pubmed_pmid,title,url,pubmed_abstract,pubmed_mesh,source,year,journal,volume,number,startpage
10371220,Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0014579399005992&_version=1&_returnURL=&md5=93bc66ac98af9f3eb4155a619d911e31,,"Animals!Genes, Protozoan!*Genome, Protozoan!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!",scirus,1999,FEBS Letters,451,3,354
10395796,Interpolated Markov models for eukaryotic gene finding.,http://cbcb.umd.edu/papers/GlimmerM-reprint-genomics-1999.pdf,"Computational gene finding research has emphasized the development of gene finders for bacterial and human DNA. This has left genome projects for some small eukaryotes without a system that addresses their needs. This paper reports on a new system, GlimmerM, that was developed to find genes in the malaria parasite Plasmodium falciparum. Because the gene density in P. falciparum is relatively high, the system design was based on a successful bacterial gene finder, Glimmer. The system was augmented with specially trained modules to find splice sites and was trained on all available data from the P. falciparum genome. Although a precise evaluation of its accuracy is impossible at this time, laboratory tests (using RT-PCR) on a small selection of predicted genes confirmed all of those predictions. With the rapid progress in sequencing the genome of P. falciparum, the availability of this new gene finder will greatly facilitate the annotation process. Maryland 20850, USA. salzberg@tigr.org","Algorithms!Alternative Splicing!Animals!Chromosomes/genetics!Comparative Study!Databases, Factual!Gene Expression!Genes, Protozoan/*genetics!Genome, Protozoan!Internet!*Markov Chains!Plasmodium falciparum/genetics!Reproducibility of Results!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Reverse Transcriptase Polymerase Chain Reaction!Sequence Alignment!",scholar,1999,Genomics,59,1,24
10562315,"Small, clonally variant antigens expressed on the surface of the Plasmodium falciparum-infected erythrocyte are encoded by the rif gene family and are the target of human immune responses.",http://intl.jem.org/cgi/content/abstract/190/10/1393,"Disease severity in Plasmodium falciparum infections is a direct consequence of the parasite's efficient evasion of the defense mechanisms of the human host. To date, one parasite-derived molecule, the antigenically variant adhesin P. falciparum erythrocyte membrane protein 1 (PfEMP1), is known to be transported to the infected erythrocyte (pRBC) surface, where it mediates binding to different host receptors. Here we report that multiple additional proteins are expressed by the parasite at the pRBC surface, including a large cluster of clonally variant antigens of 30-45 kD. We have found these antigens to be identical to the rifins, predicted polypeptides encoded by the rif multigene family. These parasite products, formerly called rosettins after their identification in rosetting parasites, are prominently expressed by fresh isolates of P. falciparum. Rifins are immunogenic in natural infections and strain-specifically recognized by human immune sera in immunoprecipitation of surface-labeled pRBC extracts. Furthermore, human immune sera agglutinate pRBCs digested with trypsin at conditions such that radioiodinated PfEMP1 polypeptides are not detected but rifins are detected, suggesting the presence of epitopes in rifins targeted by agglutinating antibodies. When analyzed by two-dimensional electrophoresis, the rifins resolved into several isoforms in the pI range of 5.5-6.5, indicating molecular microheterogeneity, an additional potential novel source of antigenic diversity in P. falciparum. Prominent polypeptides of 20, 22, 76-80, 140, and 170 kD were also detected on the surfaces of pRBCs bearing in vitro-propagated or field-isolated parasites. In this report, we describe the rifins, the second family of clonally variant antigens known to be displayed by P. falciparum on the surface of the infected erythrocyte. Swedish Institute for Infectious Disease Control, S-17177 Stockholm, Sweden.","Amino Acid Sequence!Animals!Antigens, Protozoan/*analysis/genetics/immunology!Antigens, Surface/analysis!Erythrocytes/*parasitology!Gene Expression Regulation!*Genes, Protozoan!Humans!Malaria, Falciparum/immunology!Merozoite Surface Protein 1/analysis!Molecular Sequence Data!Molecular Weight!Plasmodium falciparum/genetics/*immunology!Research Support, Non-U.S. Gov't!",scholar,1999,The Journal of Experimental Medicine,190,10,1393
10716431,Finding genes in Plasmodium falciparum.,http://www.cbi.pku.edu.cn/mirror/gene/pertea00.pdf,,"*Algorithms!Animals!*Genes, Protozoan!Plasmodium falciparum/*genetics!Software!",scholar,2000,Nature,404,6773,34
10908588,Flying through the drosophila cytoskeletal genome.,http://www.jcb.org/cgi/content/full/150/2/F63/DC1/1,,Animals!Cytoskeleton/*genetics!Drosophila melanogaster/*genetics!*Genome!*Genomic Library!Humans!,scholar,,The Journal of Cell Biology,,,
10947840,Mis3 with a conserved RNA binding motif is essential for ribosome biogenesis and implicated in the start of cell growth and S phase checkpoint.,http://www.genestocellsonline.org/cgi/content/abstract/5/7/525,"BACKGROUND: In normal somatic cell cycle, growth and cell cycle are properly coupled. Although CDK (cyclin-dependent kinase) activity is known to be essential for cell cycle control, the mechanism to ensure the coupling has been little understood. RESULTS: We here show that fission yeast Mis3, a novel evolutionarily highly conserved protein with the RNA-interacting KH motif, is essential for ribosome RNA processing, and implicated in initiating the cell growth. Growth arrest of mis3-224, a temperature sensitive mutant at the restrictive temperature, coincides with the early G2 block in the complete medium or the G1/S block in the release from nitrogen starvation, reflecting coupling of cell growth and division. Genetic interactions indicated that Mis3 shares functions with cell cycle regulators and RNA processing proteins, and is under the control of Dsk1 kinase and PP1 phosphatase. Mis3 is needed for the formation of 18S ribosome RNA, and may hence direct the level of proteins required for the coupling. One such candidate is Mik1 kinase. mis3-224 is sensitive to hydroxyurea, and the level of Mik1 protein increases during replication checkpoint in a manner dependent upon the presence of Mis3 and Cds1. CONCLUSIONS: Mis3 is essential for ribosome biogenesis, supports S phase checkpoint, and is needed for the coupling between growth and cell cycle. Whether Mis3 interacts solely with ribosomal precursor RNA remains to be determined. Biostudies, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.","Amino Acid Motifs!Amino Acid Sequence!Blotting, Northern!Blotting, Southern!Cell Cycle Proteins/*physiology!Cell Division/physiology!Centrifugation, Density Gradient!DNA-Binding Proteins/physiology!Fungal Proteins/*physiology!Genes, cdc/physiology!Immunoblotting!Microscopy, Fluorescence!Molecular Sequence Data!Plant Proteins/physiology!Protein-Serine-Threonine Kinases/physiology!RNA, Fungal/metabolism!RNA, Ribosomal/metabolism!RNA, Ribosomal, 18S/biosynthesis!RNA-Binding Proteins/*physiology!Research Support, Non-U.S. Gov't!Ribosomes/*physiology!S Phase/*physiology!Saccharomyces/*genetics!Sequence Homology, Amino Acid!",scholar,2000,Genes to Cells,5,,525
14636976,Aspartic proteases from Plasmodium chabaudi: a rodent model for human malaria.,,"Intraerythrocytic malaria parasites degrade haemoglobin to provide nutrients for their own growth and maturation. Plasmodium aspartic proteases known as plasmepsins play an important role on haemoglobin degradation and are being studied as drug targets for chemotherapy of malaria. The rodent model for human malaria, Plasmodium chabaudi, is an experimentally good model for therapy drug design. The gene encoding an aspartic protease precursor (proplasmepsin) from the rodent malaria parasite P. chabaudi was cloned and sequenced. A theoretical 3D structure model was constructed by comparative homology and used for superimposition with other known models. Analysis of the P. chabaudi and Plasmodium yoelli genomes revealed in both the presence of at least seven plasmepsins and each one has sequence similarity to its plasmepsin counterpart of the human malaria Plasmodium falciparum. The predicted proteins were confirmed as plasmepsins by detection on Blocks Database of three characteristic blocks of the eukaryotic and viral aspartic protease family. Analysis of the proline-rich loop amino acid sequence of these plasmepsins suggests that they constitute characteristic motifs of each plasmepsin group suggesting that these sequence variations are related with different substrate specificities.","Amino Acid Sequence,Humans,Plasmodium chabaudi,Aspartic Endopeptidases,Molecular Sequence Data,Mice,Genome,Polymerase Chain Reaction,Animals,Models, Molecular",NCBI,2003,Acta tropica,89,1,12-Jan
14737184,Cell-passage activity is required for the malarial parasite to cross the liver sinusoidal cell layer.,http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=314464,"Liver infection is an obligatory step in malarial transmission, but it remains unclear how the sporozoites gain access to the hepatocytes, which are separated from the circulatory system by the liver sinusoidal cell layer. We found that a novel microneme protein, named sporozoite microneme protein essential for cell traversal (SPECT), is produced by the liver-infective sporozoite of the rodent malaria parasite, Plasmodium berghei. Targeted disruption of the spect gene greatly reduced sporozoite infectivity to the liver. In vitro cell invasion assays revealed that these disruptants can infect hepatocytes normally but completely lack their cell passage ability. Their apparent liver infectivity was, however, restored by depletion of Kupffer cells, hepatic macrophages included in the sinusoidal cell layer. These results show that malarial sporozoites access hepatocytes through the liver sinusoidal cell layer by cell traversal motility mediated by SPECT and strongly suggest that Kupffer cells are main routes for this passage. Our findings may open the way for novel malaria transmission-blocking strategies that target molecules involved in sporozoite migration to the hepatocyte.","Sporozoites,Mice, Inbred BALB C,Humans,Cell Culture Techniques,Plasmodium berghei,Blotting, Western,Microscopy, Immunoelectron,Female,Liver,Kupffer Cells,Expressed Sequence Tags,DNA, Complementary,Mice,Macrophages,Cell Line,Blotting, Southern,Rats,Rats, Wistar,Hela Cells,Animals,Protozoan Proteins,Microscopy, Fluorescence,Hepatocytes",NCBI,2004,PLoS biology,2,1,E4
11099934,Assessing the impact of Plasmodium falciparum genome sequencing.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1286457900013022&_version=1&_returnURL=&md5=f371a8cb3b88b99b82385f234cf241ea,"With the publication of the complete sequences for chromosomes 2 and 3 and the increasing availability of shotgun sequence covering most of its genome, Plasmodium falciparum biology is entering its post-genomic era. Analysis of the results generated to date has identified higher-order organisation of gene families involved in parasite pathology, provided information regarding the unique biology of this parasite and allowed the identification of potential chemotherapeutic drug targets. Continuing efforts to complete the P. falciparum genome and the availability of sequences from other protozoan parasites will facilitate a broader understanding of their biology, particularly with respect to their pathogenicity. Hinxton CB10 1SA, UK. sharen@sanger.ac.uk","Animals!Base Sequence!Chromosomes!*Forecasting!*Genome, Protozoan!Genomics!Molecular Sequence Data!Plasmodium falciparum/*genetics!Protozoan Proteins/genetics!Research Support, Non-U.S. Gov't!",scirus,2000,Microbes and Infection,2,12,1479
11120681,CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts.,http://bioinformatics.oupjournals.org/cgi/content/abstract/16/10/915,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,16,10,915
11120682,The reduction of large molecular profiles to informative components using a genetic algorithm.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120683,Finding pathogenicity islands and gene transfer events in genome data.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120684,Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120685,Artemis: sequence visualization and annotation.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120686,MAD: a suite of tools for microarray data management and processing.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120687,A space-efficient algorithm for aligning large genomic sequences.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120688,MASIA: recognition of common patterns and properties in multiple aligned protein sequences.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11120689,Chips ahoy: gene expression in failing hearts surveyed by high-density microarrays.,http://bioinformatics.oupjournals.org/cgi/screenpdf/16/10/915.pdf,"MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/ of Athens, Athens GR-15701, Greece.","*Algorithms!Animals!DNA, Protozoan/*chemistry/genetics!Databases, Factual!Genes, Protozoan!Open Reading Frames!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!",scholar,2000,Bioinformatics,,,915
11173462,WWWWhy does nature stutter? A survey of strands of repeated amino acids.,http://journals.iucr.org/d/issues/2001/02/00/gr2099/gr2099.pdf,"Human stuttering is a simple example of the repetition of sounds or symbols, sometimes associated with single letters, and may be used to illustrate the amazing repetition of amino acids (symbolized by a letter, e.g. W) in proteins. A survey of available databases with highly improbable strings of single amino acids is tabulated. This paper concludes with a challenge to the crystallographic community to probe the structural origins of the structure-function relationship in this neglected area. When nature stutters, we should pay attention. University, College Station, TX 77843-2128, USA. e-meyer@tamu.edu","*Amino Acids!Animals!*Databases, Factual!Humans!Proteins/*chemistry!*Repetitive Sequences, Amino Acid!Research Support, Non-U.S. Gov't!",scholar,2001,Acta Crystallographica Section D Biological Crystallography,57,2,181
11276083,Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.,http://doi.wiley.com/10.1002/1097-0134(20010501)43:2%253C134::AID-PROT1025%253E3.3.CO%3B2-9,"With a protein structure comparison, an iterative database search with sequence profiles, and a multiple-alignment analysis, we show that two domains with the helix-grip fold, the star-related lipid-transfer (START) domain of the MLN64 protein and the birch allergen, are homologous. They define a large, previously underappreciated superfamily that we call the START superfamily. In addition to the classical START domains that are primarily involved in eukaryotic signaling mediated by lipid binding and the birch antigen family that consists of plant proteins implicated in stress/pathogen response, the START superfamily includes bacterial polyketide cyclases/aromatases (e.g., TcmN and WhiE VI) and two families of previously uncharacterized proteins. The identification of this domain provides a structural prediction of an important class of enzymes involved in polyketide antibiotic synthesis and allows the prediction of their active site. It is predicted that all START domains contain a similar ligand-binding pocket. Modifications of this pocket determine the ligand-binding specificity and may also be the basis for at least two distinct enzymatic activities, those of a cyclase/aromatase and an RNase. Thus, the START domain superfamily is a rare case of the adaptation of a protein fold with a conserved ligand-binding mode for both a broad variety of catalytic activities and noncatalytic regulatory functions. Proteins 2001;43:134-144. Medicine, National Institutes of Health, Bethesda, MD 20894, USA.","Allergens/*chemistry!Amino Acid Sequence!Binding Sites!*Carrier Proteins!Catalysis!Ligands!Membrane Proteins/*chemistry!Models, Molecular!Phylogeny!Plant Proteins/*chemistry!Protein Binding!Protein Structure, Tertiary!Sequence Alignment!Trees!",scholar,2001,Proteins Structure Function and Genetics,43,2,134
11295189,Stevor transcripts from Plasmodium falciparum gametocytes encode truncated polypeptides.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685101002250&_version=1&_returnURL=&md5=368e7713d7b9d08a8b97b03e20cd45b7,,"Amino Acid Sequence!Animals!Base Sequence!DNA, Complementary/genetics!DNA, Protozoan/genetics!Erythrocytes/parasitology!*Gametogenesis/genetics/physiology!Molecular Sequence Data!Peptides/*genetics/metabolism!Plasmodium falciparum/genetics/*growth & development/metabolism!Protozoan Proteins/*genetics/metabolism!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Sequence Analysis, DNA!*Transcription, Genetic!",scirus,2001,Molecular and Biochemical Parasitology,113,2,331
11420378,Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains.,http://www.mbe.oupjournals.org/cgi/content/abstract/18/7/1401,"Proteins are often characterized by the presence of multiple domains, which make specific contributions to their cellular function. While the gain of domains in proteins by duplication and shuffling is well established, domain loss is poorly documented. Here, we provide evidence that domain loss has played an important role in the evolution of protein architecture and function by demonstrating that fungal Zuotin proteins evolved from MIDA1-like proteins, present in animals and plants, by complete loss of the carboxyl-terminal MYB domains. Phylogenetic analyses of the DnaJ motif (the J domain) present in both Zuotin and MIDA1 proteins were complicated by the limited length and profound differences in evolutionary rates exhibited by this domain. To rigorously examine J domain phylogeny, we combined the nonparametric bootstrap with Monte Carlo simulation. This method, which we have designated the resampled parametric bootstrap, allowed us to assess type I and type II error associated with these analyses. These results revealed significant support for domain loss rather than domain gain or gene loss involving paralogs. The absence of sequences related to the MIDA1 MYB domains in Saccharomyces cerevisiae further indicates that the domains have been completely lost, consistent with known functional differences between Zuotin and MIDA1 proteins. These analyses suggest that the description of additional examples of complete domain loss may provide a method to identify orthologous proteins exhibiting functional differences using genomic sequence data. University, Columbus, 43210, USA. braun.83@osu.edu","Amino Acid Sequence!Animals!Arabidopsis/genetics!Comparative Study!DNA-Binding Proteins/chemistry/*genetics!*Evolution, Molecular!Fungal Proteins/chemistry/*genetics!Mice!Models, Genetic!Molecular Sequence Data!Phylogeny!Plant Proteins/chemistry/genetics!Protein Structure, Tertiary!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Saccharomyces cerevisiae/genetics!*Saccharomyces cerevisiae Proteins!Sequence Deletion!Sequence Homology, Amino Acid!",scholar,2001,Molecular Biology and Evolution,18,,1401
11493695,Exploring the transcriptome of the malaria sporozoite stage.,http://www.pnas.org/cgi/content/abstract/98/17/9895,"Most studies of gene expression in Plasmodium have been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far behind. We have constructed a high quality cDNA library of the Plasmodium sporozoite stage by using the rodent malaria parasite P. yoelii, an important model for malaria vaccine development. The technical obstacles associated with limited amounts of RNA material were overcome by PCR-amplifying the transcriptome before cloning. Contamination with mosquito RNA was negligible. Generation of 1,972 expressed sequence tags (EST) resulted in a total of 1,547 unique sequences, allowing insight into sporozoite gene expression. The circumsporozoite protein (CS) and the sporozoite surface protein 2 (SSP2) are well represented in the data set. A BLASTX search with all tags of the nonredundant protein database gave only 161 unique significant matches (P(N) < or = 10(-4)), whereas 1,386 of the unique sequences represented novel sporozoite-expressed genes. We identified ESTs for three proteins that may be involved in host cell invasion and documented their expression in sporozoites. These data should facilitate our understanding of the preerythrocytic Plasmodium life cycle stages and the development of preerythrocytic vaccines. Center, New York University School of Medicine, New York, NY 10016, USA. kappes01@popmail.med.nyu.edu America.","Amino Acid Motifs!Amino Acid Sequence!Animals!Anopheles/parasitology!DNA, Complementary/genetics!Expressed Sequence Tags!*Gene Expression Profiling!*Gene Expression Regulation, Developmental!*Gene Library!Host-Parasite Relations/genetics!Ligands!Malaria Vaccines!Molecular Sequence Data!Plasmodium falciparum/genetics!Plasmodium yoelii/*genetics/growth & development/pathogenicity!Protozoan Proteins/genetics!RNA, Messenger/*biosynthesis/genetics!RNA, Protozoan/*biosynthesis/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Reverse Transcriptase Polymerase Chain Reaction!Sequence Alignment!Sequence Homology, Amino Acid!Species Specificity!*Transcription, Genetic!Virulence/genetics!",scholar,2001,Proceedings of the National Academy of Sciences,98,17,9895
11523008,Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists.,http://www.springerlink.com/index/DFVT2R02QM777RX2.pdf,"Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein kinase and calmodulin genes facilitated by recombination of ancient introns. Savannah, GA 31404, USA.","Amino Acid Sequence!Animals!Ca(2+)-Calmodulin Dependent Protein Kinase/*chemistry/*genetics!Calmodulin/chemistry/genetics!Computational Biology!*Evolution, Molecular!Introns/genetics!Models, Genetic!Phylogeny!Plants/*enzymology/genetics!Protein Structure, Tertiary!Protein-Serine-Threonine Kinases/chemistry/genetics!Protozoa/*enzymology/genetics!Research Support, Non-U.S. Gov't!Sequence Alignment!",scholar,2001,Journal of Molecular Evolution,53,3,214
11591825,Evidence for a role for a Plasmodium falciparum homologue of Sec31p in the export of proteins to the surface of malaria parasite-infected erythrocytes.,http://jcs.biologists.org/cgi/content/abstract/114/18/3377,"The malaria parasite, Plasmodium falciparum, spends part of its life cycle inside the enucleated erythrocytes of its human host. The parasite modifies the cytoplasm and plasma membrane of its host cell by exporting proteins beyond the confines of its own plasma membrane. We have previously provided evidence that a plasmodial homologue of the COPII protein, Sar1p, is involved in the trafficking of proteins across the erythrocyte cytoplasm. We have now characterised an additional plasmodial COPII protein homologue, namely Sec31p. Recombinant proteins corresponding to the WD-40 and the intervening domains of the PfSec31p sequence were used to raise antibodies. The affinity-purified antisera recognised a protein with an apparent relative molecular mass of 1.6 x 10(5) on western blots of malaria parasite-infected erythrocytes but not on blots of uninfected erythrocytes. PfSec31p was shown to be largely insoluble in nonionic detergent, suggesting cytoskeletal attachment. Confocal immunofluorescence microscopy of malaria parasite-infected erythrocytes was used to show that PfSec31p is partly located within the parasite and partly exported to structures outside the parasite in the erythrocyte cytoplasm. We have also shown that PfSec31p and PfSar1p occupy overlapping locations. Furthermore, the location of PfSec31p overlaps that of the cytoadherence-mediating protein PfEMP1. These data support the suggestion that the malaria parasite establishes a vesicle-mediated trafficking pathway outside the boundaries of its own plasma membrane - a novel paradigm in eukaryotic biology. Australia.","Animals!Brefeldin A/pharmacology!Carrier Proteins/genetics/*metabolism!Cytoplasm/*metabolism!Erythrocyte Membrane/*metabolism!Erythrocytes/*parasitology!Humans!Malaria/metabolism!Molecular Sequence Data!Monomeric GTP-Binding Proteins/genetics!Phosphoproteins/genetics/*metabolism!Plasmodium falciparum/genetics/*metabolism/parasitology!Protein Transport/drug effects/physiology!Research Support, Non-U.S. Gov't!*Saccharomyces cerevisiae Proteins!Sequence Alignment!Sequence Homology, Amino Acid!",scholar,2001,Journal of Cell Science,114,,3377
1840489,The C-terminal domain of RNA polymerase II of the malaria parasite Plasmodium berghei.,,"The C-terminal domain (CTD) of RNA polymerase II (RNAP) has an essential function in the regulation of transcription. The CTD of the human malaria parasite, Plasmodium falciparum, differs dramatically from that of higher eukaryotes. To determine whether this is a general feature of malarial parasites, we have analysed the CTD of the distantly related rodent malaria parasite P.berghei. The CTDs of the two parasites enzymes are very similar in amino acid composition and contain the basic structure of most eukaryotic CTDs, which is a tandem repeat of a heptapeptide (SPTSPSY). The CTD of P.berghei differs, however, in three aspects from the CTD of P.falciparum and other eukaryotes. First, both domains show a divergence from the consensus sequence at position 6 of the heptapeptide repeat. The Ser6 is always substituted, with a bias for lysine. The latter substitution might increase the binding efficiency to the DNA template. Second, the rodent and human malarial CTDs contain a 3' extension of, respectively, 66 or 67 amino acid residues. This tail-piece is unique among eukaryotes. Third, the enlargement of the CTD of the human parasite by six heptapeptide repeats is most likely generated by a recent amplification of a specific repeat unit.","Plasmodium falciparum,Amino Acid Sequence,Restriction Mapping,Plasmodium berghei,Sequence Homology, Nucleic Acid,Macromolecular Substances,Molecular Sequence Data,RNA Polymerase II,DNA,Blotting, Southern,Base Sequence,Animals",NCBI,1991,Biochemical and biophysical research communications,180,3,1350-5
11738709,Prediction of many new exons and introns in Plasmodium falciparum chromosome 2.,http://www.biocristalografia.df.ibilce.unesp.br/publications/pdf/purine2003_74.pdf,"The current prediction of genes in the Plasmodium falciparum genome database relies upon a limited number of specially developed computer algorithms. We have re-annotated the sequence of chromosome 2 of P. falciparum by a computer-assisted manual analysis, which is described here. Of 161 newly predicted introns, we have experimentally confirmed 98. We regard 110 introns from the previously published analyses as probable, we delete 3, change 26 and add 135. We recognise 214 genes in chromosome 2. We have predicted introns in 121 genes. The increased complexity of gene structure on chromosome 2 is likely to be mirrored by the entire genome. Monash University, Clayton, Vic. 3800, Australia. robert.huestis@med.monash.edu.au","Algorithms!Animals!Antigens, Protozoan/genetics!Base Sequence!Chromosomes/*genetics!Computational Biology/*methods!Exons/*genetics!*Genes, Protozoan!Introns/*genetics!Molecular Sequence Data!Plasmodium falciparum/*genetics!Protozoan Proteins/genetics/metabolism!RNA Splice Sites!Research Support, Non-U.S. Gov't!Sequence Alignment!",scholar,2001,Mol Biochem Parasitol,118,2,187
11738711,The sequence of a 200 kb portion of a Plasmodium vivax chromosome reveals a high degree of conservation with Plasmodium falciparum chromosome 3.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685101003802&_version=1&_returnURL=&md5=dcf91da2a8b31983d37748ec68deffed,"Within a 199,866 base pair (bp) portion of a Plasmodium vivax chromosome we identified a conserved linkage group consisting of at least 41 genes homologous to Plasmodium falciparum genes located on chromosome 3. There were no P. vivax homologues of the P. falciparum cytoadherence-linked asexual genes clag 3.2, clag 3.1 and a var C pseudogene found on the P. vivax chromosome. Within the conserved linkage group, the gene order and structure are identical to those of P. falciparum chromosome 3. This conserved linkage group may extend to as many as 190 genes. The subtelomeric regions are different in size and the P. vivax segment contains genes for which no P. falciparum homologues have been identified to date. The size difference of at least 900 kb between the homologous P. vivax chromosome and P. falciparum chromosome 3 is presumably due to a translocation. There is substantial sequence divergence with a much higher guanine+cytosine (G+C) content in the DNA and a preference for amino acids using GC-rich codons in the deduced proteins of P. vivax. This structural conservation of homologous genes and their products combined with sequence divergence at the nucleotide level makes the P. vivax genome a powerful tool for comparative analyses of Plasmodium genomes. Biology Laboratory, The Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Q 4029 Brisbane, Australia. marinat@qimr.edu.au","Animals!Chromosomes/*genetics!Chromosomes, Artificial, Yeast/genetics!Comparative Study!Computational Biology/methods!*Conserved Sequence!Contig Mapping!Exons/genetics!Gene Library!Humans!Introns/genetics!Molecular Sequence Data!Plasmodium falciparum/*genetics!Plasmodium vivax/*genetics!Protozoan Proteins/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Analysis, DNA!Sequence Homology!*Synteny!",scirus,2001,Molecular and Biochemical Parasitology,118,2,211
11738712,"The high molecular mass rhoptry protein, RhopH1, is encoded by members of the clag multigene family in Plasmodium falciparum and Plasmodium yoelii.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685101003917&_version=1&_returnURL=&md5=45735215c466eadfeb126b7d648c51ee,"Malarial merozoite rhoptries contain a high molecular mass protein complex called RhopH. RhopH is composed of three polypeptides, RhopH1, RhopH2, and RhopH3, encoded by distinct genes. Using monoclonal antibody-purified protein complex from both Plasmodium falciparum and Plasmodium yoelii, peptides were obtained by digestion of RhopH1 and their sequence determined either by mass spectrometry or Edman degradation. In both species the genes encoding RhopH1 were identified as members of the cytoadherence linked asexual gene (clag) family. In P. falciparum the family members on chromosome 3 were identified as encoding RhopH1. In P. yoelii two related genes were identified and sequenced. One of the genes, pyrhoph1a, was positively identified as encoding RhopH1 by the peptide analysis and the other gene, pyrhoph1a-p, was at least transcribed. Genes in the clag family present in both parasite species have a number of conserved features. The size and location of the P. yoelii protein complex in the rhoptries was confirmed. The first clag gene identified on chromosome 9 was implicated in cytoadherence, the binding of infected erythrocytes to host endothelial cells; this study shows that other members of the family encode merozoite rhoptry proteins, proteins that may be involved in merozoite-erythrocyte interactions. We propose that the family should be renamed as rhoph1/clag. Shigenobu-cho, Ehime 791-0295, Japan.","Amino Acid Sequence!Animals!Antibodies, Monoclonal/biosynthesis/immunology!Antibodies, Protozoan/biosynthesis/immunology!Cell Adhesion!Female!Malaria/parasitology!Malaria, Falciparum/parasitology!Mice!Mice, Inbred BALB C!Molecular Sequence Data!Multigene Family!Plasmodium falciparum/*genetics/growth & development/pathogenicity!Plasmodium yoelii/*genetics/growth & development/pathogenicity!Protozoan Proteins/chemistry/*genetics/immunology/metabolism!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!",scirus,2001,Molecular and Biochemical Parasitology,118,2,223
11738715,Fine structure of Plasmodium falciparum subtelomeric sequences.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685101003620&_version=1&_returnURL=&md5=7377a0ef79f6cd9098ce5b0c64aa7d16,,"Amino Acid Sequence!Animals!Molecular Sequence Data!Plasmodium falciparum/*genetics!Protozoan Proteins/*chemistry/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Telomere/chemistry/*genetics!",scirus,2001,Molecular and Biochemical Parasitology,118,2,253
11752262,"PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).",http://nar.oupjournals.org/cgi/content/abstract/30/1/87,"PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically based queries of the database. A version of the database is also available on CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where Internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community. Avenue, Philadelphia, PA 19104-6018, USA.","Animals!Chromosome Mapping!DNA, Protozoan/genetics!Database Management Systems!*Databases, Genetic!Forecasting!Gene Expression Profiling!*Genome, Protozoan!Information Storage and Retrieval!Internet!Plasmodium/*genetics/*metabolism!Plasmodium falciparum/genetics!Protozoan Proteins/biosynthesis/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Analysis!Sequence Homology!",scholar,2002,Nucleic Acids Research,30,1,87
11788821,A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies.,http://www.nature.com/ncb/journal/v4/n2/abs/ncb743.html,"Membrane proteins with transmembrane domains (TMDs) that contain polar residues exposed to the lipid bilayer are selectively sorted into multivesicular bodies (MVBs) and delivered to the yeast vacuole. Sorting of some, although not all, proteins into these structures is mediated by ubiquitination. We have identified a transmembrane ubiquitin ligase, Tul1, that is resident in the Golgi apparatus and is required for the ubiquitination of proteins with polar TMDs, including vacuolar proteins such as carboxypeptidase S. We suggest that Tul1 provides quality control, identifying misfolded membrane proteins and marking them for transport to endosomes and degradation in the vacuole.","Amino Acid Sequence!Fluorescent Dyes/metabolism!Fungal Proteins/*metabolism!Golgi Apparatus/enzymology/metabolism!Ligases/chemistry/*metabolism!Membrane Proteins/chemistry/genetics/*metabolism!Molecular Sequence Data!Protein Sorting Signals!Protein Structure, Tertiary!Protein Transport/*physiology!Qa-SNARE Proteins!Recombinant Fusion Proteins/genetics/metabolism!Research Support, Non-U.S. Gov't!*Saccharomyces cerevisiae Proteins!*Schizosaccharomyces pombe Proteins!Two-Hybrid System Techniques!Ubiquitin/*metabolism!*Ubiquitin-Protein Ligases!Yeasts/cytology/genetics/*metabolism!",scholar,2002,Nature Cell Biology,4,,117
11836228,Physics-based gene identification: proof of concept for Plasmodium falciparum.,http://www.bioinformatics.oupjournals.org/cgi/content/abstract/18/1/190,"The ab initio prediction of new genes in eukaryotic genomes represents a difficult task, notably for the identification of complex split genes. A Physics-Based Gene Identification (PBGI) method was formulated recently (Yeramian, Gene, 255, 139-150, 151-168, 2000a,b) to address this problem, taking as a model the Plasmodium falciparum genome. Here, the predictive power of this method is put under experimental test for this genome. The presented results demonstrate the usefulness of the PBGI as a gene-identification tool for P. falciparum, notably for the discovery of new genes with no homology to known genes. Perspectives opened by this new method for other eukaryotic genomes are also mentioned. Institut Pasteur, 75724 Paris Cedex 15, France.","Algorithms!Animals!Biophysics!Computational Biology!DNA, Protozoan/chemistry/genetics!*Genes, Protozoan!*Genetic Techniques!Genome, Protozoan!Genomics/statistics & numerical data!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!",scholar,2002,Bioinformatics,18,1,190
11847128,A central role for Plasmodium falciparum subtelomeric regions in spatial positioning and telomere length regulation.,,"In the protozoan malaria parasite, Plasmodium falciparum, the telomere-associated sequences (TASs) of the 14 linear chromosomes display a similar higher order organization and form clusters of four to seven telomeres localized at the nuclear periphery. Experimental evidence has shown that the physical tethering of chromosome ends enhances the ectopic recombination between gene families involved in antigenic variation and parasite sequestration. Using FISH analysis, we observed that chromosome ends lacking the subtelomeric region are usually delocalized from telomere clusters, but still remain at the nuclear periphery. This indicates that subtelomeric DNA is necessary for cluster formation but is not essential for peripheral positioning. Intriguingly, these truncated chromosomes have unusually long telomeric tracts (up to three times longer than average length), showing that TASs play a role in telomere length regulation. On these chromosomes, the newly formed telomere frequently extends from truncated genes leading, in some cases, to the transcription of telomeric DNA. The implications of both subtelomeric gene expression and nuclear architecture in the virulence of this serious human pathogen are discussed. Pasteur, 25 rue du Dr Roux, F-75724 Paris Cedex 15, France.","Animals!Blotting, Southern!In Situ Hybridization, Fluorescence!Plasmodium falciparum/genetics/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Reverse Transcriptase Polymerase Chain Reaction!*Telomere!Transcription, Genetic!",scholar,,,,,
11861763,A family of transmembrane microneme proteins of Toxoplasma gondii contain EGF-like domains and function as escorters.,http://jcs.biologists.org/cgi/content/abstract/115/3/563,"TgMIC6, TgMIC7, TgMIC8 and TgMIC9 are members of a novel family of transmembrane proteins localized in the micronemes of the protozoan parasite Toxoplasma gondii. These proteins contain multiple epidermal growth factor-like domains, a putative transmembrane spanning domain and a short cytoplasmic tail. Sorting signals to the micronemes are encoded in this short tail. We established previously that TgMIC6 serves as an escorter for two soluble adhesins, TgMIC1 and TgMIC4. Here, we present the characterization of TgMIC6 and three additional members of this family, TgMIC7, -8 and -9. Consistent with having sorting signals localized in its C-terminal tail, TgMIC6 exhibits a classical type I membrane topology during its transport along the secretory pathway and during storage in the micronemes. TgMIC6 is processed at the N-terminus, probably in the trans-Golgi network, and the cleavage site has been precisely mapped. Additionally, like other members of the thrombospondin-related anonymous protein family, TgMIC2, TgMIC6 and TgMIC8 are proteolytically cleaved near their C-terminal domain upon discharge by micronemes. We also provide evidence that TgMIC8 escorts another recently described soluble adhesin, TgMIC3. This suggests that the existence of microneme protein complexes is not an exception but rather the rule. TgMIC6 and TgMIC8 are expressed in the rapidly dividing tachyzoites, while TgMIC7 and TgMIC9 genes are predominantly expressed in bradyzoites, where they presumably also serve as escorters. Biology, Sir Alexander Fleming Building, Imperial College Road, London, SW7 2AZ, UK.","*Adhesins, Bacterial!Amino Acid Sequence!Animals!Carrier Proteins/chemistry/genetics/*metabolism!Epidermal Growth Factor/chemistry/*genetics!Gene Expression Regulation, Developmental!Humans!Membrane Proteins/chemistry/genetics/*metabolism!Molecular Sequence Data!Protein Sorting Signals!Protein Structure, Tertiary!Protein Transport/physiology!Protozoan Proteins/chemistry/genetics/*metabolism!Recombinant Fusion Proteins/genetics/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!Toxoplasma/cytology/*physiology!",scholar,2002,Journal of Cell Science,115,,563
11943536,BSD: a novel domain in transcription factors and synapse-associated proteins.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0968000401020424&_version=1&_returnURL=&md5=aef474f2f3104da317653784dc16e489,"This article describes a novel domain, BSD, that is present in basal transcription factors, synapse-associated proteins and several hypothetical proteins. It occurs in a variety of species ranging from primal protozoan to human. The BSD domain is characterized by three predicted alpha helices, which probably form a three-helical bundle, as well as by conserved tryptophan and phenylalanine residues, located at the C terminus of the domain. Germany. doerks@embl.heidelberg.de","*Amino Acid Motifs!Amino Acid Sequence!Animals!Humans!Molecular Sequence Data!Neuropeptides/*chemistry!Sequence Homology, Amino Acid!Transcription Factors/*chemistry!",scirus,2002,Trends in Biochemical Sciences,27,4,168
12095684,Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0378111902005528&_version=1&_returnURL=&md5=4af9674bf0c8a9b10d0e641a53f2f15b,"Now that the sequencing of the complete genome of the human malaria parasite Plasmodium falciparum is now underway, importance of analyses of complementary DNAs (cDNAs) is looming up. We constructed a full-length-enriched cDNA library from erythrocytic stage P. falciparum using the 'oligo-capping' method (Nucleic Acids Res. 29 (2001) 70). In this report we describe the novel genes identified using this library and detailed characterization of transcriptional start site of knob-associated histidine rich protein gene. Contrary to the previous report we conclude all the transcripts of plasmodium genes have diverse start sites. Sequence comparisons between the cDNAs and the complete sequences of chromosomes 2 identified three novel genes that had been missed by computational predictions. Moreover, analysis of transcriptional start sites revealed that the average length of the 5' untranslated region was 346 nt, which is much longer than that in humans. The transcriptional start sites of all the genes studied were far more diverse than those of human genes. These observations may reflect unique mechanism(s) of gene expression in this organism, which has an extremely AT-rich genome. of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan. jwatanab@manage.ims.u-tokyo.ac.jp","5' Untranslated Regions/genetics!Amino Acid Sequence!Animals!Base Sequence!*Gene Library!Genes, Protozoan/genetics!Humans!Malaria, Falciparum/parasitology!Molecular Sequence Data!Peptides/genetics!Plasmodium falciparum/*genetics!Protozoan Proteins/genetics!RNA, Messenger/genetics!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Transcription Initiation Site!*Transcription, Genetic!",scirus,2002,Gene,291,1,105
12106866,"Male-specific expression of the paralog of malaria transmission-blocking target antigen Pfs230, PfB0400w.",http://www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26list_uids%3D12106866%26dopt%3DAbstract,"Malaria transmission requires that Plasmodium parasites circulating in the vertebrate host develop into male and female gametocytes, which are then taken up by a mosquito to undergo fertilization and further development into infectious sporozoites. To understand the malaria specific events involved in this process, the gene products involved require identification and characterization. This work demonstrates that antibodies generated against the paralog of malaria transmission-blocking antigen Pfs230, PfB0400w, react only with stage V male gametocytes, not gametes or asexual parasites. In contrast, Pfs230 is expressed on the surface of all gametocytes and remains associated with emerged gametes as one of the primary surface antigens for several hours. Consistent with the localization findings, a high molecular weight band is recognized by anti-PfB0400w antibodies on western blots of extracts of late stage gametocytes, not asexual parasites, early (stage II/III) gametocytes, or gametes. PfB0400w mRNA is also not observed in asexual parasites. The transcript levels peak in stage III/IV gametocytes, then sharply decline in gametes. This work identifies a novel male-specific protein with an expression pattern that is distinctly different than its paralog. Chicago, IL 60626, USA.","Animals!Antigens, Protozoan/*genetics/*metabolism!Erythrocytes/parasitology!Fluorescent Antibody Technique!*Gene Duplication!Gene Expression Regulation, Developmental!Genes, Protozoan!Malaria, Falciparum/parasitology/transmission!Plasmodium falciparum/genetics/*growth & development!Protozoan Proteins/*genetics/metabolism!Reproduction!Reproduction, Asexual!Research Support, U.S. Gov't, P.H.S.!",scholar,2002,Mol Biochem Parasitol,122,2,127
12244052,"Serine repeat antigen (SERA5) is predominantly expressed among the SERA multigene family of Plasmodium falciparum, and the acquired antibody titers correlate with serum inhibition of the parasite growth.",http://www.jbc.org/cgi/content/abstract/jbc%3B277/49/47533,"The Plasmodium falciparum serine repeat antigen (SERA) is one of the blood stage malaria vaccine candidates. The malaria genome project has revealed that SERA is a member of the SERA multigene family consisting of eight SERA homologues clustered on chromosome 2 and one SERA homologue on chromosome 9. Northern blotting and real time quantitative reverse transcription-PCR with five independent parasite strains, including three allelic representative forms of the SERA gene, have shown that all of the SERA homologues are transcribed most actively at trophozoite and schizont stages and that SERA5 (SERA/SERP) is transcribed predominantly among the family. Polyclonal antibodies were raised against recombinant proteins representing the N-terminal portions of four significantly transcribed SERA homologues (SERA3 to -6) in the center of the cluster on chromosome 2. Using these antibodies, indirect immunofluorescence microscopy detected the expression of SERA3 to -6, with similar localization, in all trophozoite- and schizont-infected erythrocytes. We have examined 40 sera from Ugandan adults for their antibody reactivity and found that enzyme-linked immunosorbent assay titer against SERA5 N-terminal domain, but not against other SERA proteins, is positively correlated with the inhibition of in vitro parasite growth by individual sera. Our data confirm the usefulness of the N-terminal domain of SERA5 as a promising malaria candidate vaccine. Diseases, Osaka University, Suita, Osaka 565-0871, Japan.","Adult!Animals!Antigens, Protozoan/*biosynthesis/*genetics!Blotting, Northern!Blotting, Western!Enzyme-Linked Immunosorbent Assay!Erythrocytes/parasitology!Humans!Malaria Vaccines/metabolism!Microscopy, Fluorescence!Models, Genetic!Multigene Family!Plasmids/metabolism!Plasmodium falciparum/*genetics/*metabolism!Protein Binding!Protein Structure, Tertiary!RNA, Messenger/metabolism!Recombinant Proteins/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Reverse Transcriptase Polymerase Chain Reaction!Transcription, Genetic!",scholar,2002,Journal of Biological Chemistry,277,49,47533
12364807,Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum.,http://www.sciencemag.org/cgi/content/abstract/sci%3B298/5591/216,"The detection of single-nucleotide polymorphisms in pathogenic microorganisms has normally been carried out by trial and error. Here we show that DNA hybridization with high-density oligonucleotide arrays provides rapid and convenient detection of single-nucleotide polymorphisms in Plasmodium falciparum, despite its exceptionally high adenine-thymine (AT) content (82%). A disproportionate number of polymorphisms are found in genes encoding proteins associated with the cell membrane. These genes are targets for only 22% of the oligonucleotide probes but account for 69% of the polymorphisms. Genetic variation is also enriched in subtelomeric regions, which account for 22% of the chromosome but 76% of the polymorphisms. Health, Boston, MA 02115, USA.","Animals!Base Sequence!Chromosomes/genetics!DNA, Protozoan/genetics!*Genes, Protozoan!Genome, Protozoan!Membrane Proteins/*genetics!Molecular Sequence Data!Nucleic Acid Hybridization!Oligonucleotide Probes!Plasmodium falciparum/*genetics!*Polymorphism, Single Nucleotide!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Analysis, DNA!Variation (Genetics)!",scholar,2002,Science,298,5591,216
8940993,Molecular cloning and antigenic mapping of heat-shock protein 70 from the malaria species Plasmodium bergheI.,,"We have isolated a 70-kD heat-shock protein (hsp-70) cDNA from Plasmodium berghei. A cDNA clone encoding the P. berghei hsp-70 was isolated and sequenced, demonstrating that it is highly homologous with other Plasmodium hsp-70s. One of the common features is a series of GGMP amino acid repeats at the carboxy terminus; there is also a long, AT-rich 5' untranslated region, a hallmark of other malarial RNAs. Hydropathy and antigenicity analyses suggest the presence of two hydrophilic domains. Recombinant peptides comprising different fragments of hsp-70 were expressed in Escherichia coli and assessed for antigenicity with antiserum from mice immunized with sonicated extracts of P. berghei. Antigenic sites map to regions that include the two hydrophilic domains.","Amino Acid Sequence,Recombinant Proteins,Plasmodium berghei,Plasmids,Epitope Mapping,Cloning, Molecular,Molecular Sequence Data,HSP70 Heat-Shock Proteins,Gene Expression Regulation,Escherichia coli,Sequence Homology, Amino Acid,Base Sequence,Animals",NCBI,1996,The American journal of tropical medicine and hygiene,55,5,570-6
9010839,Further characterization of a 58 kDa Plasmodium berghei phosphoprotein as a cochaperone.,,"Molecular chaperones are important for proper protein folding during protein biogenesis. This report describes a protein from Plasmodium berghei which is 30% identical and 40% similar to a recently described mammalian cochaperone, or heat shock protein 70 interacting protein. The P. berghei cochaperone accumulates throughout the trophozoite stage and decreases during the schizont stage. The stage specific expression is consistent with its presumed role in protein folding or protein-protein interactions. The largest difference between the Plasmodium and mammalian sequences is a more extensive domain of imperfect glycine-glycine-methionine-proline (GGMP) tandem repeats in the parasite's cochaperone sequence. Immunofluorescence studies show that the protein is an abundant cytosolic protein of the parasite. However, antibodies raised against the GGMP repeat domain, which is also found in other parasite chaperones, react with both the parasite and host erythrocyte membrane. The reactivity with the host membrane suggests that the parasite exports molecular chaperones into the infected erythrocyte.","Molecular Chaperones,Fluorescent Antibody Technique,Amino Acid Sequence,Plasmodium berghei,Cloning, Molecular,Sequence Homology, Nucleic Acid,Immunoblotting,Sequence Analysis, DNA,Molecular Sequence Data,Sequence Homology, Amino Acid,Base Sequence,Phosphoproteins,Animals,Protozoan Proteins",NCBI,1996,Molecular and biochemical parasitology,83,1,25-33
2651910,High level sequence homology between a Plasmodium chabaudi heat shock protein gene and its Plasmodium falciparum equivalent.,,,"Plasmodium falciparum,Genes,Amino Acid Sequence,Molecular Sequence Data,Heat-Shock Proteins,Base Sequence,Animals,Plasmodium",NCBI,1989,Molecular and biochemical parasitology,33,1,101-3
12377259,Selective pressures that decrease synonymous mutations in Plasmodium falciparum.,https://qspace.library.queensu.ca/dspace/html/1974/136/pfalcip01.htm,"Rich and Ayala propose that the zero rate of non-amino-acid-changing (synonymous) mutations in some proteins of Plasmodium falciparum reflects a recent population bottleneck. Alternatively, Arnot and Saul propose sequence conservation in response to selective pressures other than the pressure to encode protein. Among these are fold pressure and purine-loading pressure. Genomes adapt to these by acquisition of introns and/or low-complexity (simple-sequence) segments in proteins. Adaptive explanations include facilitation of intragenic recombination (and hence diversification of the encoded protein) by DNA stem-loop secondary structures. K7L3N6. forsdyke@post.queensu.ca","Amino Acid Sequence/genetics!Animals!Antigens, Protozoan/genetics!Base Composition!Base Sequence/genetics!*Evolution, Molecular!Herpesvirus 4, Human/genetics!Plasmodium falciparum/*genetics!Point Mutation/*genetics!Protein Folding!Protozoan Proteins/genetics!Selection (Genetics)!",scholar,2002,Trends Parasitol,18,9,411
11413195,Antibodies against merozoite surface protein (MSP)-1(19) are a major component of the invasion-inhibitory response in individuals immune to malaria.,,"Antibodies that bind to antigens expressed on the merozoite form of the malaria parasite can inhibit parasite growth by preventing merozoite invasion of red blood cells. Inhibitory antibodies are found in the sera of malaria-immune individuals, however, the specificity of those that are important to this process is not known. In this paper, we have used allelic replacement to construct a Plasmodium falciparum parasite line that expresses the complete COOH-terminal fragment of merozoite surface protein (MSP)-1(19) from the divergent rodent malaria P. chabaudi. By comparing this transfected line with parental parasites that differ only in MSP-1(19), we show that antibodies specific for this domain are a major component of the inhibitory response in P. falciparum-immune humans and P. chabaudi-immune mice. In some individual human sera, MSP-1(19) antibodies dominated the inhibitory activity. The finding that antibodies to a small region of a single protein play a major role in this process has important implications for malaria immunity and is strongly supportive of further understanding and development of MSP-1(19)-based vaccines.","Plasmodium falciparum,Parasitic Sensitivity Tests,Cell Division,Amino Acid Sequence,Humans,Recombinant Fusion Proteins,Sequence Alignment,Plasmodium chabaudi,Merozoite Surface Protein 1,Peptide Fragments,Malaria, Falciparum,Molecular Sequence Data,Adult,Mice,Antibody Specificity,Epidermal Growth Factor,Cell Line,Antibodies, Protozoan,Protein Structure, Tertiary,Transfection,Animals",NCBI,2001,The Journal of experimental medicine,193,12,1403-12
12435438,Stochastic versus stable transcriptional differences on Plasmodium falciparum DNA microarrays.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751902001820&_version=1&_returnURL=&md5=a9d37e5db67654b985ff4bf3278b1dc5,"The recent availability of the Plasmodium falciparum genome sequence has opened up convenient, large-scale analysis of transcriptional products in malaria. Protocols for cDNA labelling, cDNA hybridisation, and fluorescent signal detection developed for other organisms can be applied directly to malaria. However, P. falciparum offers unique challenges in data analysis due to stochastic variability in expression of some gene products, such as variable erythrocyte surface proteins. Careful comparison of global transcriptional patterns in two well-studied clones of P. falciparum (Dd2 and HB3) indicates that reliable, stable transcriptional alterations in malaria can be readily distinguished from stochastic processes. To do this, we utilised a complex experimental design which involves a combination of self-hybridisations and cross-hybridisations between two independently grown parasite populations for each clone being examined (for short, we call this a '2x2 CombiScan'). While even a simple 2x2 CombiScan required 12 microarray hybridisations, the effort generated output that was highly interpretable. Reliable RNA transcriptional differences between Dd2 and HB3 could be readily visualised using public algorithms for data normalisation and clustering.","Animals!DNA, Complementary/genetics!DNA, Protozoan/*genetics!Oligonucleotide Array Sequence Analysis/*methods!Plasmodium falciparum/*genetics!RNA, Protozoan/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Stochastic Processes!Transcription, Genetic/*genetics!",scirus,2002,International Journal for Parasitology,32,13,1543
12458198,Conserved N-terminal motifs of telomerase reverse transcriptase required for ribonucleoprotein assembly in vivo.,http://www.jbc.org/cgi/content/abstract/278/6/3882,"Telomerase is a ribonucleoprotein (RNP) reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The key protein subunit of the telomerase complex, known as TERT, possesses reverse transcriptase (RT)-like motifs that directly mediate nucleotide addition. The RT motifs are located in the C-terminal region of the polypeptide. Sequence alignments also revealed the existence of four conserved motifs (named GQ, CP, QFP, and T) in the N-terminal region of TERT. The GQ motif of yeast TERT has been demonstrated previously to be essential for telomerase catalysis and may participate in RNP formation. In this report, we show that substitution of conserved residues in the CP, QFP, and T motifs of yeast TERT also impairs both telomere maintenance and telomerase activity, thus confirming the validity of the sequence alignment. The extent of telomere shortening correlates with the extent of reduction in the level of telomerase activity, TERT protein, and TERT-associated TLC1 RNA. Overexpression of the mutant proteins does not result in telomere shortening, implying that assembly rather than catalytic function was affected. This notion was further supported by comparing the efficiency of RNP formation in the wild type and the overexpression strains. Taken together, our results show that three of the four N-terminal motifs are required for efficient telomerase RNP formation in vivo but not for the enzymatic function of telomerase. We also show that the majority of telomerase-associated TLC1 RNA has a more upstream 3' end than previously reported, consistent with additional processing events during RNP maturation. Research Center, Weill Medical College of Cornell University, New York, New York 10021, USA.","Amino Acid Motifs!Amino Acid Sequence!Base Sequence!Catalysis!DNA Primers!DNA-Binding Proteins!Molecular Sequence Data!RNA/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Ribonucleoproteins/*metabolism!Sequence Homology, Amino Acid!Telomerase/chemistry/*metabolism!",scholar,2003,Journal of Biological Chemistry,278,6,3882
12556470,A novel erythrocyte binding antigen-175 paralogue from Plasmodium falciparum defines a new trypsin-resistant receptor on human erythrocytes.,http://www.jbc.org/cgi/content/abstract/278/16/14480,"The recognition and invasion of human erythrocytes by the most lethal malaria parasite Plasmodium falciparum is dependent on multiple ligand-receptor interactions. Members of the erythrocyte binding-like (ebl) family, including the erythrocyte binding antigen-175 (EBA-175), are responsible for high affinity binding to glycoproteins on the surface of the erythrocyte. Here we describe a paralogue of EBA-175 and show that this protein (EBA-181/JESEBL) binds in a sialic acid-dependent manner to erythrocytes. EBA-181 is expressed at the same time as EBA-175 and co-localizes with this protein in the microneme organelles of asexual stage parasites. The receptor binding specificity of EBA-181 to erythrocytes differs from other members of the ebl family and is trypsin-resistant and chymotrypsin-sensitive. Furthermore, using glycophorin B-deficient erythrocytes we show that binding of EBA-181 is not dependent on this sialoglycoprotein. The level of expression of EBA-181 differs among parasite lines, and the importance of this ligand for invasion appears to be strain-dependent as the EBA-181 gene can be disrupted in W2mef parasites, without affecting the invasion phenotype, but cannot be targeted in 3D7 parasites. Australia.","Animals!Antigens/metabolism!Antigens, Protozoan/*chemistry/*metabolism!Antigens, Surface!Carrier Proteins/chemistry/metabolism!Chymotrypsin/pharmacology!Electrophoresis, Polyacrylamide Gel!Erythrocytes/*immunology/metabolism/*parasitology!Humans!Immunoblotting!Ligands!Microscopy, Fluorescence!Models, Genetic!Phenotype!Plasmids/metabolism!Plasmodium falciparum/*metabolism!Protein Binding!Protein Structure, Tertiary!Protozoan Proteins/chemistry/metabolism!Recombination, Genetic!Research Support, Non-U.S. Gov't!Sialoglycoproteins/chemistry!Time Factors!Transfection!Trypsin/*pharmacology!",scholar,2003,Journal of Biological Chemistry,278,16,14480
12603733,Widespread functional specialization of Plasmodium falciparum erythrocyte membrane protein 1 family members to bind CD36 analysed across a parasite genome.,http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2958.2003.03378.x,"Plasmodium falciparum-infected erythrocytes sequester from blood circulation by binding host endothelium. A large family of variant proteins mediates cytoadherence and their binding specificity determines parasite sequestration patterns and potential for disease. The aim of the present study was to understand how binding properties are encoded into family members and to develop sequence algorithms for predicting binding. To accomplish these goals computational approaches and a binding assay were used to characterize adhesion across Plasmodium falciparum erythrocyte membrane 1 (PfEMP1) proteins in the 3D7 parasite genome. We report that most family members encode the capacity to bind CD36 in the protein's semi-conserved head structure and describe the sequence characteristics of a group of PfEMP1 proteins that do not. Structural and functional grouping of PfEMP1 proteins based upon head structure and additional domain architectural properties provide new insights into the protein family. These can be used to investigate the role of proteins in malaria pathogenesis and potentially tailor vaccines to recognize particular binding variants. University, Fort Collins, CO 80525, USA.","Algorithms!Amino Acid Sequence!Animals!Antigens, CD36/*metabolism!Cell Adhesion!Comparative Study!Erythrocytes/parasitology!Genes, Protozoan!Genome!Humans!Malaria Vaccines!Molecular Sequence Data!Multigene Family!Mutagenesis, Site-Directed!Phylogeny!Plasmodium falciparum/genetics/*physiology!Protein Binding!Protein Structure, Tertiary!Protozoan Proteins/chemistry/genetics/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Homology, Amino Acid!",scholar,2003,Mol Microbiol,47,5,1265
12615322,Expression of a recombinant IRP-like Plasmodium falciparum protein that specifically binds putative plasmodial IREs.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685102002785&_version=1&_returnURL=&md5=dffb323d91cc56a6ef02b72e2ee08e3d,"Plasmodium falciparum iron regulatory-like protein (PfIRPa, accession AJ012289) has homology to a family of iron-responsive element (IRE)-binding proteins (IRPs) found in different species. We have previously demonstrated that erythrocyte P. falciparum PfIRPa binds a mammalian consensus IRE and that the binding activity is regulated by iron status. In the work we now report, we have cloned a C-terminus histidine-tagged PfIRPa and overexpressed it in a bacterial expression system in soluble form capable of binding IREs. To overexpress PfIRPa, we used the T7 promoter-driven vector, pET28a(+), in conjunction with the Rosetta(DE3)pLysS strain of E. coli, which carries extra copies of tRNA genes usually found in organisms such as P. falciparum whose genome is (A+T)-rich. The histidine-tagged recombinant protein (rPfIRPa) in soluble form was partially purified using His-bind resin. We searched the plasmodial database, plasmoDB, to identify sequences capable of forming IRE loops using a specially developed algorithm, and found three plasmodial sequences matching the search criteria. In gel retardation assays, rPfIRPa bound three 32P-labeled putative plasmodial IREs with affinity exceeding the affinity for the mammalian consensus IRE. The binding was concentration-dependent and was not inhibited by heparin, an inhibitor of non-specific binding. Immunodepletion of rPfIRPa resulted in substantial inhibition of the signal intensity in the gel retardation assays and in Western blot-determinations of rPfIRPa protein levels. Endogenous PfIRPa retained all three putative 32P-IREs at the same position on the gel as the recombinant PfIRPa. NW, Washington, DC 20059, USA. mloyevsky@howard.edu","Animals!Base Sequence!Binding Sites!DNA Primers!Humans!Iron-Regulatory Proteins/biosynthesis/genetics/*metabolism!Jurkat Cells!Molecular Sequence Data!Nucleic Acid Conformation!Plasmodium falciparum/*metabolism!Protein Binding!Protein-Tyrosine Kinase/metabolism!Proto-Oncogene Proteins/*metabolism!Protozoan Proteins/biosynthesis/genetics/*metabolism!RNA, Protozoan/chemistry/genetics!Recombinant Proteins/metabolism!Research Support, U.S. Gov't, P.H.S.!Wnt Proteins!*Zebrafish Proteins!",scirus,2003,Molecular and Biochemical Parasitology,126,2,231
12620119,Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.,http://www.biomedcentral.com/content/pdf/gb-2003-4-2-r9.pdf,"BACKGROUND: The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development. RESULTS: We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages. CONCLUSIONS: DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development. Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA.","Animals!Blotting, Northern!*Gene Expression Profiling!Oligonucleotide Array Sequence Analysis/*methods!Plasmodium falciparum/*genetics/growth & development!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!",scholar,2003,Genome Biol,4,2,R9
12637517,RNA recognition motif-type RNA-binding proteins in Trypanosoma cruzi form a family involved in the interaction with specific transcripts in vivo.,http://www.jbc.org/cgi/reprint/M301756200v1.pdf,"Trypanosomes, protozoan parasites from the order Kinetoplastida, have to deal with environmental changes during the interaction with their hosts. Trypanosoma cruzi, the causative agent of Chagas' disease, uses post-transcriptional mechanisms to regulate gene expression. However, few RNA-binding proteins involved in mRNA turnover control have been identified to date. In this work, an RNA recognition motif (RRM)-type RNA-binding protein family named T. cruzi RNA-binding protein (TcRBP) and composed of at least six members was identified. The genomic organization of four members revealed a head to tail arrangement within a region of 15 kilobase pairs. TcRBP members have a common RRM and different auxiliary domains with a high content of glycine, glutamine, and histidine residues within their N- and C-terminal regions. TcRBPs differ in their expression patterns as well as in their homoribopolymer binding interaction in vitro, although they preferentially recognize poly(U) and poly(G) RNAs. An interesting observation was the relaxed RNA-binding interactions with several trypanosome transcripts in vitro. In contrast, co-immunoprecipitation experiments of TcRBP-containing ribonucleoprotein complexes formed in vivo revealed a highly restricted binding interaction with specific RNAs. Several TcRBP-containing complexes are stage-specific and, in some cases, bear the poly(A)-binding protein TcPABP1. Altogether, these results suggest that TcRBPs might be modulated in vivo, to favor or preclude the interaction with specific transcripts in a developmentally regulated manner. Chascomus, CONICET-UNSAM, 1650 San Martin, Provincia de Buenos Aires, Argentina.","3' Untranslated Regions!5' Untranslated Regions!Amino Acid Sequence!Animals!Base Sequence!Blotting, Northern!Blotting, Southern!Comparative Study!DNA/chemistry!DNA Restriction Enzymes/metabolism!Glutamine/analysis!Glycine/analysis!Histidine/analysis!Molecular Sequence Data!Phylogeny!Poly G/metabolism!Poly U/metabolism!Protein Structure, Secondary!Protozoan Proteins/chemistry/genetics/metabolism!RNA/*metabolism!RNA, Messenger/analysis/*metabolism!RNA-Binding Proteins/*chemistry/*genetics/metabolism!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Sequence Alignment!Trypanosoma cruzi/*chemistry!",scholar,,Journal of Biological Chemistry,,,
12657463,The Plasmodium falciparum family of Rab GTPases.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0378111903003810&_version=1&_returnURL=&md5=22460a44366384205fcb261bed6683f9,"Rab GTPases are key regulators of vesicular traffic in eukaryotic cells. Here we sought a global characterization and description of the Plasmodium falciparum family of Rab GTPases. We used a combination of bioinformatic analyses, experimental testing of predictions, structure modelling and phylogenetics. These analyses led to the identification of seven new parasite Rabs. Accordingly we estimate that the P. falciparum family is made up of 11 genes. We show that ten members of this family are transcribed in infected erythrocytes. Concerning the various members of the family, a series of specific as well as global conclusions can be drawn. Rabs predicted to be compartment-specific show different subcellular distributions. This is demonstrated for PfRab1A and PfRab11A, with the generation of specific antisera. The sequence analyses reveal several peculiarities, with possible functional implications. One of the transcribed genes, Pfrab5b, does not encode a classical C-terminus, suggestive of a novel regulatory role for this GTPase. Another, Pfrab5a, previously identified as a rab gene located on chromosome 2, possesses a 30-amino-acid insertion in its GTP-binding domain. Structural considerations suggest that this insertion could represent a novel interaction interface. We used conserved RabF and RabSF motifs to discriminate between specific parasite Rabs, and followed their predicted change in position on the structure of PfRab6, as GTP is hydrolysed to GDP. This allowed us to propose their involvement in potential interaction surfaces, that we extended to human Rab6 and the motifs known to mediate Rabkinesine-6 binding. Finally, we compared the P. falciparum Rab family to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe and found that parasite Rabs segregate into possible functional clads. Such grouping into clads may give clues to parasite Rab function, and may shed light on P. falciparum secretory/endocytic pathways. of Parasitology, Institut Pasteur, Paris, France.","Amino Acid Sequence!Animals!DNA, Complementary/chemistry/genetics!Erythrocytes/parasitology!Gene Expression Regulation, Enzymologic!Guanosine Triphosphate/chemistry/metabolism!Humans!Models, Molecular!Molecular Sequence Data!Multigene Family/*genetics!Phylogeny!Plasmodium falciparum/enzymology/*genetics!Protein Binding!Protein Conformation!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Analysis, DNA!Sequence Homology, Amino Acid!rab GTP-Binding Proteins/chemistry/*genetics/metabolism!",scirus,2003,Gene,306,.,13
12671001,Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite.,http://intl.genome.org/cgi/content/abstract/13/4/601,"The search for novel antimalarial drug targets is urgent due to the growing resistance of Plasmodium falciparum parasites to available drugs. Proteases are attractive antimalarial targets because of their indispensable roles in parasite infection and development, especially in the processes of host erythrocyte rupture/invasion and hemoglobin degradation. However, to date, only a small number of proteases have been identified and characterized in Plasmodium species. Using an extensive sequence similarity search, we have identified 92 putative proteases in the P. falciparum genome. A set of putative proteases including calpain, metacaspase, and signal peptidase I have been implicated to be central mediators for essential parasitic activity and distantly related to the vertebrate host. Moreover, of the 92, at least 88 have been demonstrated to code for gene products at the transcriptional levels, based upon the microarray and RT-PCR results, and the publicly available microarray and proteomics data. The present study represents an initial effort to identify a set of expressed, active, and essential proteases as targets for inhibitor-based drug design. Virginia 20110, USA. development/pathogenicity","Amino Acid Sequence/genetics!Animals!Calpain/genetics!Comparative Study!Endopeptidases/*genetics!Evolution, Molecular!Gene Expression Profiling/methods!Gene Expression Regulation, Enzymologic/genetics!*Genome, Protozoan!Humans!Malaria, Falciparum/*enzymology/parasitology!*Membrane Proteins!Molecular Sequence Data!Multigene Family/*genetics!Plasmodium falciparum/*enzymology/*genetics/growth &!Predictive Value of Tests!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment/methods!Serine Endopeptidases/genetics!",scholar,2003,Genome Research,13,4,601
12706793,Low-complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103000392&_version=1&_returnURL=&md5=68b10d8da12029545f146efc97165b3e,"Protein segments that contain few of the possible 20 amino acids, sometimes in tandem repeat arrays, are referred to as containing "simple" or "low-complexity" sequence. Many Plasmodium falciparum proteins are longer than their homologs in other species by virtue of their content of such low-complexity segments that have no known function; these are interspersed among segments of higher complexity to which function can often be ascribed. If there is low complexity at the protein level, there is likely to be low complexity at the corresponding nucleic acid level (departure from equifrequency of the four bases). Thus, low complexity may have been selected primarily at the nucleic acid level and low complexity at the protein level may be secondary. In this case, the amino acid composition of low-complexity segments should be more reflective than that of high complexity segments on forces operating at the nucleic acid level, which include GC-pressure and AG-pressure. Consistent with this, for amino acid determining first and second codon positions, open reading frames containing low-complexity segments show increased contributions to downward GC-pressure (revealed as decreased percentage of G+C) and to upward AG-pressure (revealed as increased percentage A+G). When not countermanded by high contributions to AG-pressure, low-complexity segments can contribute to base order-dependent fold potential; in this respect, they resemble introns. Thus, in P. falciparum, low-complexity segments appear as adaptations primarily serving nucleic acid level functions. Canada.","Amino Acids/chemistry/genetics!Animals!Base Composition!Chromosomes/genetics!Codon/genetics!DNA Transposable Elements/genetics!DNA, Protozoan/chemistry/genetics!Evolution, Molecular!Herpesvirus 4, Human/genetics!Introns/genetics!Plasmodium falciparum/chemistry/*genetics!Protein Structure, Tertiary/genetics!Protozoan Proteins/*chemistry/genetics!Repetitive Sequences, Amino Acid!",scirus,2003,Molecular and Biochemical Parasitology,128,1,21
12706803,Striated fiber assemblin in apicomplexan parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103000380&_version=1&_returnURL=&md5=ef1bc35185e45c5420fcfdcfcb94b8ca,,"Amino Acid Sequence!Animals!*Apicomplexa/chemistry/classification!Base Sequence!Chlamydomonas reinhardtii/chemistry/genetics!Cloning, Molecular!DNA Primers/genetics!Microtubule-Associated Proteins/*analysis/*chemistry/classification!Molecular Sequence Data!Phylogeny!Protozoan Proteins/*analysis/*chemistry/classification!Research Support, Non-U.S. Gov't!Toxoplasma/chemistry/genetics/ultrastructure!",scirus,2003,Molecular and Biochemical Parasitology,128,1,95
12737636,Sympatric Plasmodium falciparum isolates from Venezuela have structured var gene repertoires.,http://www.malariajournal.com/content/2/1/7,"BACKGROUND: The human malaria parasite Plasmodium falciparum expresses adhesins belonging to the erythrocyte membrane protein 1 (PfEMP1) family on the surface of the infected host erythrocyte. These antigens elicit a strain-specific antibody response that is associated with protection from disease. During clonal expansion of blood-stage parasites, the surface phenotype of the infected erythrocyte changes because of transcriptional switching among the 40 to 50 members of the highly polymorphic var multi-gene family which encode PfEMP1 variants. Studies to date have compared var repertoires of natural isolates from various geographical locations but have not addressed any within-population structure that may exist among repertoires. METHODS: Distinct parasite genotypes from a single population co-circulating among a defined group of hosts were selected. PCR products encoding the DBL-alpha domain of PfEMP-1 were cloned and sequenced from each of three isolates. Repertoire similarity was statistically evaluated using combinatorial analysis. The chromosomal location of shared sequences was inferred from similarity to dbl-alpha of known location in the 3D7 genome. RESULTS: Sympatric parasites were found to share few var gene sequences, even when alleles at other polymorphic loci were shared. A number of the sequences shared by at least two of the isolates studied were found to be related to 3D7 genomic sequences with non-telomeric chromosomal locations, or atypical domain structures, which may represent globally conserved loci. CONCLUSION: The parasite population studied is structured, with minimal overlap in PfEMP1 repertoires. The var gene family accumulates diversity more rapidly than other antigen genes examined. This may be facilitated by ectopic recombination among the sub-telomeric regions of P. falciparum chromosomes. School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK. adriana.tami@lshtm.ac.uk","Adolescent!Adult!Animals!Antigens, Protozoan/genetics!Conserved Sequence/genetics!Cross-Sectional Studies!DNA, Protozoan/genetics!Gene Frequency/genetics!*Genes, Protozoan!Genetics, Population/statistics & numerical data!Genotype!Humans!Malaria, Falciparum/epidemiology!Male!Merozoite Surface Protein 1/genetics!Plasmodium falciparum/*genetics/*isolation & purification!Protein Structure, Tertiary/genetics!Protozoan Proteins/genetics!Research Support, Non-U.S. Gov't!Variation (Genetics)!Venezuela/epidemiology!",scirus,2003,Malaria Journal,2,1,7
12743798,Molecular cloning and characterization of an SRCAP chromatin remodeling homologue in Toxoplasma gondii.,http://www.springerlink.com/index/Y8BHBKF8EVWVRCAE.pdf,"We have identified and mapped a gene in Toxoplasma gondii that encodes a homologue of SRCAP (Snf2-related CBP activator protein), a member of the SNF/SWI family of chromatin remodeling factors. The genomic locus (TgSRCAP) is present as a single copy and contains 16 introns. The predicted cDNA contains an open reading frame of 8,775 bp and encodes a protein of 2,924 amino acids. We have identified additional SRCAP-like sequences in Apicomplexa for comparison by screening genomic databases. An analysis of SRCAP homologues between species reveals signature features that may be indicative of SRCAP members. Expression of mRNA encoding TgSRCAP is upregulated when tachyzoite (invasive form) parasites are induced to differentiate into bradyzoites (encysted form) in vitro. Recombinant TgSRCAP protein is functionally equivalent to the human homologue, being capable of increasing transcription mediated by CREB. School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202-5120, USA. wjsulliv@iupui.edu","Adenosinetriphosphatase/analysis/*chemistry/*genetics!Amino Acid Sequence!Animals!CREB-Binding Protein!Chromatin/*genetics!Cloning, Molecular!Gene Expression Regulation!*Genes, Protozoan!Hela Cells!Humans!Molecular Sequence Data!Nuclear Proteins/metabolism!RNA, Messenger/genetics!Sequence Homology, Amino Acid!Toxoplasma/*genetics/isolation & purification!Trans-Activators/metabolism!Transcription, Genetic!",scholar,2003,Parasitology Research,90,1,1
12756555,A Plasmodium homologue of cochaperone p23 and its differential expression during the replicative cycle of the malaria parasite.,http://www.springerlink.com/index/V7JC9026CHRQ9A2M.pdf,"The complete gene sequence of a major phosphoprotein from the malaria parasite reveals that it is a homologue to cochaperone p23. This p23 homologue is highly conserved between Plasmodium falciparum and other malaria parasites and exhibits 44% sequence identity with the Schizosaccharomyces pombe p23 homologue. The Plasmodium p23 is a relatively abundant cytoplasmic protein with a molecular mass of 34-36 kDa depending on species. Expression of this 34 kDa protein and its mRNA commences in the early ring stage and continues throughout the trophozoite stage. At the beginning of schizogony there is a decrease in the transcription and translation rates and a decline in the amount of the 34 kDa protein. The exact role of the 34 kDa phosphoprotein in parasite replication and differentiation is not known, but the Plasmodium p23 homologue may play a role in parasite proliferation and differentiation through its interactions with protein kinases and other chaperones. and Tropical Medicine, 1440 Canal Street, SL17, New Orleans, LA 70112, USA. wiser@tulane.edu",Animals!Base Sequence!DNA Replication!Fluorescent Antibody Technique!Life Cycle Stages/genetics!Molecular Chaperones/*metabolism!Phosphoproteins/*metabolism!Plasmodium/genetics/growth & development/*metabolism/physiology!Protozoan Proteins/*metabolism!*Schizosaccharomyces pombe Proteins!Sequence Alignment!,scholar,2003,Parasitology Research,90,2,166
12798510,New tools to identify var sequence tags and clone full-length genes using type-specific primers to Duffy binding-like domains.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103000999&_version=1&_returnURL=&md5=3d723384a7659838e428428f78b57b3f,"Cytoadherence of infected erythrocytes is a hallmark of Plasmodium falciparum infection and a key determinant in the particular virulence of this species. Infected erythrocytes bind a variety of host receptors but certain adhesion traits are associated with more severe disease. A large, diverse protein family named P. falciparum erythrocyte membrane protein 1 (PfEMP1) is responsible for sequestration of mature stage infected erythrocytes and orchestrates parasite binding tropism. To better understand the molecular basis for malaria disease, more study is needed to identify the subset of PfEMP1 variants that contribute to basic disease phenotypes. PfEMP1 proteins have multiple receptor-like domains that group into different homology types based upon sequence similarity. Universal primers have been developed that recognize some, but not all PfEMP1 adhesion domain types. In this study, we designed and validated a new series of type-discriminatory primers to the DBL-beta, -gamma, and -delta adhesion types for epidemiological profiling. In addition, we used new primers to the var upstream region and exon 2 to demonstrate how the strategic placement of primers throughout the gene structure can be exploited to efficiently clone the var gene coding region. These new approaches provide valuable tools to gain novel insights into cytoadherence and malaria pathogenesis. 98109, USA.","Animals!Antigens, Protozoan/metabolism!Base Sequence!Binding Sites!*Cloning, Molecular!*DNA Primers!Databases, Genetic!Duffy Blood-Group System/metabolism!*Genes, Protozoan!Models, Genetic!Phylogeny!Plasmodium falciparum/genetics!Protein Structure, Tertiary!Protozoan Proteins/chemistry/*genetics/metabolism!Receptors, Cell Surface/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sensitivity and Specificity!Sequence Homology!*Sequence Tagged Sites!",scirus,2003,Molecular and Biochemical Parasitology,129,1,91
12809568,Characterisation of methionine adenosyltransferase from Mycobacterium smegmatis and M. tuberculosis.,http://www.biomedcentral.com/content/pdf/1471-2180-3-12.pdf,"BACKGROUND: Tuberculosis remains a serious world-wide health threat which requires the characterisation of novel drug targets for the development of future antimycobacterials. One of the key obstacles in the definition of new targets is the large variety of metabolic alterations that occur between cells in the active growth and chronic/dormant phases of tuberculosis. The ideal biochemical target should be active in both growth phases. Methionine adenosyltransferase, which catalyses the formation of S-adenosylmethionine from methionine and ATP, is involved in polyamine biosynthesis during active growth and is also required for the methylation and cyclopropylation of mycolipids necessary for survival in the chronic phase. RESULTS: The gene encoding methionine adenosyltransferase has been cloned from Mycobacterium tuberculosis and the model organism M. smegmatis. Both enzymes retained all amino acids known to be involved in catalysing the reaction. While the M. smegmatis enzyme could be functionally expressed, the M. tuberculosis homologue was insoluble and inactive under a large variety of expression conditions. For the M. smegmatis enzyme, the Vmax for S-adenosylmethionine formation was 1.30 micromol/min/mg protein and the Km for methionine and ATP was 288 microM and 76 microM respectively. In addition, the enzyme was competitively inhibited by 8-azaguanine and azathioprine with a Ki of 4.7 mM and 3.7 mM respectively. Azathioprine inhibited the in vitro growth of M. smegmatis with a minimal inhibitory concentration (MIC) of 500 microM, while the MIC for 8-azaguanine was >1.0 mM. CONCLUSION: The methionine adenosyltransferase from both organisms had a primary structure very similar those previously characterised in other prokaryotic and eukaryotic organisms. The kinetic properties of the M. smegmatis enzyme were also similar to known prokaryotic methionine adenosyltransferases. Inhibition of the enzyme by 8-azaguanine and azathioprine provides a starting point for the synthesis of higher affinity purine-based inhibitors. Box 4000, Medicine Hat, AB, T1A 8K6, Canada. Brad.Berger@drdc-rddc.gc.ca inhibitors/*genetics/metabolism","Azaguanine/pharmacology!Azathioprine/pharmacology!Cloning, Molecular!Enzyme Inhibitors/pharmacology!Gene Expression!Methionine Adenosyltransferase/antagonists &!Mycobacterium smegmatis/*enzymology/genetics!Mycobacterium tuberculosis/*enzymology/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Species Specificity!",scholar,2003,BMC Microbiology,3,,12
12823820,Selective upregulation of a single distinctly structured var gene in chondroitin sulphate A-adhering Plasmodium falciparum involved in pregnancy-associated malaria.,http://www.ingentaconnect.com/content/bsc/mole/2003/00000049/00000001/art00015,"Cytoadhesion of infected red blood cells (iRBC) is mediated through parasite-encoded, clonally variant surface antigens (VSA) and is a central process in the pathogenesis of Plasmodium falciparum malaria. Pregnancy-associated malaria (PAM) has been linked to VSA-mediated adhesion of iRBC to the glycosaminoglycan chondroitin sulphate A (CSA) in the placental intervillous space. Several studies have pointed to members of the PfEMP1 VSA family as mediators of CSA-specific iRBC sequestration in the placenta. Here, we report marked upregulation of a single var gene in several P. falciparum parasite isolates after selection for adhesion to CSA in vitro. The gene belongs to a highly conserved and common var gene subfamily (var2csa). The var2csa genes are structurally distinct from all other var genes in the parasite genome in lacking both CIDR and DBL-gamma domains. These domains have previously been implicated in PfEMP1-mediated adhesion to CD36 and CSA. We also show that var2csa was transcribed at higher levels in three placental parasite isolates compared with transcription in parasites from peripheral blood of two children with P. falciparum malaria. This var gene thus has the properties expected of a gene encoding the parasite adhesion molecule that initiates the pathology associated with PAM. and Immunology, University of Copenhagen, Panum Institute 24-2, and Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Denmark. hecmp@biobase.dk","Adult!Animals!Antigens, Protozoan/*genetics/metabolism!Antigens, Surface/genetics/metabolism!Cell Adhesion!Child!Chondroitin Sulfates/*metabolism!Erythrocytes/parasitology/physiology!Female!Genome, Protozoan!Humans!Malaria, Falciparum/*parasitology!Male!Multigene Family!Placenta/parasitology!Plasmodium falciparum/*genetics/metabolism!Pregnancy!Pregnancy Complications, Parasitic/*parasitology!Protozoan Proteins/*genetics/metabolism!Research Support, Non-U.S. Gov't!Transcription, Genetic!Up-Regulation!",scholar,2003,Molecular Microbiology,49,1,179
12824434,GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives.,http://nar.oupjournals.org/cgi/content/abstract/31/13/3843,"The GeneFizz (http://pbga.pasteur.fr/GeneFizz) web tool permits the direct comparison between two types of segmentations for DNA sequences (possibly annotated): the coding/non-coding segmentation associated with genomic annotations (simple genes or exons in split genes) and the physics-based structural segmentation between helix and coil domains (as provided by the classical helix-coil model). There appears to be a varying degree of coincidence for different genomes between the two types of segmentations, from almost perfect to non-relevant. Following these two extremes, GeneFizz can be used for two purposes: ab initio physics-based identification of new genes (as recently shown for Plasmodium falciparum) or the exploration of possible evolutionary signals revealed by the discrepancies observed between the two types of information. 75724 Paris Cedex 15, France. yeramian@pasteur.fr","Algorithms!Animals!DNA/chemistry!Drosophila melanogaster/genetics!*Evolution, Molecular!*Genes!Genetic Code!Genomics/methods!Internet!Models, Genetic!Nucleic Acid Conformation!Plasmodium falciparum/genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!*Software!User-Computer Interface!",scholar,2003,Nucleic Acids Research,31,13,3843
12857354,PEST sequences in the malaria parasite Plasmodium falciparum: a genomic study.,http://bmc.ub.uni-potsdam.de/cgi-bin/show.pl%3F1475-2875-2-16/1475-2875-2-16.pdf,"BACKGROUND: Inhibitors of the protease calpain are known to have selectively toxic effects on Plasmodium falciparum. The enzyme has a natural inhibitor calpastatin and in eukaryotes is responsible for turnover of proteins containing short sequences enriched in certain amino acids (PEST sequences). The genome of P. falciparum was searched for this protease, its natural inhibitor and putative substrates. METHODS: The publicly available P. falciparum genome was found to have too many errors to permit reliable analysis. An earlier annotation of chromosome 2 was instead examined. PEST scores were determined for all annotated proteins. The published genome was searched for calpain and calpastatin homologs. RESULTS: Typical PEST sequences were found in 13% of the proteins on chromosome 2, including a surprising number of cell-surface proteins. The annotated calpain gene has a non-biological "intron" that appears to have been created to avoid an unrecognized frameshift. Only the catalytic domain has significant similarity with the vertebrate calpains. No calpastatin homologs were found in the published annotation. CONCLUSION: A calpain gene is present in the genome and many putative substrates of this enzyme have been found. Calpastatin homologs may be found once the re-annotation is completed. Given the selective toxicity of calpain inhibitors, this enzyme may be worth exploring further as a potential drug target. Republic of Ireland. dmitchel@tcd.ie","Amino Acid Sequence!Animals!Calcium-Binding Proteins/genetics!Calpain/genetics!Cysteine Proteinase Inhibitors/genetics!Databases, Genetic!*Genome, Protozoan!Malaria, Falciparum/*genetics!Plasmodium falciparum/chemistry/*genetics!Protozoan Proteins/analysis/genetics!",scholar,2003,Malaria Journal,2,,16
12864851,"Mapping of the Plasmodium falciparum multidrug resistance gene 5'-upstream region, and evidence of induction of transcript levels by antimalarial drugs in chloroquine sensitive parasites.",http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2958.2003.03597.x/abs/,"The Plasmodium falciparum multidrug resistance gene, pfmdr1, has been shown to be involved in the mediation of the parasite's response to various antimalarial drugs. Previous studies of pfmdr1 expression have shown that transcript levels are increased in drug-resistant isolates. However, a detailed examination of the transcriptional regulation of this gene has not been completed. The aim of this study was to map the 5' UTR of pfmdr1, and to examine the transcriptional profile of the gene in sensitive parasites treated with four different antimalarial drugs. RT-PCR and 5'-RACE mapping showed that the 5' UTR has a length of 1.94 kb. A putative promoter has been identified via transient transfection. Northern analysis revealed a 2.1- to 2.7-fold increase in pfmdr1 expression in 3D7 parasites treated with 50 nM chloroquine for 6 h, confirming results from Serial Analysis of Gene Expression. 3D7 parasites were subsequently treated with experimentally derived IC50 concentrations of mefloquine, quinine and pyrimethamine. pfmdr1 transcript levels specifically increased 2.5-fold at 6 h in mefloquine-treated parasites and threefold in parasites treated with quinine for 30 min. There was no evidence of transcript induction in pyrimethamine-treated parasites. This is the first evidence of induction of pfmdr1 expression in sensitive cells; and suggests a novel method of transcriptional control for this gene. Health, Boston MA, USA.","5' Untranslated Regions/*genetics!ATP-Binding Cassette Transporters/biosynthesis/*genetics!Animals!Antimalarials/*pharmacology!Base Sequence!Chloroquine/*pharmacology!Chromosome Mapping!Comparative Study!Drug Resistance, Multiple/*genetics!Gene Expression Regulation/*drug effects!*Genes, MDR!*Genes, Protozoan!Genes, Reporter!Luciferases/biosynthesis/genetics!Mefloquine/pharmacology!Molecular Sequence Data!Plasmodium falciparum/drug effects/*genetics!Polymerase Chain Reaction!Protozoan Proteins/biosynthesis/*genetics!Pyrimethamine/pharmacology!Quinine/pharmacology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Reverse Transcriptase Polymerase Chain Reaction!Sequence Alignment!Sequence Homology, Nucleic Acid!Transcription, Genetic/*drug effects!",scholar,2003,Molecular Microbiology,49,3,671
12869562,Identification and initial characterization of three novel cyclin-related proteins of the human malaria parasite Plasmodium falciparum.,http://www.jbc.org/cgi/reprint/M301625200v1.pdf,"The molecular mechanisms regulating cell proliferation and development during the life cycle of malaria parasites remain to be elucidated. The peculiarities of the cell cycle organization during Plasmodium falciparum schizogony suggest that the modalities of cell cycle control in this organism may differ from those in other eukaryotes. Indeed, existing data concerning Plasmodium cell cycle regulators such as cyclin-dependent kinases reveal structural and functional properties that are divergent from those of their homologues in other systems. The work presented here lies in the context of the exploitation of the recently available P. falciparum genome sequence toward the characterization of putative cell cycle regulators. We describe the in silico identification of three open reading frames encoding proteins with maximal homology to various members of the cyclin family and demonstrate that the corresponding polypeptides are expressed in the erythrocytic stages of the infection. We present evidence that these proteins possess cyclin activity by demonstrating either their association with histone H1 kinase activity in parasite extracts or their ability to activate PfPK5, a P. falciparum cyclin-dependent kinase homologue, in vitro. Furthermore, we show that RINGO, a protein with no sequence homology to cyclins but that is nevertheless a strong activator of mammalian CDK1/2, is also a strong activator of PfPK5 in vitro. This raises the possibility that "cryptic" cell cycle regulators may be found among the 50% of the open reading frames in the P. falciparum genome that display no homology to any known proteins. College, 56 Dumbarton Road, Glasgow G11 6NU, Scotland, United Kingdom.","Amino Acid Sequence!Animals!Base Sequence!Cell Cycle!Cell Cycle Proteins/metabolism!Cyclins/genetics/isolation & purification/*metabolism!DNA, Protozoan/genetics!Erythrocytes/parasitology!Gene Expression Regulation, Developmental!Genes, Protozoan!Humans!In Vitro!Malaria, Falciparum/parasitology!Molecular Sequence Data!Open Reading Frames!Plasmodium falciparum/cytology/genetics/growth & development/*metabolism!Protein Kinases/metabolism!Protozoan Proteins/genetics/isolation & purification/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Homology, Amino Acid!",scholar,,Journal of Biological Chemistry,,,
12886016,Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data.,http://www.pnas.org/cgi/content/abstract/100/17/9952,"The recent explosion in genomic sequencing has made available a wealth of data that can now be analyzed to identify protein antigens, potential targets for vaccine development. Here we present, in the context of Plasmodium falciparum, a strategy that rapidly identifies target antigens from large and complex genomes. Sixteen antigenic proteins recognized by volunteers immunized with radiation-attenuated P. falciparum sporozoites, but not by mock immunized controls, were identified. Several of these were more antigenic than previously identified and well characterized P. falciparum-derived protein antigens. The data suggest that immune responses to Plasmodium are dispersed on a relatively large number of parasite antigens. These studies have implications for our understanding of immunodominance and breadth of responses to complex pathogens. 20910-7500, USA. America.","Adult!Algorithms!Alleles!Animals!Antigens, Protozoan/*genetics/isolation & purification!Genes, Protozoan!Genome, Protozoan!Genomics!Humans!Immunization!In Vitro!Interferon Type II/biosynthesis!Malaria Vaccines/genetics/immunology/isolation & purification!Male!Middle Aged!Molecular Sequence Data!Plasmodium falciparum/*genetics/*immunology!Proteomics!Protozoan Proteins/genetics/immunology/isolation & purification!Research Support, U.S. Gov't, Non-P.H.S.!T-Lymphocytes/immunology!",scholar,2003,Proceedings of the National Academy of Sciences,100,17,9952
12893887,Discovery of gene function by expression profiling of the malaria parasite life cycle.,http://www.sciencemag.org/cgi/reprint/1087025v1.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,2003,Science,301,5639,1503
12893888,A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893889,Radiology 2003--science to practice.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893890,"Science to practice: blood flow quantification with contrast-enhanced US: entrance in the section"" phenomenon--phantom and rabbit study.""",http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893892,The end of life.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893893,Lymphoscintigraphy for lymphatic mapping in breast carcinoma.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893894,Opportunities and challenges for the National Institute of Biomedical Imaging and Bioengineering.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893895,Image-guided tumor ablation: proposal for standardization of terms and reporting criteria.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893896,Self-referred whole-body CT imaging: current implications for health care consumers.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893897,Dose reduction in pediatric CT: a rational approach.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893898,Intrapleural fibrinolysis for parapneumonic effusion and empyema in children.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893899,The deep sulcus sign.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893900,Irreversible JPEG compression of digital chest radiographs for primary interpretation: assessment of visually lossless threshold.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12893901,Celiac artery compression by the median arcuate ligament: a pitfall of end-expiratory MR imaging.,http://plantbio.berkeley.edu/~taylor/pmb290/genomics.pdfs/LeRoche.Science.2003.pdf,"The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes. North Torrey Pines Road, La Jolla, CA 92037, USA. leroch@scripps.edu","Animals!Anopheles/parasitology!Cell Cycle!Chromosomes/genetics!Cluster Analysis!Erythrocytes/parasitology!*Gene Expression!*Gene Expression Profiling!Gene Expression Regulation, Developmental!*Genes, Protozoan!Humans!Life Cycle Stages!Liver/parasitology!Malaria, Falciparum/parasitology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/*growth & development/metabolism!Proteome!Protozoan Proteins/genetics/metabolism/physiology!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Salivary Glands/parasitology!Sporozoites/genetics/growth & development!Transcription, Genetic!",scholar,,,,,
12929205,The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum.,http://biology.plosjournals.org/perlserv/%3Frequest%3Dget-document%26doi%3D10.1371%252Fjournal.pbio.0000005,"Plasmodium falciparum is the causative agent of the most burdensome form of human malaria, affecting 200-300 million individuals per year worldwide. The recently sequenced genome of P. falciparum revealed over 5,400 genes, of which 60% encode proteins of unknown function. Insights into the biochemical function and regulation of these genes will provide the foundation for future drug and vaccine development efforts toward eradication of this disease. By analyzing the complete asexual intraerythrocytic developmental cycle (IDC) transcriptome of the HB3 strain of P. falciparum, we demonstrate that at least 60% of the genome is transcriptionally active during this stage. Our data demonstrate that this parasite has evolved an extremely specialized mode of transcriptional regulation that produces a continuous cascade of gene expression, beginning with genes corresponding to general cellular processes, such as protein synthesis, and ending with Plasmodium-specific functionalities, such as genes involved in erythrocyte invasion. The data reveal that genes contiguous along the chromosomes are rarely coregulated, while transcription from the plastid genome is highly coregulated and likely polycistronic. Comparative genomic hybridization between HB3 and the reference genome strain (3D7) was used to distinguish between genes not expressed during the IDC and genes not detected because of possible sequence variations. Genomic differences between these strains were found almost exclusively in the highly antigenic subtelomeric regions of chromosomes. The simple cascade of gene regulation that directs the asexual development of P. falciparum is unprecedented in eukaryotic biology. The transcriptome of the IDC resembles a "just-in-time" manufacturing process whereby induction of any given gene occurs once per cycle and only at a time when it is required. These data provide to our knowledge the first comprehensive view of the timing of transcription throughout the intraerythrocytic development of P. falciparum and provide a resource for the identification of new chemotherapeutic and vaccine candidates. Francisco, USA.","Animals!Antimalarials/pharmacology!Chromosome Mapping!Chromosomes/ultrastructure!Erythrocytes/*parasitology!Gene Expression Regulation!*Gene Expression Regulation, Developmental!Genes, Protozoan!Genome!Genome, Protozoan!Humans!Nucleic Acid Hybridization!Oligonucleotide Array Sequence Analysis!Oligonucleotides/chemistry!Open Reading Frames!Plasmodium falciparum/*metabolism!Plastids!Protozoan Proteins!RNA, Messenger/metabolism!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Time Factors!*Transcription, Genetic!",scholar,,,,,
9373142,Partial nucleotide sequence and organisation of extrachromosomal plastid-like DNA in Plasmodium berghei.,,"The murine malaria parasite Plasmodium berghei contains a plastid-like extrachromosomal genome. This genome is 30.7 kb in size and is transcriptionally active as shown by RT-PCR. DNA sequence analysis of the genome reveals 69.9-95.5% homology to sequences of the 35-kb extrachromosomal circle found in the human malaria species Plasmodium falciparum. Homologous sequences include regions of genes for the ssu-rRNA, lsu-rRNA, rpo B and clusters of t-RNAs. Sequence variation between the two Plasmodium species exists in the non-coding interspacing regions. A physical map has been constructed for the P. berghei circle, indicating the EcoRI and HindIII restriction sites as well as the arrangement of the rRNA, rpo B and tRNA genes. Arrangement of these genes is similar to that found on the P. falciparum 35-kb circle. The P. berghei circular element is distinct from the mitochondrial 6-kb DNA of both the murine and the human Plasmodium species. Preliminary results indicate that the circle may be a useful target for drug therapy.","Plasmodium falciparum,Restriction Mapping,Humans,Plasmodium berghei,DNA, Protozoan,Variation (Genetics),Sequence Homology, Nucleic Acid,Plastids,Mice,Base Sequence,RNA, Protozoan,DNA, Mitochondrial,Polymerase Chain Reaction,Animals",NCBI,1997,Gene,200,2-Jan,91-8
12952885,OrthoMCL: identification of ortholog groups for eukaryotic genomes.,http://intl.genome.org/cgi/content/abstract/13/9/2178,"The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences. Methods successfully exploited for prokaryotic genome analysis have proved difficult to apply to eukaryotes, however, as larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs. This method performs similarly to the INPARANOID algorithm when applied to two genomes, but can be extended to cluster orthologs from multiple species. OrthoMCL clusters are coherent with groups identified by EGO, but improved recognition of "recent" paralogs permits overlapping EGO groups representing the same gene to be merged. Comparison with previously assigned EC annotations suggests a high degree of reliability, implying utility for automated eukaryotic genome annotation. OrthoMCL has been applied to the proteome data set from seven publicly available genomes (human, fly, worm, yeast, Arabidopsis, the malaria parasite Plasmodium falciparum, and Escherichia coli). A Web interface allows queries based on individual genes or user-defined phylogenetic patterns (http://www.cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome. Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.","Animals!Arabidopsis/genetics!Caenorhabditis elegans/genetics!Comparative Study!Computational Biology/methods!Drosophila melanogaster/genetics!Eukaryotic Cells/*chemistry/*metabolism!*Genome!Genome, Fungal!Genome, Plant!Genome, Protozoan!Humans!Internet!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Saccharomyces cerevisiae/*genetics!*Sequence Homology, Nucleic Acid!*Software!",scholar,2003,Genome Research,13,9,2178
12956414,"Protein prenyltransferases: anchor size, pseudogenes and parasites.",https://www.degruyter.com/journals/bc/2003/pdf/384_977.pdf,"Lipid modification of eukaryotic proteins by protein prenyltransferases is required for critical signaling pathways, cell cycle progression, cytoskeleton remodeling, induction of apoptosis and vesicular trafficking. This review analyzes the influence of distinct states of sequential posttranslational processing that can be obtained after single or double prenylation, reversible palmitoylation, proteolytic cleavage of the C-terminus and possible reversible carboxymethylation. This series of modifications, as well as the exact length of the prenyl anchor, are determinants in protein-membrane and specific protein-protein interactions of protein prenyltransferase substrates. Furthermore, the occurrence and distribution of pseudogenes of protein prenyltransferase subunits are discussed. Besides being developed as anti-cancer agents, prenyltransferase inhibitors are effective against an increasing number of parasitic diseases. Extensive screens for protein prenyltransferases in genomic data of fungal and protozoan pathogens unveil a series of new pharmacologic targets for prenyltransferase inhibition, including the parasites Brugia malayi, Onchocerca volvulus, Aspergillus nidulans, Pneumocystis carinii, Entamoeba histolytica, Strongyloides stercoralis, Trichinella spiralis and Cryptosporidium parvum. Vienna, Austria. stroh@imp.univie.ac.at inhibitors/classification/genetics/*metabolism","Animals!Antineoplastic Agents/pharmacology/therapeutic use!Comparative Study!Dimethylallyltranstransferase/antagonists &!Enzyme Inhibitors/pharmacology/therapeutic use!Humans!Parasites/drug effects/*enzymology/genetics!Plants/parasitology!*Protein Isoprenylation!Protein Processing, Post-Translational!Pseudogenes/*physiology!Research Support, Non-U.S. Gov't!Substrate Specificity!rab GTP-Binding Proteins/genetics/metabolism!ras Proteins/genetics/metabolism!",scholar,2003,Biol. Chem,384,,977
14509838,Histone H3 and H3.3 variants in the protozoan pathogens Plasmodium falciparum and Toxoplasma gondii.,http://taylorandfrancis.metapress.com/index/RT0YLF6EFJYL5U30.pdf,"Histones constitute the fundamental component of chromatin and participate in the regulation of gene expression by virtue of covalent modifications to their N-terminal domains. The discovery that histone-modifying enzymes are targeted by the antiprotozoal agent apicidin has prompted further investigation of gene expression regulation in protozoan parasites; consequently, several chromatin remodeling homologues with unusual features have been isolated. To facilitate investigation of these chromatin remodeling homologues using parasite-specific substrates, we sought to clone and characterize histone H3 from two medically significant pathogens in the phylum Apicomplexa: Plasmodium falciparum (malaria) and Toxoplasma gondii (opportunistic pathogen of immunocompromised individuals). Like most eukaryotic organisms, these parasites each contain at least two histone H3 variants, termed H3 and H3.3. Sequence analysis reveals the Apicomplexan H3 proteins harbor novel and rare features. Expression and purification of recombinant H3 variants will provide species-specific substrate for the analysis of the histone-modifying machinery of these parasites. A517, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202-5120, USA. wjsulliv@iupui.edu","Amino Acid Sequence!Animals!Base Sequence!Comparative Study!DNA Primers!Histones/*genetics!Molecular Sequence Data!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Analysis, DNA!Toxoplasma/*genetics!*Variation (Genetics)!",scholar,2003,DNA Sequence-The Journal of Sequencing and Mapping,14,3,227
14514358,"The heat shock protein 90 of Plasmodium falciparum and antimalarial activity of its inhibitor, geldanamycin.",http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D201030%26tools%3Dbot,"BACKGROUND: The naturally occurring benzoquinone ansamycin compound, geldanamycin (GA), is a specific inhibitor of heat shock protein 90 (Hsp90) and is a potential anticancer agent. Since Plasmodium falciparum has been reported to have an Hsp90 ortholog, we tested the possibility that GA might inhibit it and thereby display antiparasitic activity. RESULTS: We provide direct recombinant DNA evidence for the Hsp90 protein of Plasmodium falciparum, the causative agent of fatal malaria. While the mRNA of Hsp90 was mainly expressed in ring and trophozoite stages, the protein was found in all stages, although schizonts contained relatively lower amounts. In vitro the parasitic Hsp90 exhibited an ATP-binding activity that could be specifically inhibited by GA. Plasmodium growth in human erythrocyte culture was strongly inhibited by GA with an IC50 of 20 nM, compared to the IC50 of 15 nM for chloroquine (CQ) under identical conditions. When used in combination, the two drugs acted synergistically. GA was equally effective against CQ-sensitive and CQ-resistant strains (3D7 and W2, respectively) and on all erythrocytic stages of the parasite. CONCLUSIONS: Together, these results suggest that an active and essential Hsp90 chaperone cycle exists in Plasmodium and that the ansamycin antibiotics will be an important tool to dissect its role in the parasite. Additionally, the favorable pharmacology of GA, reported in human trials, makes it a promising antimalarial drug. South Alabama, College of Medicine, 307 University Blvd, Mobile, AL 36688-0002, USA. rkumar@usouthal.edu development/physiology","Adenosine Triphosphate/metabolism!Animals!Antimalarials/metabolism/*pharmacology!Chloroquine/metabolism!Cloning, Molecular!Drug Resistance/physiology!Drug Synergism!Gene Expression Regulation, Developmental/drug effects/genetics!HSP90 Heat-Shock Proteins/*antagonists & inhibitors/genetics/metabolism!Plasmodium falciparum/*drug effects/genetics/growth &!Protozoan Proteins/*antagonists & inhibitors/genetics/metabolism!Quinones/metabolism/*pharmacology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scholar,2003,Malaria Journal,2,1,30
14521577,Pfs230: from malaria transmission-blocking vaccine candidate toward function.,http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-3024.2003.00643.x/abs/,,"Animals!Antibodies, Protozoan/pharmacology!Antigens, Protozoan/genetics/*immunology!Culicidae/parasitology!Female!Genes, Protozoan!Humans!Malaria Vaccines/immunology/*pharmacology!Malaria, Falciparum/immunology/prevention & control/transmission!Male!Plasmodium falciparum/genetics/growth & development/immunology!Protozoan Proteins/genetics/*immunology!Recombinant Proteins/genetics/immunology!Research Support, U.S. Gov't, P.H.S.!",scholar,2003,Parasite Immunology,25,7,351
14550891,"Plasmepsin 4, the food vacuole aspartic proteinase found in all Plasmodium spp. infecting man.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103001373&_version=1&_returnURL=&md5=a8977d38641cefad64dd892caf31dce6,"Plasmepsins are aspartic proteinases of the malaria parasite, and seven groups of plasmepsins have been identified by comparing genomic sequence data available for the genes encoding these enzymes from Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium berghei, and Plasmodium yoelii. The food vacuole plasmepsins typified by plasmepsin 4 from P. falciparum (PfPM4) constitute one of these groups. Genes encoding the ortholog of PfPM4 have been cloned from Plasmodium ovale, Plasmodium malariae, and P. vivax. In addition, P. falciparum contains three paralagous food vacuole plasmepsins or plasmepsin-like enzymes that appear to have arisen by gene duplication, plasmepsins 1 (PfPM1), 2 (PfPM2) and HAP, and all four were localized to purified food vacuole preparations by two-dimensional gel electrophoresis and mass spectroscopic analysis. The three paralogs of PfPM4 do not have counterparts in the six other Plasmodium spp. examined by genomic DNA blot analysis and by review of available genomic sequence data. The presence of these paralogs among the food vacuole plasmepsins in P. falciparum as compared with the other three species causing malaria in man will impact efforts to rationally design antimalarials targeting the food vacuole plasmepsins. Florida, Box 110880, Gainesville, FL 32611-0880, USA. damej@mail.vetmed.ufl.edu","Amino Acid Sequence!Animals!*Aspartic Endopeptidases/chemistry/genetics/metabolism!Cloning, Molecular!Electrophoresis, Gel, Two-Dimensional!Humans!Malaria/*parasitology!Molecular Sequence Data!Plasmodium/classification/*enzymology!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Analysis, DNA!Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization!Vacuoles/*enzymology!",scirus,2003,Molecular and Biochemical Parasitology,130,1,1
14565852,Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D222925%26tools%3Dbot,"BACKGROUND: The variant surface antigen family Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. The sequence diversity and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub-grouped into three major groups (group A, B and C) and two intermediate groups B/A and B/C representing transitions between the three major groups. The best defined var group, group A, comprises telomeric genes transcribed towards the telomere encoding PfEMP1s with complex domain structures different from the 4-domain type dominant of groups B and C. Two sequences belonging to the var1 and var2 subfamilies formed independent groups. A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged. This organization appeared to be unique for the group A var genes CONCLUSION: The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite. Immunology, University of Copenhagen, Denmark. thomaslavstsen@vip.cybercity.dk","Animals!Antigens, Protozoan/genetics!Chromosome Mapping/methods!Cloning, Molecular!DNA, Intergenic/*genetics!Erythrocyte Membrane/genetics!Exons/*genetics!Introns/genetics!Membrane Proteins/genetics!Multigene Family!Plasmodium falciparum/*genetics!Protein Structure, Tertiary/genetics!Protozoan Proteins/genetics!Pseudogenes!Research Support, Non-U.S. Gov't!*Sequence Analysis, DNA/methods!*Variation (Genetics)!",scholar,2003,Malaria Journal,2,,27
14569009,Induction of crossreactive antibodies against the Plasmodium falciparum variant protein.,http://www.pnas.org/cgi/content/abstract/100/22/13007%3Fetoc,"The variant antigen Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), present on the surface of P. falciparum-parasitized erythrocytes (PE), plays a central role in naturally acquired immunity, although antibodies to PfEMP1 are predominantly variant specific. To overcome this major limitation for vaccine development, we immunized mice with three cysteine-rich interdomain 1 (CIDR1) domains of PfEMP1 that have the critical function of binding the PE to CD36 on endothelium and thus preventing spleen-dependent killing of the parasite. The immunizations consisted of different combinations of three CIDR1 encoded by DNA followed by recombinant protein boost. Immunizations with a single variant in a prime-boost regimen induced no or low cross-reactivity toward heterologous CIDR1; however, a broad range of crossreactivity was detected in mice that were immunized with all three variants simultaneously. The induced crossreactivity suggests that an anti-PfEMP1 vaccine may be possible. Infectious Diseases/National Institutes of Health, Rockville, MD 20852, USA. America.","Animals!Antibodies, Protozoan/*immunology!Base Sequence!CHO Cells!Cloning, Molecular!Cricetinae!Cross Reactions/*immunology!DNA Primers!Enzyme-Linked Immunosorbent Assay!Female!Malaria, Falciparum/immunology!Mice!Mice, Inbred BALB C!Molecular Sequence Data!Plasmodium falciparum/*immunology!Protozoan Proteins/*genetics/*immunology/isolation & purification!Protozoan Vaccines!Recombinant Proteins/immunology!Restriction Mapping!Transfection!",scholar,2003,Proceedings of the National Academy of Sciences,100,22,13007
14607282,"Adenylyl cyclases from Plasmodium, Paramecium and Tetrahymena are novel ion channel/enzyme fusion proteins.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0898656803001293&_version=1&_returnURL=&md5=94c975d7a8858d86b7ad857b64bb22bd,"In Paramecium, cAMP formation is stimulated by a potassium conductance, which is an intrinsic property of the adenylyl cyclase. We cloned a full-length cDNA and several gDNA fragments from Paramecium and Tetrahymena coding for adenylyl cyclases with a novel domain composition. A putative N-terminal ion channel domain contains a canonical S4 voltage-sensor and a canonical potassium pore-loop located C-terminally after the last transmembrane span on the cytoplasmic side. The adenylyl cyclase catalyst is C-terminally located. DNA microinjection of a green fluorescent protein (GFP)-tagged construct into the macronucleus of Paramecium resulted in ciliary localization of the expressed protein. An identical gene coding for an ion-channel adenylyl cyclase was cloned from the malaria parasite Plasmodium falciparum. Expression of the catalytic domain of the latter in Sf9 cells yielded an active homodimeric adenylyl cyclase. The occurrence of this highly unique subtype of adenylyl cyclase appears to be restricted to ciliates and apicomplexa. Universitat Tubingen, Morgenstelle 8, 72076 Tubingen, Germany.","Adenylate Cyclase/genetics/isolation & purification/*metabolism!Amino Acid Sequence/genetics!Animals!Base Sequence/genetics!Cilia/genetics/metabolism!Cyclic AMP/biosynthesis!DNA, Complementary/analysis/genetics!Gene Expression Regulation, Enzymologic/genetics!Green Fluorescent Proteins!Luminescent Proteins!Molecular Sequence Data!Paramecium/*enzymology/genetics!Plasmodium falciparum/*enzymology/genetics!Potassium/metabolism!Potassium Channels/genetics/isolation & purification/*metabolism!Protein Isoforms/genetics/isolation & purification/metabolism!Protein Structure, Tertiary/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Sequence Homology, Amino Acid!Species Specificity!Tetrahymena/*enzymology/genetics!",scirus,2004,Cellular Signalling,16,1,115
14612390,A conserved telomerase motif within the catalytic domain of telomerase reverse transcriptase is specifically required for repeat addition processivity.,http://mcb.asm.org/cgi/content/abstract/23/23/8440,"Telomerase is a ribonucleoprotein reverse transcriptase responsible for the maintenance of one strand of the telomere terminal repeats. The catalytic protein subunit of the telomerase complex, known as TERT, possesses a reverse transcriptase (RT) domain that mediates nucleotide addition. The RT domain of TERT is distinguishable from retroviral and retrotransposon RTs in having a sizable insertion between conserved motifs A and B', within the so-called fingers domain. Sequence analysis revealed the existence of conserved residues in this region, named IFD (insertion in fingers domain). Mutations of some of the conserved residues in Saccharomyces cerevisiae TERT (Est2p) abolished telomerase function in vivo, testifying to their importance. Significant effects of the mutations on telomerase activity in vitro were observed, with most of the mutants exhibiting a uniform reduction in activity regardless of primer sequence. Remarkably, one mutant manifested a primer-specific defect, being selectively impaired in extending primers that form short hybrids with telomerase RNA. This mutant also accumulated products that correspond to one complete round of repeat synthesis, implying an inability to effect the repositioning of the DNA product relative to the RNA template that is necessary for multiple repeat addition. Our results suggest that the ability to stabilize short RNA-DNA hybrids is crucial for telomerase function in vivo and that this ability is mediated in part by a more elaborate fingers domain structure. Research Center, Weill Medical College of Cornell University, New York, New York 10021, USA. nflue@med.cornell.edu","Amino Acid Motifs!Amino Acid Sequence!Amino Acid Substitution!Catalytic Domain!Conserved Sequence!DNA-Binding Proteins!Kinetics!Models, Molecular!Molecular Sequence Data!Mutagenesis, Site-Directed!Protein Structure, Tertiary!Recombinant Proteins/chemistry/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Saccharomyces cerevisiae/enzymology/genetics!Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism!Sequence Homology, Amino Acid!Telomerase/*chemistry/genetics/*metabolism!Telomere/metabolism!",scholar,,Molecular and Cellular Biology,,,
14617379,Integrative analysis of intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum.,http://bmc.ub.uni-potsdam.de/cgi-bin/show.pl%3F1475-2875-2-38/1475-2875-2-38.pdf,"BACKGROUND: The intraerythrocytic development of Plasmodium falciparum, the most virulent human malaria parasite involves asexual and gametocyte stages. There has been a significant increase in disparate datasets derived from genomic and post-genomic analysis of the parasite that necessitates delivery of integrated analysis from which biological processes important to the survival of the parasite can be determined. METHODS: In order to resolve genes associated with stage differentially expressed transcripts, we have developed and implemented an integrative approach that combines evidence from P. falciparum expressed sequence tags (ESTs), genomic, microarray, proteomic and gene ontology data. RESULTS: A total of 143 gametocyte-overexpressed and 51 asexual-overexpressed transcripts were identified. A subset of 74 genes associated with these transcripts showed evidence of stage-correlated protein expression, of which 53 have not been experimentally characterised. Our study has revealed (1) possible regulatory mechanisms in malaria parasites' gametocyte maturation, (2) correlation between EST and microarray data for a P. falciparum gene family to present unique EST-derived information, (3) candidate drug and antigenic targets on which computational and experimental studies can be performed, and (4) the need for more empirical studies on gene and protein expression in malaria parasites. CONCLUSION: Applying different domains of data to the same underlying gene set has yielded novel insights into the biology of the parasite and presents an approach to appraise critically the data quality of post-genomic datasets from malaria parasites. Cape, Bellville 7535, South Africa. raphael@sanbi.ac.za",,scholar,2003,Malaria Journal,2,,38
14627712,Analysis of the Plasmodium and Anopheles transcriptional repertoire during ookinete development and midgut invasion.,http://www.jbc.org/cgi/reprint/M307582200v1.pdf,"Plasmodium, the causative agent of malaria, has to undergo sexual differentiation and development in anopheline mosquitoes for transmission to occur. To isolate genes specifically induced in both organisms during the early stages of Plasmodium differentiation in the mosquito, two cDNA libraries were constructed, one enriched for sequences expressed in differentiating Plasmodium berghei ookinetes and another enriched for sequences expressed in Anopheles stephensi guts containing invading ookinetes and early oocysts. Sequencing of 457 ookinete library clones and 652 early oocyst clones represented 175 and 346 unique expressed sequence tags, respectively. Nine of 13 Plasmodium and four of the five Anopheles novel expressed sequence tags analyzed on Northern blots were induced during ookinete differentiation and mosquito gut invasion. Ancaspase-7, an Anopheles effector caspase, is proteolytically activated during Plasmodium invasion of the midgut. WARP, a gene encoding a Plasmodium surface protein with a von Willebrand factor A-like adhesive domain, is expressed only in ookinetes and early oocysts. An anti-WARP polyclonal antibody strongly inhibits (70-92%) Plasmodium development in the mosquito, making it a candidate antigen for transmission blocking vaccines. The present results and those of an accompanying report (Srinivasan, P., Abraham, E. G., Ghosh, A. K., Valenzuela, J., Ribeiro, J. M. C., Dimopoulos G., Kafatos, F. C., Adams, J. H., and Jacobs-Lorena, M. (2004) J. Biol. Chem. 279, 5581-5587) provide the foundation for further analysis of Plasmodium differentiation in the mosquito and of mosquito responses to the parasite. 44106, USA.","Amino Acid Sequence!Animals!Anopheles/*metabolism!Blotting, Northern!Cloning, Molecular!DNA, Complementary/metabolism!Digestive System/*embryology!Disease Vectors!Drosophila!Expressed Sequence Tags!Gene Library!Immunoblotting!Insect Vectors!Mice!Microscopy, Fluorescence!Molecular Sequence Data!Multigene Family!Oocytes/metabolism!Plasmodium/*metabolism!Plasmodium berghei/metabolism!Protein Structure, Tertiary!RNA/chemistry!Research Support, U.S. Gov't, P.H.S.!Sequence Homology, Amino Acid!Species Specificity!Time Factors!*Transcription, Genetic!",scholar,,Journal of Biological Chemistry,,,
14651636,Evidence for the importance of genetic structuring to the structural and functional specialization of the Plasmodium falciparum var gene family.,http://www.blackwell-synergy.com/links/doi/10.1046%252Fj.1365-2958.2003.03814.x,"The var gene family encodes Plasmodium falciparum erythrocyte membrane 1 (PfEMP1) proteins that act as virulence factors responsible for both antigenic variation and cytoadherence of infected erythrocytes. These proteins orchestrate infected erythrocyte sequestration from blood circulation and contribute to adhesion-based complications of P. falciparum malaria infections. For this study, we analysed the genetic organization and strain structure of var genes and present evidence for three separately evolving groups that have, in part, functionally diverged and differ between subtelomeric and central chromosomal locations. Our analyses suggest that a recombination hierarchy limits reassortment between groups and may explain why some var genes are unusually conserved between parasite strains. This recombination hierarchy, coupled with binding and immune selection, shapes the variant antigen repertoire and has structural, functional and evolutionary consequences for the PfEMP1 protein family that are directly relevant to malaria pathogenesis. 98109, USA.","Animals!Antigens, CD36/metabolism!Cell Adhesion!Erythrocytes/parasitology!Evolution, Molecular!*Genome, Protozoan!Molecular Sequence Data!Multigene Family!*Phylogeny!Plasmodium falciparum/classification/*genetics/metabolism!*Protozoan Proteins/chemistry/genetics/metabolism!*Recombination, Genetic!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Analysis, DNA!Structure-Activity Relationship!Telomere/*genetics!",scholar,2003,Molecular Microbiology,50,5,1527
14653531,"Sex ratios in the rodent malaria parasite, Plasmodium chabaudi.",http://www.journals.cambridge.org/abstract_S0031182003004013,"The sex ratios of malaria and related Apicomplexan parasites play a major role in transmission success. Here, we address 2 fundamental issues in the sex ratios of the rodent malaria parasite, Plasmodium chabaudi. First we test the accuracy of empirical methods for estimating sex ratios in malaria parasites, and show that sex ratios made with standard thin smears may overestimate the proportion of female gametocytes. Secondly, we test whether the mortality rate differs between male and female gametocytes, as assumed by sex ratio theory. Conventional application of sex ratio theory to malaria parasites assumes that the primary sex ratio can be accurately determined from mature gametocytes circulating in the peripheral circulation. We stopped gametocyte production with chloroquine in order to study a cohort of gametocytes in vitro. The mortality rate was significantly higher for female gametocytes, with an average half-life of 8 h for female gametocytes and 16 h for male gametocytes. West Mains Road, University of Edinburgh, Edinburgh EH9 37T, UK. sarah.reece@ed.ac.uk","Animals!Antimalarials/pharmacology!Chloroquine/pharmacology!Disease Models, Animal!Female!Malaria/*parasitology/transmission!Male!Mice!Mice, Inbred C57BL!Plasmodium chabaudi/*growth & development!Research Support, Non-U.S. Gov't!Sex Ratio!",scholar,2003,Parasitology,127,5,419
14662742,Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice.,http://nramm.scripps.edu/publications/JCB%2520163%2520-%2520Moores.pdf,"KinI kinesins are important in regulating the complex dynamics of the microtubule cytoskeleton. They are unusual in that they depolymerize, rather than move along microtubules. To determine the attributes of KinIs that distinguish them from translocating kinesins, we examined the ATPase activity, microtubule affinity, and three-dimensional microtubule-bound structure of a minimal KinI motor domain. Together, the kinetic, affinity, and structural data lead to the conclusion that on binding to the microtubule lattice, KinIs release ADP and enter a stable, low-affinity, regulated state, from which they do not readily progress through the ATPase cycle. This state may favor detachment, or diffusion of the KinI to its site of action, the microtubule ends. Unlike conventional translocating kinesins, which are microtubule lattice-stimulated ATPases, it seems that with KinIs, nucleotide-mediated modulation of tubulin affinity is only possible when it is coupled to protofilament deformation. This provides an elegant mechanistic basis for their unique depolymerizing activity. 92037, USA.","Adenosinetriphosphatase/*metabolism!Animals!Cryoelectron Microscopy!Kinesin/chemistry/*metabolism!Macromolecular Substances!Microtubules/chemistry/*metabolism!Models, Molecular!Molecular Motors/*metabolism!Plasmodium falciparum/metabolism!Protein Binding!Protein Conformation!Protozoan Proteins/metabolism!Research Support, U.S. Gov't, P.H.S.!Tubulin/metabolism!",scholar,2003,The Journal of Cell Biology,163,5,963
14662988,Expression of equi merozoite antigen 2 during development of Babesia equi in the midgut and salivary gland of the vector tick Boophilus microplus.,http://jcm.asm.org/cgi/content/abstract/41/12/5803,"Equi merozoite antigens 1 and 2 (EMA-1 and EMA-2) are Babesia equi proteins expressed on the parasite surface during infection in horses and are orthologues of proteins in Theileria spp., which are also tick-transmitted protozoal pathogens. We determined in this study whether EMA-1 and EMA-2 were expressed within the vector tick Boophilus microplus. B. equi transitions through multiple, morphologically distinct stages, including sexual stages, and these transitions culminate in the formation of infectious sporozoites in the tick salivary gland. EMA-2-positive B. equi stages in the midgut lumen and midgut epithelial cells of Boophilus microplus nymphs were identified by reactivity with monoclonal antibody 36/253.21. This monoclonal antibody also recognized B. equi in salivary glands of adult Boophilus microplus. In addition, quantification of B. equi in the mammalian host and vector tick indicated that the duration of tick feeding and parasitemia levels affected the percentage of nymphs that contained morphologically distinct B. equi organisms in the midgut. In contrast, there was no conclusive evidence that B. equi EMA-1 was expressed in either the Boophilus microplus midgut or salivary gland when monoclonal antibody 36/18.57 was used. The expression of B. equi EMA-2 in Boophilus microplus provides a marker for detecting the various development stages and facilitates the identification of novel stage-specific Babesia proteins for testing transmission-blocking immunity. and Pathology, Washington State University, Pullman, Washington 99164-7040, USA.","Animals!Antigens, Protozoan/*genetics!Digestive System/immunology!Epithelial Cells/immunology!Humans!Insect Vectors!Ixodidae/growth & development/*parasitology!Membrane Proteins/*genetics!Polymerase Chain Reaction!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Salivary Glands/immunology!",scholar,,Journal of Clinical Microbiology,,,
14668007,Common trafficking pathway for variant antigens destined for the surface of the Plasmodium falciparum-infected erythrocyte.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103002391&_version=1&_returnURL=&md5=c98f0f04e6dbae5cad96aceb1e1bf825,"Intraerythrocytic Plasmodium falciparum exports proteins to the cytosol and to the plasma membrane of the host cell. We here present data revealing the existence of a unique common pathway for the surface bound traffic of the clonally variant antigens, repeated-interspersed-antigen (RIFINS) and P. falciparum erythrocyte-membrane-protein-1 (PfEMP1). RIFIN- and PfEMP1-specific antibodies were found to stain single small vesicles (SSV) that bud off from the parasitophorus vacuolar membrane (PMV) at 6-10 h post-invasion. Large multimeric vesicle (LMV) assemblies, composed of subunits each of a similar size to that of a SSV, appeared as the dominant vesicle type carrying the variant antigens in the cytosol as the parasites developed into early trophozoite stages (> or = 16 h post-invasion). Later, more than 24 h post-invasion, large spinle-like vesicles (LSLV) built up as the LMV approached and accumulated underneath the erythrocyte membrane. LMV were found to associate both with the Maurer's cleft antigen Pf332 and with lipids as seen by fluorescent BODIPY-Ceramide staining. Co-traffic of Pf332 with RIFINS and PfEMP1 occurred in sub-compartmentalized LMV, as the variant antigens co-localized at the outer rim while Pf332 occupied the core of the vesicle complex. Formation of LMV for the trafficking of RIFINS and PfEMP1 is a prominent feature of freshly isolated P. falciparum and of in vitro propagated K+ as well as K- parasites, seemingly independent of the knob-associated histidine-rich protein (KAHRP). In vitro cultured 3D7 clones lack LMV formation and traffic the variant antigens in vesicles of a similar size to that of the SSV. 16, Box 280, SE-171 77 Stockholm, Sweden.","Animals!Antigens, Protozoan/*metabolism!Cell Membrane/chemistry!Cytoplasm/metabolism/ultrastructure!Cytoplasmic Vesicles/metabolism/ultrastructure!Erythrocytes/cytology/*metabolism/*parasitology!Humans!Malaria, Falciparum/parasitology!Membrane Proteins/metabolism!Peptides/metabolism!Plasmodium falciparum/immunology/*pathogenicity!Protein Transport!Protozoan Proteins/*metabolism!",scirus,2004,Molecular and Biochemical Parasitology,133,1,1
14668008,A member of a conserved Plasmodium protein family with membrane-attack complex/perforin (MACPF)-like domains localizes to the micronemes of sporozoites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103002536&_version=1&_returnURL=&md5=789c6e663f8dd9f3221a15c122b3ce26,"Pore-forming proteins are employed by many pathogens to achieve successful host colonization. Intracellular pathogens use pore-forming proteins to invade host cells, survive within and productively interact with host cells, and finally egress from host cells to infect new ones. The malaria-causing parasites of the genus Plasmodium evolved a number of life cycle stages that enter and replicate in distinct cell types within the mosquito vector and vertebrate host. Despite the fact that interaction with host-cell membranes is a central theme in the Plasmodium life cycle, little is known about parasite proteins that mediate such interactions. We identified a family of five related genes in the genome of the rodent malaria parasite Plasmodium yoelii encoding secreted proteins all bearing a single membrane-attack complex/perforin (MACPF)-like domain. Each protein is highly conserved among Plasmodium species. Gene expression analysis in P. yoelii and the human malaria parasite Plasmodium falciparum indicated that the family is not expressed in the parasites blood stages. However, one of the genes was significantly expressed in P. yoelii sporozoites, the stage transmitted by mosquito bite. The protein localized to the micronemes of sporozoites, organelles of the secretory invasion apparatus intimately involved in host-cell infection. MACPF-like proteins may play important roles in parasite interactions with the mosquito vector and transmission to the vertebrate host. University School of Medicine, New York, NY 10016, USA. development/metabolism/ultrastructure","Amino Acid Motifs!Amino Acid Sequence!Animals!Complement Membrane Attack Complex/chemistry/genetics/physiology!Conserved Sequence!*Gene Expression!Membrane Glycoproteins/chemistry/genetics/physiology!Molecular Sequence Data!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/genetics/growth & development/metabolism!Plasmodium yoelii/*genetics/*growth &!Protozoan Proteins/chemistry/*genetics/*metabolism/physiology!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sporozoites/*genetics/metabolism!",scirus,2004,Molecular and Biochemical Parasitology,133,1,15
14678570,Construction and use of Plasmodium falciparum phage display libraries to identify host parasite interactions.,http://bmc.ub.uni-potsdam.de/cgi-bin/show.pl%3F1475-2875-2-47/1475-2875-2-47.pdf,"BACKGROUND: The development of Plasmodium falciparum within human erythrocytes induces a wide array of changes in the ultrastructure, function and antigenic properties of the host cell. Numerous proteins encoded by the parasite have been shown to interact with the erythrocyte membrane. The identification of new interactions between human erythrocyte and P. falciparum proteins has formed a key area of malaria research. To circumvent the difficulties provided by conventional protein techniques, a novel application of the phage display technology was utilised. METHODS: P. falciparum phage display libraries were created and biopanned against purified erythrocyte membrane proteins. The identification of interacting and in-frame amino acid sequences was achieved by sequencing parasite cDNA inserts and performing bioinformatic analyses in the PlasmoDB database. RESULTS: Following four rounds of biopanning, sequencing and bioinformatic investigations, seven P. falciparum proteins with significant binding specificity toward human erythrocyte spectrin and protein 4.1 were identified. The specificity of these P. falciparum proteins were demonstrated by the marked enrichment of the respective in-frame binding sequences from a fourth round phage display library. CONCLUSION: The construction and biopanning of P. falciparum phage display expression libraries provide a novel approach for the identification of new interactions between the parasite and the erythrocyte membrane. Laboratory Services, School of Pathology, University of the Witwatersrand, Parktown, Johannesburg 2193, South Africa. theresa.coetzer@nhls.ac.za",,scholar,2003,Malaria Journal,2,,47
14685263,Identification of a family of animal sphingomyelin synthases.,,"Sphingomyelin (SM) is a major component of animal plasma membranes. Its production involves the transfer of phosphocholine from phosphatidylcholine onto ceramide, yielding diacylglycerol as a side product. This reaction is catalysed by SM synthase, an enzyme whose biological potential can be judged from the roles of diacylglycerol and ceramide as anti- and proapoptotic stimuli, respectively. SM synthesis occurs in the lumen of the Golgi as well as on the cell surface. As no gene for SM synthase has been cloned so far, it is unclear whether different enzymes are present at these locations. Using a functional cloning strategy in yeast, we identified a novel family of integral membrane proteins exhibiting all enzymatic features previously attributed to animal SM synthase. Strikingly, human, mouse and Caenorhabditis elegans genomes each contain at least two different SM synthase (SMS) genes. Whereas human SMS1 is localised to the Golgi, SMS2 resides primarily at the plasma membrane. Collectively, these findings open up important new avenues for studying sphingolipid function in animals. Biomembranes, Utrecht University, Utrecht, The Netherlands. Groups)/*chemistry/genetics/*metabolism","Amino Acid Motifs!Amino Acid Sequence!Amino Acid Substitution!Animals!Binding Sites!Cell Membrane/chemistry/metabolism!Cloning, Molecular!Comparative Study!Computational Biology!Consensus Sequence!Conserved Sequence!Databases, Factual!Golgi Apparatus/chemistry/metabolism!Hela Cells!Humans!Hydrophobicity!Models, Biological!Molecular Sequence Data!Phylogeny!Protein Structure, Tertiary!Research Support, Non-U.S. Gov't!Saccharomyces cerevisiae/enzymology!Sequence Homology, Amino Acid!Sphingomyelins/biosynthesis!Transferases (Other Substituted Phosphate!",scholar,,,,,
14697197,Plasmodium biology: genomic gleanings.,http://adenina.biomol.unb.br/~brigido/tebm/genoma_comparativo/Malaria.pdf,"The highly A+T rich genomes of human and rodent malarial parasites offer unprecedented glimpses of a lineage that is distinct from other model organisms. Plasmodium is distinguished by the presence of numerous low complexity inserts within globular domains of proteins. It displays several peculiarities in its transcription apparatus, and its DNA repair system appears to favor a certain innate level of mutability. Plasmodium possesses many cell surface molecules with "animal-like" adhesion modules. Potential genetic footprints of the ancestral eukaryotic algal precursor of the apicoplast are also detectable in its genome. Medicine, National Institutes of Health, Bethesda, MD 20894, USA. aravind@ncbi.nlm.nih.gov","Animals!Evolution, Molecular!*Genome, Protozoan!Host-Parasite Relations/genetics!Humans!Life Cycle Stages/genetics!Phylogeny!Plasmodium/cytology/*genetics/metabolism!Protein Structure, Tertiary/genetics!Protozoan Proteins/genetics/metabolism!",scholar,2003,Cell,115,7,771
14720308,Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi.,http://www.biomedcentral.com/1471-2164/5/5/,"BACKGROUND: The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the ER membrane. The SRP of metazoans is well characterized and composed of an RNA molecule and six polypeptides. The particle is organized into the S and Alu domains. The Alu domain has a translational arrest function and consists of the SRP9 and SRP14 proteins bound to the terminal regions of the SRP RNA. So far, our understanding of the SRP and its evolution in lower eukaryotes such as protozoa and yeasts has been limited. However, genome sequences of such organisms have recently become available, and we have now analyzed this information with respect to genes encoding SRP components. RESULTS: A number of SRP RNA and SRP protein genes were identified by an analysis of genomes of protozoa and fungi. The sequences and secondary structures of the Alu portion of the RNA were found to be highly variable. Furthermore, proteins SRP9/14 appeared to be absent in certain species. Comparative analysis of the SRP RNAs from different Saccharomyces species resulted in models which contain features shared between all SRP RNAs, but also a new secondary structure element in SRP RNA helix 5. Protein SRP21, previously thought to be present only in Saccharomyces, was shown to be a constituent of additional fungal genomes. Furthermore, SRP21 was found to be related to metazoan and plant SRP9, suggesting that the two proteins are functionally related. CONCLUSIONS: Analysis of a number of not previously annotated SRP components show that the SRP Alu domain is subject to a more rapid evolution than the other parts of the molecule. For instance, the RNA portion is highly variable and the protein SRP9 seems to have evolved into the SRP21 protein in fungi. In addition, we identified a secondary structure element in the Saccharomyces RNA that has been inserted close to the Alu region. Together, these results provide important clues as to the structure, function and evolution of SRP. 30 Goteborg, Sweden. magnus.alm@medkem.gu.se","Amino Acid Sequence!Animals!Base Sequence!Comparative Study!Databases, Genetic!Fungal Proteins/genetics!Fungi/*genetics/metabolism!Genome, Fungal!Genome, Protozoan!Molecular Sequence Data!Nucleic Acid Conformation!Phylogeny!Protozoa/*genetics/metabolism!Protozoan Proteins/genetics!RNA, Fungal/chemistry/genetics!RNA, Protozoan/chemistry/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Homology, Amino Acid!Signal Recognition Particle/*genetics/metabolism!",scholar,2004,BMC Genomics,5,5,
14739451,Stable SNPs in malaria antigen genes in isolated populations.,http://www.sciencemag.org/cgi/data/309/5731/134/DC1/1,,"Alleles!Amino Acid Sequence!Animals!Antigens, Protozoan/chemistry/*genetics!Antimalarials/pharmacology!Chloroquine/pharmacology!Drug Resistance!Epitopes/genetics!Genes, Protozoan!Geography!Haplotypes!Humans!Malaria, Falciparum/parasitology!Membrane Proteins/chemistry/genetics!Merozoite Surface Protein 1/chemistry/genetics!Molecular Sequence Data!Plasmodium falciparum/drug effects/*genetics/*immunology!*Polymorphism, Single Nucleotide!Protozoan Proteins/chemistry/genetics!Repetitive Sequences, Nucleic Acid!Research Support, Non-U.S. Gov't!Tandem Repeat Sequences!Vanuatu!",scholar,,Science,,,
14747018,Annotating the Plasmodium genome and the enigma of the shikimate pathway.,http://www.biochemistry.tugraz.at/pdf/McConkeyetal2004TiP.pdf,"The completion of the Plasmodium falciparum genome sequence heralds a new era in the effort to identify all the parasite's genes along with their cellular functions. A combination of bioinformatics and experimental proof will facilitate this process. Many enzymes in metabolic processes have been identified, but several examples exist of incomplete pathways, such as the shikimate pathway. This review uses the example of the shikimate pathway to examine the application of bioinformatics to lead experimental design in post-genomic biology. 9JT, Leeds, UK. g.a.mcconkey@leeds.ac.uk","Amino Acid Sequence!Animals!Computational Biology!Folic Acid/*metabolism!*Genome, Protozoan!Models, Biological!Phosphotransferases (Alcohol Group Acceptor)/chemistry/metabolism!Plasmodium falciparum/enzymology/*genetics/*metabolism!Sequence Alignment!Shikimic Acid/*metabolism!",scholar,2004,Trends Parasitol,20,2,60
14747137,"var genes, PfEMP1 and the human host.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003207&_version=1&_returnURL=&md5=c7a49ac144273a83233e7f03acf5ef9f,"Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is an important virulence factor encoded by a family of roughly 60 var genes and is used by the parasite to interact with the human host. The parasite regularly exchanges the expressed var gene generating antigenic variation of the infected RBCs (pRBC) surface which is crucial for successful proliferation and transmission. PfEMP1 is also an adhesive molecule that binds to an array of human receptors. By sequestration in the post-capillary venules, pRBCs are able to escape the spleen-mediated clearance but severe malaria may develop if the local binding is extensive. Anti-PfEMP1 immunity is important for preventing the development of both cerebral malaria and placental malaria, but more immunological studies on PfEMP1 antigens and their interaction with the human host are needed. Over the last few years our knowledge about var genes and PfEMP1s has increased dramatically through genetic, biochemical, immunological and epidemiological studies. In addition, the genome sequence has also provided us with a new platform for further dissecting its biological functions. This review highlights the recent analyses of var genes in the P. falciparum genome and postulates significance of genome recombination to the diversity of parasite virulence. Swedish Institute for Infectious Disease Control, Box 280, SE-171 77 Stockholm, Sweden.","Animals!Antigenic Variation/*genetics/physiology!Antigens, Protozoan/genetics/immunology/physiology!Genes, Protozoan!Humans!Malaria, Falciparum/parasitology!Plasmodium falciparum/*genetics/immunology/*pathogenicity!Protozoan Proteins/*genetics/immunology/*physiology!Recombination, Genetic!Research Support, Non-U.S. Gov't!Virulence/*genetics!",scirus,2004,Molecular and Biochemical Parasitology,134,1,3
14747145,Identification of regulatory elements in the Plasmodium falciparum genome.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003268&_version=1&_returnURL=&md5=eace5b21d7ec1beaaecdd8c6e97bdcad,"There is little information regarding regulatory sequences in the newly sequenced genome of the malaria parasite, Plasmodium falciparum. Thus, for the first time, a bioinformatic strategy was utilized to identify regulatory elements in this genome using the P. falciparum heat shock protein (hsp) gene family as a model system. Our analysis indicates that the P. falciparum hsp genes do not contain standard eukaryotic regulatory elements. However, a novel G-rich regulatory element named the G-box was identified upstream of several P. falciparum hsp genes and the P. yoelii yoelii, P. berghei, and P. vivax hsp86 genes. Remarkably, the Plasmodium sp. G-boxes were required for maximal reporter gene expression in transient transfection assays. The G-box is not homologous to known eukaryotic elements, and is the best-defined functional element elucidated from Plasmodium sp. Our analysis also revealed several other elements necessary for reporter gene expression including an upstream sequence element, the region surrounding the transcription start site, and the 5' and 3' untranslated regions. These data demonstrate that unique regulatory elements are conserved in the genomes of Plasmodium sp., and demonstrate the feasibility of bioinformatic approaches for their identification. Health, Boston, MA 02115, USA.","3' Untranslated Regions!5' Untranslated Regions!Animals!Base Composition!Base Sequence!Computational Biology!Conserved Sequence!Gene Expression!Genes, Reporter!*Genome, Protozoan!Heat-Shock Proteins/genetics!Luciferases/genetics/metabolism!Molecular Sequence Data!Plasmodium falciparum/*genetics/*metabolism!Promoter Regions (Genetics)!*Regulatory Sequences, Nucleic Acid!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Transcription Initiation Site!Transfection!",scirus,2004,Molecular and Biochemical Parasitology,134,1,75
14747157,The use of DsRED in single- and dual-color fluorescence labeling of mitochondrial and plastid organelles in Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003554&_version=1&_returnURL=&md5=925349401c9c341a5ea63dde545349b4,,"Acyl Carrier Protein/analysis/genetics!Aldehydes/analysis!Animals!Chaperonin 60/analysis/genetics!Green Fluorescent Proteins!Luminescent Proteins/*analysis/genetics!Microscopy, Fluorescence!Mitochondria/*chemistry!Plasmodium falciparum/chemistry/*ultrastructure!Plastids/*chemistry!Protein Transport!Protozoan Proteins/*analysis!Recombinant Fusion Proteins/analysis!Research Support, Non-U.S. Gov't!Staining and Labeling/*methods!Transfection!",scirus,2004,Molecular and Biochemical Parasitology,134,1,175
14962358,Plasmodium falciparum thioredoxins and glutaredoxins as central players in redox metabolism.,http://www.ingentaconnect.com/content/maney/rer/2003/00000008/00000005/art00005,"Over the last few years, an increasing number of different functions have been ascribed to small redox-active proteins like thioredoxins (Trx) and glutaredoxins (Grx). These functions include redox regulation of transcription and translation, antioxidant defence, involvement in protein folding and cellular signalling, and reduction of ribonucleotide reductase. In the malarial parasite Plasmodium falciparum, a classical Trx and a typical Grx have been described as well as a number of Trx- and Grx-like proteins including monothiol glutaredoxins. Furthermore, plasmoredoxin, a redox-active protein related to Trx, has been characterized; plasmoredoxin is unique for malarial parasites, therefore having great potential as diagnostic tool. In this minireview, we summarize the current knowledge on members of the thioredoxin superfamily and their function in the malarial parasite P. falciparum. Germany.","Amino Acid Sequence!Animals!Forecasting!Humans!Molecular Sequence Data!Oxidation-Reduction!*Oxidoreductases!Plasmodium falciparum/*physiology!Proteins/*metabolism!Protozoan Proteins/*physiology!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Thioredoxin/*metabolism!",scholar,2003,Redox Report,8,5,
14962373,"PlasmoDB: exploring genomics and post-genomics data of the malaria parasite, Plasmodium falciparum.",http://hfes.publisher.ingentaconnect.com/content/maney/rer/2003/00000008/00000005/art00020,"The recent completion of the genome sequence of Plasmodium falciparum 3D7 provides the foundation for genome-wide analysis of the parasite. In addition to DNA and gene sequence data, postgenomic methods including microarray-based transcript profiling and high-throughput proteomics are now accessible to Plasmodium researchers. The Plasmodium Genome database (<http://PlasmoDB.org>) was developed to provide rapid and convenient access to the terabytes of genomic-scale data now being generated around the world. All data are available in a relational framework, permitting convenient downloading, browsing, and analysis. Combinatorial use of data analysis tools enables powerful data mining queries, such as combining gene and protein expression data to monitor changes through various life-cycle stages. Functional predictions can be used to explore potential targets for antimalarial drug development. This report outlines the use of PlasmoDB to examine redox-active functions in Plasmodium. Pennsylvania 19104-6018, USA. fraunhol@sas.upenn.edu","Animals!*Computational Biology!*Databases, Genetic!Gene Expression!*Genome, Protozoan!Plasmodium falciparum/*genetics/metabolism!Proteomics!Software!",scholar,2003,Redox Report,8,5,
12967707,Crystal structure of Plasmodium berghei lactate dehydrogenase indicates the unique structural differences of these enzymes are shared across the Plasmodium genus.,,"As Plasmodium rely extensively on homolactic fermentation for energy production, Plasmodium falciparum lactate dehydrogenase (PfLDH)--the key enzyme in this process--has previously been suggested as a novel target for antimalarials. This enzyme has distinctive kinetic and structural properties that distinguish it from its human homologues. In this study, we now describe the expression, kinetic characterisation and crystal structure determination of the LDH from Plasmodium berghei. This enzyme is seen to have a similar kinetic profile to its P. falciparum counterpart, exhibiting the characteristic lack of substrate inhibition that distinguishes plasmodial from human LDHs. The crystal structure of P. berghei lactate dehydrogenase (PbLDH) shows a very similar active site arrangement to the P. falciparum enzyme. In particular, an insertion of five amino acid residues in the active site loop creates an enlarged volume in the substrate binding site, and characteristic changes in the residues lining the NADH cofactor binding pocket result in displacement of the cofactor relative to its observed position in mammalian and all other LDH structures. These results imply the special features previously described for PfLDH may be shared across the Plasmodium genus, supporting the universal application of therapeutics targeting this enzyme.","Plasmodium falciparum,Amino Acid Sequence,Humans,Kinetics,Crystallography, X-Ray,Plasmodium berghei,Cloning, Molecular,Models, Animal,Sequence Analysis, DNA,Molecular Sequence Data,L-Lactate Dehydrogenase,Crystallization,Animals,Models, Molecular",NCBI,2003,Molecular and biochemical parasitology,131,1,10-Jan
14989696,Parasite-specific eIF2 (eukaryotic initiation factor-2) kinase required for stress-induced translation control.,http://www.biochemj.org/bj/imps/pdf/BJ20040262.pdf,"The ubiquitous intracellular parasite Toxoplasma gondii (phylum Apicomplexa) differentiates into an encysted form (bradyzoite) that can repeatedly re-emerge as a life-threatening acute infection (tachyzoite) upon impairment of immunity. Since the switch from tachyzoite to bradyzoite is a stress-induced response, we sought to identify components related to the phosphorylation of the alpha subunit of eIF2 (eukaryotic initiation factor-2), a well-characterized event associated with stress remediation in other eukaryotic systems. In addition to characterizing Toxoplasma eIF2alpha (TgIF2alpha), we have discovered a novel eIF2 protein kinase, designated TgIF2K-A (Toxoplasma gondii initiation factor-2kinase). Although the catalytic domain of TgIF2K-A contains sequence and structural features that are conserved among members of the eIF2 kinase family, TgIF2K-A has an extended N-terminal region that is highly divergent from other eIF2 kinases. TgIF2K-A specifically phosphorylates the regulatory serine residue of yeast eIF2alpha in vitro and in vivo, and can modulate translation when expressed in the yeast model system. We also demonstrate that TgIF2K-A phosphorylates the analogous regulatory serine residue of recombinant TgIF2alpha in vitro. Finally, we demonstrate that TgIF2alpha phosphorylation in tachyzoites is enhanced in response to heat shock or alkaline stress, conditions known to induce parasite differentiation in vitro. Collectively, this study suggests that eIF2 kinase-mediated stress responses are conserved in Apicomplexa, and a novel family member exists that may control parasite-specific events, including the clinically relevant conversion into bradyzoite cysts. Medicine, 635 Barnhill Drive, Medical Sciences Bldg, Indianapolis, IN 46202, USA. wjsulliv@iupui.edu","Amino Acid Sequence/genetics!Animals!Cloning, Molecular/methods!Eukaryotic Initiation Factor-2/chemistry/genetics/physiology!Metamorphosis, Biological/genetics/physiology!Molecular Sequence Data!Peptide Synthases/physiology!Phosphorylation!Protein Biosynthesis/*physiology!Protein-Serine-Threonine Kinases/chemistry/genetics/physiology!Protozoan Proteins/chemistry/physiology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment/methods!Species Specificity!Toxoplasma/*enzymology/growth & development/pathogenicity!eIF-2 Kinase/chemistry/genetics/*physiology!",scholar,,,,,
14990449,Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics.,http://bioinformatics.oupjournals.org/cgi/content/abstract/20/4/534,"MOTIVATION: Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive automatic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annotation or multiple-genomic tree constructions. Extreme value distribution based on the Karlin-Altschul model, usually advised for large-scale comparisons are not always valid, particularly in the case of comparisons of non-biased with nucleotide-biased genomes (such that of Plasmodium falciparum). Z-values estimates based on Monte Carlo technics, can be calculated experimentally for any alignment output, whatever the method used. Empirically, a Z-value higher than approximately 8 is supposed reasonable to assess that an alignment score is significant, but this arbitrary figure was never theoretically justified. RESULTS: In this paper, we used the Bienayme-Chebyshev inequality to demonstrate a theorem of the upper limit of an alignment score probability (or P-value). This theorem implies that a computed Z-value is a statistical test, a single-linkage clustering criterion and that 1/Z-value(2) is an upper limit to the probability of an alignment score whatever the actual probability law is. Therefore, this study provides the missing theoretical link between a Z-value cut-off used for an automatic clustering of putative orthologs and/or paralogs, and the corresponding statistical risk in such genome-scale comparisons (using non-biased or biased genomes). Dynamique Cellulaire, UMR 5168 CNRS-CEA-INRA-Universite J. Fourier, CEA Grenoble, 17 rue des Martyrs, F-38054, Grenoble cedex 09, France.","*Algorithms!Amino Acid Sequence!Amino Acids/chemistry!Cluster Analysis!Comparative Study!*Data Interpretation, Statistical!Molecular Sequence Data!Proteins/*chemistry!Quality Control!Reproducibility of Results!Sensitivity and Specificity!Sequence Alignment/*methods!Sequence Analysis, Protein/*methods!Sequence Homology, Amino Acid!",scholar,,Bioinformatics,20,,4
14997358,Binding of chimeric metal-binding green fluorescent protein to lipid monolayer.,http://www.springerlink.com/index/0VJ02AM9Y1E2NTEG.pdf,"Membrane-based bioanalytical devices for metal determination using green fluorescent protein as the sensor molecule may be a useful future biomimetic material. However, in order to develop such a device, it is necessary first to understand the interaction of the protein with lipid membranes. Thus we have investigated the interaction between chimeric cadmium-binding green fluorescent proteins (CdBPGFPs) and lipid monolayers, using a film-balance technique complemented with epifluorescence microscopy. The binding avidity was monitored from the surface pressure vs. area isotherms or from the measured increase in the lateral pressure upon injection of the chimeric CdBPGFPs beneath the lipid monolayer. Increased fluidization as well as expansion of the surface area were shown to depend on the concentration of the CdBPGFPs. The kinetics of the protein-induced increase in lateral pressure was found to be biphasic. The chimeric CdBPGFPs possessed high affinity to the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayer with a dissociation constant of Kd = 10(-8)M. Epifluorescence measurements showed that this affinity is due to the presence of the Cd-binding peptide, which caused the GFP to incorporate preferentially to the liquid phase and defect part of the rigid domain at low interfacial pressure. At high compression, the Cd-binding peptide could neither incorporate nor remain in the lipid core. However, specific orientation of the chimeric CdBPGFPs underneath the air-water interface was achieved, even under high surface pressure, when the proteins were applied to the metal-chelating lipid-containing surfaces. This specific binding could be controlled reversibly by the addition of metal ions or metal chelator. The reversible binding of the chimeric CdBPGFPs to metal-chelating lipids provided a potential approach for immobilization, orientation and lateral organization of a protein at the membrane interface. Furthermore, the feasibility of applying the chelator lipids for the codetermination of metal ions with specific ligands was also revealed. Our finding clearly demonstrates that a strong interaction, particularly with fluid lipid domains, could potentially be used for sensor development in the future. Mahidol University, 2 Prannok Road, Bangkok-Noi, 10700 Bangkok, Thailand.","1,2-Dipalmitoylphosphatidylcholine/*chemistry!Binding Sites!Biosensing Techniques/*methods!Green Fluorescent Proteins/analysis/*chemistry/genetics/ultrastructure!Membrane Lipids/*chemistry!Metals/*analysis/*chemistry!Microscopy, Fluorescence/*methods!Protein Binding!Recombinant Fusion Proteins/analysis/chemistry/ultrastructure!Research Support, Non-U.S. Gov't!",scholar,2004,European Biophysics Journal,33,6,522
15003839,Transcription of subtelomerically located var gene variant in Plasmodium falciparum appears to require the truncation of an adjacent var gene.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003578&_version=1&_returnURL=&md5=776f048b069343a9bd47f1a983277c4b,"The Plasmodium falciparum R29 clone preferentially transcribes the R29var gene variant on rosette selection, unlike other isogenic clones from the same parasite lineage. Characterisation of the R29var gene locus revealed that this gene lies internal to, and is in a tail-to-tail orientation with, a second var gene variant (A4var) at one end of chromosome 13. In the R29 clone, a spontaneous deletion event between these two var variants deletes all of the A4var gene and the subtelomeric repetitive sequence arrays. We have previously shown that a simple disruption of the A4var gene is not sufficient to preferentially activate the R29var gene in rosette-selected parasites. We therefore hypothesised that the truncation of the chromosome end may be a key factor in predisposing the R29var variant to transcription under rosette selection conditions. Here, we have generated a panel of isogenic parasite clones with both intact and truncated A4var-R29var loci, and show that R29var transcription is only detected in rosette-selected clones with a truncated locus. Furthermore, we present provisional data describing the relative frequency with which this spontaneous deletion event occurs. These data have implications in our understanding of how spontaneous deletion events within subtelomeric var loci may affect transcription of these var gene variants. Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK. horrocks@hammer.imm.ox.ac.uk","Animals!Antigenic Variation/genetics!Antigens, Protozoan/genetics!Blotting, Northern!DNA, Protozoan/analysis/genetics!Gene Expression Regulation!Gene Order!*Genes, Protozoan!Plasmodium falciparum/*genetics!Protozoan Proteins/*genetics!RNA, Protozoan/analysis/genetics!Repetitive Sequences, Nucleic Acid!Research Support, Non-U.S. Gov't!Restriction Mapping!Sequence Deletion!Telomere/genetics!*Transcription, Genetic!",scirus,2004,Molecular and Biochemical Parasitology,134,2,193
15003842,PTRAMP; a conserved Plasmodium thrombospondin-related apical merozoite protein.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003736&_version=1&_returnURL=&md5=a3726d6ff1a6e494216d66ea3ccb07d8,"A gene encoding a 352 amino acid protein with a putative signal sequence, transmembrane domain and thrombospondin structural homology repeat was identified in the genome of the human malaria parasite, Plasmodium falciparum and the rodent malaria parasite, Plasmodium berghei. The protein localises in the apical organelles of P. falciparum and P. berghei merozoites within intraerythrocytic schizonts and has, therefore, been termed the Plasmodium thrombospondin-related apical merozoite protein (PTRAMP). PTRAMP co-localises with the Apical Merozoite Antigen-1 (AMA-1) in developing micronemes and subsequently relocates onto the merozoite surface. Although the gene appears to be specific to the Plasmodium genus, orthologues are present in the genomes of all malaria parasite species examined suggesting a conserved function in host-cell invasion. PTRAMP, therefore, has all the features to merit further evaluation as a malaria vaccine candidate. The King's Buildings, Edinburgh EH9 3JT, UK. Joanne.Thompson@ed.ac.uk","Amino Acid Motifs!Amino Acid Sequence!Animals!Antigens, Protozoan/metabolism!Erythrocytes/parasitology!Gene Expression Regulation!Membrane Proteins/*chemistry/genetics/*metabolism!Molecular Sequence Data!Plasmodium/cytology/*genetics/growth & development/metabolism!Plasmodium berghei/cytology/genetics/growth & development/metabolism!Plasmodium falciparum/cytology/genetics/growth & development/metabolism!Protein Sorting Signals!Protein Structure, Tertiary!Protozoan Proteins/*chemistry/*genetics/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Homology!Thrombospondins/genetics!",scirus,2004,Molecular and Biochemical Parasitology,134,2,225
15003844,"Human malaria parasite orotate phosphoribosyltransferase: functional expression, characterization of kinetic reaction mechanism and inhibition profile.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685103003773&_version=1&_returnURL=&md5=ffd32f041090258e4cfb34b1f12bc116,"Plasmodium falciparum, the causative agent of the most lethal form of human malaria, relies on de novo pyrimidine biosynthesis. A gene encoding orotate phosphoribosyltransferase (OPRT), the fifth enzyme of the de novo pathway catalyzing formation of orotidine 5'-monophosphate (OMP) and pyrophosphate (PP(i)) from 5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate, was identified from P. falciparum (pfOPRT). The deduced amino acid sequence for pfOPRT was compared with OPRTs from other organisms and found to be most similar to that of Escherichia coli. The catalytic residues and consensus sequences for substrate binding in the enzyme were conserved among other organisms. The pfOPRT was exceptional in that it contained a unique insertion of 20 amino acids and an amino-terminal extension of 66 amino acids, making the longest amino acid sequence (281 amino acids with a predicted molecular mass of 33kDa). The cDNA of the pfOPRT gene was cloned, sequenced and functionally expressed in soluble form. The recombinant pfOPRT was purified from the E. coli lysate by two steps, nickel metal-affinity and gel-filtration chromatography. From 1l E. coli culture, 1.2-1.5mg of pure pfOPRT was obtained. SDS-PAGE revealed that the pfOPRT had a molecular mass of 33kDa and analytical gel-filtration chromatography showed that the enzyme activity eluted at approximately 67kDa. Using dimethyl suberimidate to cross-link neighboring subunits of the pfOPRT, it was confirmed that the native enzyme exists in a dimeric form. The steady state kinetics of initial velocity and product inhibition studies indicate that the enzyme pfOPRT follows a random sequential kinetic mechanism. Compounds aimed at the pfOPRT nexus may act against the parasite through at least two mechanisms: by directly inhibiting the enzyme activity, or be processed to an inhibitor of thymidylate synthase. This study provides a working system with which to investigate new antimalarial agents targeted against P. falciparum OPRT. Diseases, Osaka University, Suita, Osaka 565-0871, Japan. fmedjkk@md2.md.chula.ac.th inhibitors/chemistry/genetics/*metabolism","Amino Acid Sequence!Animals!Antimalarials/pharmacology!Binding Sites/genetics!Catalytic Domain/genetics!Chromatography!Cloning, Molecular!DNA, Protozoan/chemistry/isolation & purification!Dimerization!Enzyme Inhibitors/pharmacology!Escherichia coli/genetics/metabolism!Genes, Protozoan!Kinetics!Molecular Sequence Data!Molecular Weight!Orotate Phosphoribosyltransferase/*antagonists &!Plasmodium falciparum/*enzymology/*genetics!Protein Subunits!Recombinant Proteins/isolation & purification/metabolism!Research Support, Non-U.S. Gov't!Salmonella typhimurium/genetics!Sequence Alignment!Substrate Specificity!",scirus,2004,Molecular and Biochemical Parasitology,134,2,245
15032631,Mitochondrial and plastid functions as antimalarial drug targets.,http://www.ingentaconnect.com/content/ben/cdtid/2004/00000004/00000001/art00003,"Malaria parasites possess three genomes: the nuclear chromosomes, the mitochondrial genome, and the plastid genome. Realization that the parasites contain a plastid remnant with its own genome has created much excitement not only from a basic biological point of view but also from the prospects for developing new antimalarial drugs. Both the mitochondrial and the plastid genomes are the smallest examples of their kind known to date. The plastid appears to be derived from an ancestral secondary endosymbiotic event. Interestingly, the main functions usually associated with a mitochondrion and a plastid, i.e. oxidative phosphorylation and photosynthesis, do not appear to be conserved in malaria parasites. Completion of the parasite genome sequence has provided the opportunity to assess functions assigned to these highly derivatized organelles. It is clear that these organelles serve vital functions since interference with their activity is incompatible with parasite growth. A number of antimalarial compounds target functions of either the mitochondrion or the plastid. This review will survey our current understanding of mitochondrial and plastid functions with a view to identify processes that are or have a potential to be targets for antimalarial drugs. Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA 19129, USA. av27@drexel.edu","Animals!Antimalarials/metabolism/*therapeutic use!Cell Nucleus/genetics!Chromosomes/genetics!Electron Transport!Fatty Acids/biosynthesis!Humans!Mitochondria/drug effects/*metabolism!Models, Biological!Plastids/drug effects/*metabolism!Research Support, U.S. Gov't, P.H.S.!Symbiosis!Terpenes/metabolism!",scholar,2004,Current Drug Targets--Infectious Disorders,4,,11
15032632,Computer assisted searches for drug targets with emphasis on malarial proteases and their inhibitors.,http://www.ingentaconnect.com/content/ben/cdtid/2004/00000004/00000001/art00004,"The creation of databases that make enormous and diverse amounts of information available, the coding of algorithms that allow the collection and investigation of these data and the wide availability of desktop computers capable of handling the data and running the algorithms have set the stage for innovative approaches to drug target identification. Here we review the main currents in this new field, providing an overview of some of the databases and software used to generate and shorten the lists of potential drug targets using in silico methods. As a case study, we look at the identification and investigation of malarial proteases as therapeutic targets in the Plasmodium spp. parasites. 1604 West, San Antonio, Texas 78249, USA. ywang@utsa.edu","Algorithms!Animals!Antimalarials/*pharmacology!Computational Biology!*Computers!Databases, Factual!*Drug Design!Endopeptidases/*drug effects!Evolution!Genome, Protozoan!Genomics!Humans!Malaria/drug therapy!Malaria, Falciparum/drug therapy!Plasmodium falciparum/drug effects!Protease Inhibitors/*pharmacology!Proteomics!Research Support, Non-U.S. Gov't!Software!",scholar,2004,Current Drug Targets--Infectious Disorders,4,,25
15037302,Toxoplasma as a novel system for motility.,http://therion.dna.uba.ar/bmei/teo/SAngel_motility.pdf,"Motility is a characteristic of most living organisms and often requires specialized structures like cilia or flagella. An alternative is amoeboid movement, where the polymerization/depolymerization of actin leads to the formation of pseudopodia, filopodia and/or lamellipodia that enable the cell to crawl along a surface. Despite their lack of locomotive organelles and in absence of cell deformation, members of the apicomplexan parasites employ a unique form of locomotion called gliding motility to promote their migration across biological barriers and to power host-cell invasion and egress. Detailed studies in Toxoplasma gondii and Plasmodium species have revealed that this unique mode of movement is dependent on a myosin of class XIV and necessitates actin dynamics and the concerted discharge and processing of adhesive proteins. Gliding is essential for the survival and infectivity of these obligate intracellular parasites, which cause severe disease in humans and animals. Fleming Building, South Kensington Campus, London UK, SW7 2AZ. d.soldati@ic.ac.uk","Actins/metabolism!Animals!Cytoskeleton/*physiology!*Locomotion!Models, Animal!Myosins/genetics!Plasmodium falciparum/chemistry/physiology!Research Support, Non-U.S. Gov't!Signal Transduction!Toxoplasma/cytology/*physiology!",scholar,2004,Curr Opin Cell Biol,16,1,32
15048989,Mass spectrometric analysis of Plasmodium falciparum erythrocyte membrane protein-1 variants expressed by placental malaria parasites.,http://doi.wiley.com/10.1002/pmic.200300666,"Surface proteins from Plasmodium falciparum are important malaria vaccine targets. However, the surface proteins previously identified are highly variant and difficult to study. We used tandem mass spectrometry to characterize the variant antigens (Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1)) expressed on the surface of malaria-infected erythrocytes that bind to chondroitin sulfate A (CSA) in the placenta. Whereas PfEMP1 variants previously implicated as CSA ligands were detected, in unselected parasites four novel variants were detected in CSA-binding or placental parasites but not in unselected parasites. These novel PfEMP1 variants require further study to confirm whether they play a role in placental malaria. mfried@sbri.org","Animals!Chondroitin Sulfates/metabolism!Electrophoresis, Polyacrylamide Gel!Erythrocyte Membrane/metabolism/parasitology!Erythrocytes/metabolism/*parasitology!Female!Malaria/metabolism!Malaria Vaccines/*immunology!Placenta/metabolism/parasitology!Plasmodium falciparum/immunology/*metabolism!Pregnancy!*Pregnancy Complications, Parasitic!Protozoan Proteins/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization!",scholar,2004,Proteomics,4,4,1086
15049814,The Plasmodium falciparum clag9 gene encodes a rhoptry protein that is transferred to the host erythrocyte upon invasion.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2003.03969.x/abs/,"The first gene characterizing the clag (cytoadherence linked asexual gene) family of Plasmodium falciparum was identified on chromosome 9. The protein product (Clag9) was implicated in cytoadhesion, the binding of infected erythrocytes to host endothelial cells, but little information on the biochemical characteristics of this protein is available. Other genes related to clag9 have been identified on different chromosomes. These genes encode similar amino acid sequences, but clag9 shows least conservation. Clag9 was detected in schizonts, merozoites and ring-stage parasites after protease digestion and peptide analysis by mass spectrometry. Using antisera raised against unique regions of Clag9 and against RhopH2, a component of the RhopH high-molecular-mass protein complex of merozoites, immunofluorescence co-localized the two proteins to the apical region of merozoites. Immunoelectron microscopy co-localized Clag9 and RhopH2 exclusively to the basal bulb region of rhoptries rather than to their apical ducts. The same Clag9-specific antibodies bound the RhopH complex, and the protein was detected in the complex purified by antibodies to RhopH2. Clag9 protein was also shown to be present in ring-stage parasites, carried through from the previous cycle with the RhopH complex, in a location identical to that of RhopH2. Transcription of the clag9 gene was shown to occur at the same time as the genes for other members of the RhopH complex, rhoph2 and 3. The results indicate that Clag9 is part of the RhopH complex and suggest that, within this complex, the protein previously designated RhopH1 is composed of more than one protein product of the clag gene family. The results cast doubt on a direct role for Clag9 in cytoadhesion; we suggest that the primary role of the RhopH complex is in remodelling the infected red blood cell after invasion by the merozoite. The complex may have multiple functions dependent on its exact composition, which may include, with respect to Clag9, a contribution to the mechanism of cytoadhesion. Hill, London NW7 1AA, UK. iling@nimr.mrc.ac.uk development/metabolism/pathogenicity","Amino Acid Sequence!Animals!Antigens, Protozoan/genetics/metabolism/physiology!Cell Adhesion!Cell Adhesion Molecules/chemistry/*genetics/*metabolism!Erythrocytes/*parasitology!Gene Expression Regulation!Genes, Protozoan!Microscopy, Fluorescence!Microscopy, Immunoelectron!Molecular Sequence Data!Plasmodium falciparum/*genetics/growth &!Protein Transport!Protozoan Proteins/chemistry/*genetics/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Sequence Analysis, Protein!Transcription, Genetic!",scholar,2004,Molecular Microbiology,52,1,107
15055736,Eukaryotic operon genes can define highly conserved syntenies.,http://www.img.cas.cz/fb/pdf/2004-50-1-6.pdf,"The synteny conservation of the members of eukaryotic operons was investigated by mapping their orthologues in Drosophila, human, and other eukaryotes. While the homologues of the operon members are generally not linked, some examples of highly conserved syntenies were found. The most significant synteny involves two members of one C. elegans operon, encoding fibrillarin and ribosomal protein S16. Their homologues are linked in human, mouse, Drosophila, Anopheles gambiae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Plasmodium falciparum, and Guillardia theta, but not in five other genomes. The distances between the genes are larger than in the nematode, suggesting the prevalence of intrachromosomal rearrangements. Genomics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic. trachtul@biomed.cas.cz","Animals!Databases, Factual!Evolution, Molecular!Gene Rearrangement!Genome!Humans!Linkage (Genetics)!Molecular Sequence Data!Operon/*genetics!Research Support, Non-U.S. Gov't!*Synteny!",scholar,2004,Folia Biologica (Praha),50,,1
15075257,"Plasmodium falciparum histone acetyltransferase, a yeast GCN5 homologue involved in chromatin remodeling.",http://ec.asm.org/cgi/content/abstract/3/2/264,"The yeast transcriptional coactivator GCN5 (yGCN5), a histone acetyltransferase (HAT), is part of large multimeric complexes that are required for chromatin remodeling and transcriptional activation. Like other eukaryotes, the malaria parasite DNA is organized into nucleosomes and the genome encodes components of chromatin-remodeling complexes. Here we show that GCN5 is conserved in Plasmodium species and that the most homologous regions are within the HAT domain and the bromodomain. The Plasmodium falciparum GCN5 homologue (PfGCN5) is spliced with three introns, encoding a protein of 1,464 residues. Mapping of the ends of the PfGCN5 transcript suggests that the mRNA is 5.2 to 5.4 kb, consistent with the result from Northern analysis. Using free core histones, we determined that recombinant PfGCN5 proteins have conserved HAT activity with a substrate preference for histone H3. Using substrate-specific antibodies, we determined that both Lys-8 and -14 of H3 were acetylated by the recombinant PfGCN5. In eukaryotes, GCN5 homologues interact with yeast ADA2 homologues and form large multiprotein HAT complexes. We have identified an ADA2 homologue in P. falciparum, PfADA2. Yeast two-hybrid and in vitro binding assays verified the interactions between PfGCN5 and PfADA2, suggesting that they may be associated with each other in vivo. The conserved function of the HAT domain in PfGCN5 was further illustrated with yeast complementation experiments, which showed that the PfGCN5 region corresponding to the full-length yGCN5 could partially complement the yGCN5 deletion mutation. Furthermore, a chimera comprising the PfGCN5 HAT domain fused to the remainder of yeast GCN5 (yGCN5) fully rescued the yGCN5 deletion mutant. These data demonstrate that PfGCN5 is an authentic GCN5 family member and may exist in chromatin-remodeling complexes to regulate gene expression in P. falciparum. Dalian 116023, China.","Acetyltransferases/*genetics/metabolism/*physiology!Amino Acid Sequence!Animals!Chromatin Assembly and Disassembly/*genetics!DNA-Binding Proteins/genetics/metabolism!Gene Expression!Genetic Complementation Test!Glutathione Transferase/genetics!Histone Acetyltransferases!Molecular Sequence Data!Mutation!Nucleosomes/metabolism!Plasmodium falciparum/*enzymology/*genetics!Protein Kinases/genetics/metabolism!Recombinant Fusion Proteins/genetics/metabolism!Research Support, U.S. Gov't, P.H.S.!Saccharomyces cerevisiae Proteins/genetics/metabolism!Sequence Alignment!Transcription Factors/metabolism!Two-Hybrid System Techniques!",scholar,,Eukaryotic Cell,,,
15075278,A Theileria annulata DNA binding protein localized to the host cell nucleus alters the phenotype of a bovine macrophage cell line.,http://ec.asm.org/cgi/content/abstract/3/2/495,"The apicomplexan parasite Theileria annulata is the only intracellular eukaryote that is known to induce the proliferation of mammalian cells. However, as the parasite undergoes stage differentiation, host cell proliferation is inhibited, and the leukocyte is eventually destroyed. We have isolated a parasite gene (SuAT1) encoding an AT hook DNA binding polypeptide that has a predicted signal peptide, PEST motifs, nuclear localization signals, and domains which indicate interaction with regulatory components of the higher eukaryotic cell cycle. The polypeptide is localized to the nuclei of macroschizont-infected cells and was detected at significant levels in cells that were undergoing parasite stage differentiation. Transfection of an uninfected transformed bovine macrophage cell line, BoMac, demonstrated that SuAT1 can modulate cellular morphology and alter the expression pattern of a cytoskeletal polypeptide in a manner similar to that found during the infection of leukocytes by the parasite. Our findings indicate that Theileria parasite molecules that are transported to the leukocyte nucleus have the potential to modulate the phenotype of infected cells. University of Glasgow, Glasgow G61 1QH, United Kingdom. B.Shiels@vet.gla.ac.uk","AT-Hook Motifs!Amino Acid Sequence!Animals!Antibodies, Protozoan/immunology!Cattle/*parasitology!Cell Line!Cell Nucleus/*chemistry/metabolism/ultrastructure!Cinnamates/pharmacology!Cytoskeletal Proteins/metabolism!DNA-Binding Proteins/*analysis/genetics/metabolism!Hygromycin B/*analogs & derivatives/pharmacology!Macrophages/metabolism/*parasitology/ultrastructure!Microscopy, Fluorescence!Molecular Sequence Data!Phenotype!Protein Binding!Protozoan Proteins/*analysis/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Theileria annulata/genetics/metabolism/*pathogenicity!Transfection!",scholar,,Eukaryotic Cell,,,
15078855,Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery.,http://intl.genome.org/cgi/content/abstract/14/5/917,"Identification of novel targets for the development of more effective antimalarial drugs and vaccines is a primary goal of the Plasmodium genome project. However, deciding which gene products are ideal drug/vaccine targets remains a difficult task. Currently, a systematic disruption of every single gene in Plasmodium is technically challenging. Hence, we have developed a computational approach to prioritize potential targets. A pathway/genome database (PGDB) integrates pathway information with information about the complete genome of an organism. We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. In addition to the annotations provided in the genome database, we add 956 additional annotations to proteins annotated as "hypothetical" using the GeneQuiz annotation system. We apply a novel computational algorithm to PlasmoCyc to identify 216 "chokepoint enzymes." All three clinically validated drug targets are chokepoint enzymes. A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets. USA.","Algorithms!Animals!Catalysis/drug effects!Comparative Study!Computational Biology/*methods!Databases, Genetic!Enzyme Inhibitors/pharmacology!Escherichia coli/enzymology/genetics/metabolism!Escherichia coli Proteins/genetics/metabolism/physiology!Genes, Bacterial/genetics/physiology!Genes, Essential/drug effects/physiology!Genes, Protozoan/genetics/physiology!*Genome, Protozoan!Genomics/*methods!Humans!Models, Chemical!Plasmodium falciparum/drug effects/enzymology/*genetics/*metabolism!Predictive Value of Tests!Protozoan Proteins/antagonists & inhibitors/genetics/metabolism/physiology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Software!Substrate Specificity/genetics/physiology!",scholar,2004,Genome Research,14,5,917
15094163,Molecular aspects of malaria pathogenesis.,http://www.blackwell-synergy.com/doi/abs/10.1016/j.femsim.2004.01.010,"Plasmodium falciparum being the most lethal plasmodiae is still a major cause of the disease burden and mortality in malaria endemic areas. Due to the wide spread drug resistance in combination with poor socio-economic situation in the vast majority of the endemic countries, malaria is today a great global challenge. The scientific community is, however, progressing. The 23 Mb genome of P. falciparum has been decoded and publicly available. Data of transcriptional profiling at certain developmental stages have already been generated. More than 50% of P. falciparum genes are transcribed constitutively in all the developmental stages of parasite life cycle. Functional disruption of these genes might have implications for parasite growth and development. Available microarray data indicate that P. falciparum preferentially expresses rif and stevor gene families at gametocyte and sporozoite stages while var genes are predominantly expressed at the erythrocytic stage. Gene regulation mechanisms of the variant gene families in P. falciparum are still not understood though some regulatory elements have been proposed. The occurrence of severe malaria is determined by both parasite and human host factors. Sequestration and antigenic variation are two of the evasion mechanisms utilized by P. falciparum in order to escape the human host defences. Understanding the molecular mechanisms underlying these phenomena is of a major importance and interest in malaria research. Here, we summarize and highlight the recent progress in molecular aspects of severe malaria. Institute for Infectious Disease Control, Box 280, 171 77 Stockholm, Sweden.","Animals!Antigenic Variation!Cell Adhesion Molecules/metabolism!Erythrocyte Membrane/parasitology!Female!Genes, Protozoan!Humans!Malaria, Falciparum/genetics/immunology/*parasitology/*physiopathology!Male!Phenotype!Plasmodium falciparum/*genetics/*pathogenicity!Pregnancy!Pregnancy Complications, Parasitic/parasitology/physiopathology!Protozoan Proteins/*physiology!Research Support, Non-U.S. Gov't!Virulence!",scholar,2004,FEMS Immunol. Med. Microbiol,41,,9
15099555,Plasmodium falciparum--do killers commit suicide?,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492204000273&_version=1&_returnURL=&md5=85250fd7ede5e4e85a13f4338d9a0b33,,"Animals!*Apoptosis!Biological Markers!Caspases/metabolism!Erythrocyte Aggregation!Erythrocytes/*parasitology/physiology!Gene Expression Regulation!Host-Parasite Relations!Humans!Plasmodium falciparum/pathogenicity/*physiology!Research Support, Non-U.S. Gov't!",scirus,2004,Trends in Parasitology,20,4,165
15103554,CLAG 9 is located in the rhoptries of Plasmodium falciparum.,http://www.springerlink.com/index/MGDNA88EMYGXD33K.pdf,"Clag 9, a gene located on chromosome 9 of Plasmodium falciparum has previously been associated with the cytoadherence of parasitized erythrocytes to CD36. This gene is part of a multi-gene family found in all Plasmodium species studied to date. Using data from the Malaria Genome Sequencing Project, peptides specific for clag 9 were designed, synthesized and used to immunize mice. This antisera was used in Western blotting and immunofluorescence experiments to determine the cellular localization of CLAG 9 in the parasitized erythrocyte. Co-localization using immunofluorescence of wildtype and knockout parasites unequivocally shows that CLAG 9 is localized to the rhoptry organelles of P. falciparum. Tropical Health and Nutrition, Queensland Institute of Medical Research, 300 Herston Road, 4006 Herston, Queensland, Australia. donG@qimr.edu.au","Amino Acid Sequence!Animals!Antibodies, Protozoan!Cell Adhesion Molecules/chemistry/genetics/immunology/*metabolism!Erythrocytes/parasitology!Fluorescent Antibody Technique!Humans!Malaria, Falciparum/parasitology!Mice!Mice, Inbred BALB C!Molecular Sequence Data!Organelles/*metabolism!Peptides/chemistry/immunology!Plasmodium falciparum/genetics/*metabolism!Protozoan Proteins/chemistry/genetics/immunology/*metabolism!Research Support, Non-U.S. Gov't!",scholar,2004,Parasitology Research,93,1,64
15118727,Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum.,http://volatility.cgr.harvard.edu/Nature428.pdf,"Selective pressures on proteins are usually measured by comparing nucleotide sequences. Here we introduce a method to detect selection on the basis of a single genome sequence. We catalogue the relative strength of selection on each gene in the entire genomes of Mycobacterium tuberculosis and Plasmodium falciparum. Our analysis confirms that most antigens are under strong selection for amino-acid substitutions, particularly the PE/PPE family of putative surface proteins in M. tuberculosis and the EMP1 family of cytoadhering surface proteins in P. falciparum. We also identify many uncharacterized proteins that are under strong selection in each pathogen. We provide a genome-wide analysis of natural selection acting on different stages of an organism's life cycle: genes expressed in the ring stage of P. falciparum are under stronger positive selection than those expressed in other stages of the parasite's life cycle. Our method of estimating selective pressures requires far fewer data than comparative sequence analysis, and it measures selection across an entire genome; the method can readily be applied to a large range of sequenced organisms. Divinity Avenue, Cambridge, Massachusetts 02138, USA. jplotkin@fas.harvard.edu","Animals!Bacterial Proteins/genetics!Codon/genetics!Evolution, Molecular!Gene Expression Regulation!Genes, Bacterial/*genetics!Genes, Protozoan/*genetics!*Genome, Bacterial!*Genome, Protozoan!Mutation/genetics!Mycobacterium tuberculosis/*genetics!Plasmodium falciparum/*genetics/growth & development!Protozoan Proteins/genetics!*Selection (Genetics)!",scholar,2004,Nature,428,6986,942
15120625,Molecular cloning of a K(+) channel from the malaria parasite Plasmodium falciparum.,http://www.binf.ku.dk/users/tlitman/publications/BBRC_2004_318_477_Ellekvist_Ricke_Litman.pdf,"In most living cells, K(+) channels are important for the generation of the membrane potential and for volume regulation. The parasite Plasmodium falciparum, which causes malignant malaria, must be able to deal with large variations in the ambient K(+) concentration: it is exposed to high concentrations of K(+) when inside the erythrocyte and low concentrations when in plasma. In the recently published genome of P. falciparum, we have identified a gene, pfkch1, encoding a potential K(+) channel, which to some extent resembles the big-conductance (BK) K(+) channel. We have cloned the approximately 6000 nucleotide (nt) fragment from cDNA, studied the pattern of expression of pfkch1 throughout the intraerythrocytic part of the parasite's life-cyclus, and characterized the channel on the basis of similarity to other K(+) channels from pro- and eukaryotic organisms. This P. falciparum K(+) channel could be a potential drug target. ellekvist@immi.ku.dk","Amino Acid Sequence!Animals!Base Sequence!Cloning, Molecular!Conserved Sequence!Erythrocytes/parasitology!Gene Expression!Humans!Malaria/parasitology!Membrane Proteins/genetics/metabolism!Molecular Sequence Data!Phylogeny!Plasmodium falciparum/genetics/growth & development/*metabolism!Potassium Channels/*genetics/metabolism!Protozoan Proteins/*genetics/metabolism!RNA, Messenger/biosynthesis!Research Support, Non-U.S. Gov't!Sequence Alignment!",scholar,2004,Biochemical and Biophysical Research Communications,318,,477
15122533,Longitudinal assessment of Plasmodium falciparum var gene transcription in naturally infected asymptomatic children in Papua New Guinea.,http://www.journals.uchicago.edu/cgi-bin/resolve%3Fid%3Ddoi:10.1086/383250,"Sequestration and antigenic variation are essential for Plasmodium falciparum survival in vivo contributing to severe pathologic findings and, also, chronic infection. Both are conferred by P. falciparum erythrocyte membrane proteins encoded by ~60 var genes. To study the dynamics of var gene expression, we conducted a 4-month longitudinal study of semi-immune children from Papua New Guinea. By use of magnetic bead-anchored reverse-transcription polymerase chain reaction analysis performed over 5 var regions, as well as cloning and sequencing, the longitudinal distribution of full-length var transcripts was analyzed. We identified a dynamic picture of var gene expression with rapid switches but with identical var transcripts recurring for up to 10 weeks. The number of var transcripts was correlated to the number of infections, with a mean of 1.7 var transcripts identified per sample and infecting strain. Analysis of 158 different Duffy binding-like 1 alpha sequences confirmed the recombinogenic nature of var genes. This is the first report of the dynamics of var gene expression in chronically infected children.","Animals!Base Sequence!Child!Cloning, Molecular!Humans!Longitudinal Studies!Malaria, Falciparum/blood/immunology/*parasitology!Molecular Sequence Data!Papua New Guinea!Plasmodium falciparum/*genetics/immunology!Protozoan Proteins/*genetics/immunology!RNA, Protozoan/chemistry/genetics!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Sequence Analysis, DNA!Transcription, Genetic/genetics!",scholar,2004,J. infect. Dis,189,,1942
15123742,Plasmodium falciparum associated with severe childhood malaria preferentially expresses PfEMP1 encoded by group A var genes.,http://www.jem.org/cgi/content/abstract/199/9/1179,"Parasite-encoded variant surface antigens (VSAs) like the var gene-encoded Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family are responsible for antigenic variation and infected red blood cell (RBC) cytoadhesion in P. falciparum malaria. Parasites causing severe malaria in nonimmune patients tend to express a restricted subset of VSA (VSA(SM)) that differs from VSA associated with uncomplicated malaria and asymptomatic infection (VSA(UM)). We compared var gene transcription in unselected P. falciparum clone 3D7 expressing VSA(UM) to in vitro-selected sublines expressing VSA(SM) to identify PfEMP1 responsible for the VSA(SM) phenotype. Expression of VSA(SM) was accompanied by up-regulation of Group A var genes. The most prominently up-regulated Group A gene (PFD1235w/MAL7P1.1) was translated into a protein expressed on the infected RBC surface. The proteins encoded by Group A var genes, such as PFD1235w/MAL7P1.1, appear to be involved in the pathogenesis of severe disease and are thus attractive candidates for a vaccine against life-threatening P. falciparum malaria. Building 24-2, Blegdamsvej 3, 2200 Copenhagen, Denmark. atrj@biobase.dk","Amino Acid Sequence!Animals!Antibodies, Protozoan/blood!Antigens, Protozoan/*genetics!Base Sequence!Child!Cloning, Molecular!DNA Primers!Erythrocyte Membrane/parasitology!Gene Expression Regulation/genetics!Genes, Protozoan/*genetics!Humans!Malaria, Falciparum/blood/*physiopathology!Molecular Sequence Data!Plasmodium falciparum/*genetics/*pathogenicity!Polymerase Chain Reaction/methods!Protozoan Proteins/*genetics!Recombinant Proteins/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!Sequence Homology, Amino Acid!Transcription, Genetic/genetics!",scholar,,Journal of Experimental Medicine,199,9,1179
15125686,Copper pathways in Plasmodium falciparum infected erythrocytes indicate an efflux role for the copper P-ATPase.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1133890,"Copper, like iron, is a transition metal that can generate oxygen radicals by the Fenton reaction. The Plasmodium parasite invades an erythrocyte host cell containing 20 microM copper, of which 70% is contained in the Cu/Zn SOD (cuprozinc superoxide dismutase). In the present study, we follow the copper pathways in the Plasmodium-infected erythrocyte. Metal-determination analysis shows that the total copper content of Percoll-purified trophozoite-stage-infected erythrocytes is 66% that of uninfected erythrocytes. This decrease parallels the decrease seen in Cu/Zn SOD levels in parasite-infected erythrocytes. Neocuproine, an intracellular copper chelator, arrests parasites at the ring-to-trophozoite stage transition and also specifically decreases intraparasitic levels of Cu/Zn SOD and catalase. Up to 150 microM BCS (2,9-dimethyl-4,7-diphenyl-1,10-phenanthrolinedisulphonic acid), an extracellular copper chelator, has no effect on parasite growth. We characterized a single copy PfCuP-ATPase (Plasmodium falciparum copper P-ATPase) transporter, which, like the Crypto-sporidium parvum copper P-ATPase, has a single copper-binding domain: 'Met-Xaa-Cys-Xaa-Xaa-Cys'. Recombinant expression of the N-terminal metal-binding domain reveals that the protein specifically binds reduced copper. Transcription of the PfCuP-ATPase gene is the highest at late ring stage/early trophozoite, and is down-regulated in the presence of neocuproine. Immunofluorescence and electron microscopy indicate the transporter to be both in the parasite and on the erythrocyte membrane. Both the decrease in total copper and the location of the PfCuP-ATPase gene indicate a copper-efflux pathway from the infected erythrocyte. Microbiology and Immunology, Bloomberg School of Public Health, The Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA.","Adenosinetriphosphatase/genetics/*physiology!Amino Acid Sequence/genetics!Animals!Arabidopsis Proteins/genetics!Caenorhabditis elegans Proteins/genetics!Cation Transport Proteins/genetics/*physiology!Chelating Agents/pharmacology!Chromosome Mapping/methods!Comparative Study!Copper/*metabolism!DNA, Protozoan/genetics!Drosophila Proteins/genetics!Erythrocyte Membrane/enzymology/metabolism/pathology!Erythrocytes/chemistry/enzymology/*metabolism/*parasitology!Humans!Mice!Molecular Sequence Data!Open Reading Frames/genetics!Phenanthrolines/pharmacology!Plasmodium falciparum/drug effects/growth & development/*metabolism!Protozoan Proteins/chemistry/physiology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Saccharomyces cerevisiae Proteins/genetics!Sequence Analysis, Protein/methods!Superoxide Dismutase/metabolism!",scholar,2004,Biochem. J,381,,803
15130119,Dissecting the loci of low-level quinine resistance in malaria parasites.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04035.x/abs/,"Quinine (QN) remains effective against Plasmodium falciparum, but its decreasing efficacy is documented from different continents. Multiple genes are likely to contribute to the evolution of QN resistance. To locate genes contributing to QN response variation, we have searched a P. falciparum genetic cross for quantitative trait loci (QTL). Results identify additive QTL in segments of chromosomes (Chrs) 13, 7 and 5, and pairwise effects from two additional loci of Chrs 9 and 6 that interact, respectively, with the QTL of Chrs 13 and 7. The mapped segments of Chrs 7 and 5 contain pfcrt, the determinant of chloroquine resistance (CQR), and pfmdr1, a gene known to affect QN responses. Association of pfcrt with a QTL of QN resistance supports anecdotal evidence for an evolutionary relationship between CQR and reduced QN sensitivity. The Chr 13 segment contains several candidate genes, one of which (pfnhe-1) encodes a putative Na(+)/H(+) exchanger. A repeat polymorphism in pfnhe-1 shows significant association with low QN response in a collection of P. falciparum strains from Asia, Africa and Central and South America. Dissection of the genes and modifiers involved in QN response will require experimental strategies that can evaluate multiple genes from different chromosomes in combination. and Infectious Diseases, National Institutes of Health, Building 4, Room 126, NIH Campus, Bethesda, MD 20892-0425, USA.","ATP-Binding Cassette Transporters/genetics/physiology!Amino Acid Sequence!Animals!Antimalarials/pharmacology!Chloroquine/pharmacology!Chromosome Mapping!Drug Resistance/*genetics!Genes, Protozoan!Membrane Proteins/genetics/physiology!Molecular Sequence Data!Multifactorial Inheritance!Plasmodium falciparum/drug effects/*genetics!Polymorphism, Genetic!Protozoan Proteins/genetics/physiology!Quantitative Trait Loci!Quantitative Trait, Heritable!Quinine/*pharmacology!Repetitive Sequences, Nucleic Acid!Research Support, U.S. Gov't, P.H.S.!Sodium-Hydrogen Antiporter/genetics/physiology!",scholar,2004,Molecular Microbiology,52,4,985
15137943,Calcium and a calcium-dependent protein kinase regulate gamete formation and mosquito transmission in a malaria parasite.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0092867404004490&_version=1&_returnURL=&md5=f884d7c714e04301070cfedc2e779d64,"Transmission of malaria parasites to mosquitoes is initiated by the obligatory sexual reproduction of the parasite within the mosquito bloodmeal. Differentiation of specialized transmission stages, the gametocytes, into male and female gametes is induced by a small mosquito molecule, xanthurenic acid (XA). Using a Plasmodium berghei strain expressing a bioluminescent calcium sensor, we show that XA triggers a rapid rise in cytosolic calcium specifically in gametocytes that is essential for their differentiation into gametes. A member of a family of plant-like calcium dependent protein kinases, CDPK4, is identified as the molecular switch that translates the XA-induced calcium signal into a cellular response by regulating cell cycle progression in the male gametocyte. CDPK4 is shown to be essential for the sexual reproduction and mosquito transmission of P. berghei. This study reveals an unexpected function for a plant-like signaling pathway in cell cycle regulation and life cycle progression of a malaria parasite. 2AZ, United Kingdom. o.billker@imperial.ac.uk","Amino Acid Sequence/genetics!Animals!Base Sequence/genetics!Calcium/*metabolism!Calcium Signaling/genetics!Cell Differentiation/genetics!Culicidae/parasitology!DNA, Complementary/analysis/genetics!Female!Flagella/enzymology/ultrastructure!Germ Cells/*enzymology/growth & development/ultrastructure!Host-Parasite Relations/physiology!Male!Microscopy, Electron, Scanning!Molecular Sequence Data!Mutation/genetics!Plant Proteins/genetics/isolation & purification/*metabolism!Plasmodium berghei/*enzymology/growth & development/ultrastructure!Protein Kinases/genetics/isolation & purification/*metabolism!Reproduction/*genetics!Research Support, Non-U.S. Gov't!S Phase/genetics!Transgenes/genetics!Xanthurenates/metabolism!",scirus,2004,Cell,117,4,503
15138065,Widespread distribution of antisense transcripts in the Plasmodium falciparum genome.,http://plasmodb.org/resources/pubpdfs/Gunasekeraetal2004.pdf,"The availability of the complete genome sequence of Plasmodium falciparum has facilitated high-throughput profiling of its complex life cycle, following the application of micro-array, proteomic, and serial analysis of gene expression (SAGE) technologies in this system. These, in turn, have yielded unprecedented insight into global gene expression, including the foremost demonstration of antisense transcription in the parasite. For example, owing to its inherent ability to sample novel ORFs and to predict transcript orientation, SAGE analysis in asexual forms led to the initial discovery of highly abundant antisense RNAs. To determine the extent of this phenomenon in P. falciparum, we have surveyed the distribution of both sense and antisense transcripts across the asexual transcriptome for the first time. To this end, a relational database integrating SAGE expression data with genome annotation information was constructed. This allowed the comprehensive annotation of a total of 17245 SAGE tags, extending over a 350-fold expression range. Transcripts from approximately 30% of the estimated 3D7 gene loci were present at detectable levels in mixed asexual stages, where loci involved in invasion and immune evasion; and carbohydrate metabolism were highly represented in the sense transcriptome. Approximately 12% of SAGE tags, however, were derived from the non-coding strand of nuclear-encoded ORFs, indicating that endogenous antisense RNAs are widespread in this system. Notably, these antisense transcripts were absent from the mitochondrial genome. Interestingly, we note that sense and antisense tag counts from single loci across the transcriptome were inversely related. Taken together, this data may provide first hints as to the possible function of antisense transcription in this system. Health, Harvard University, 665 Huntington Avenue, Boston, MA 02115, USA.","Animals!Databases, Nucleic Acid!Expressed Sequence Tags!Gene Expression Profiling/*methods!*Genome, Protozoan!Plasmodium falciparum/*genetics!Proteome!Protozoan Proteins/genetics/metabolism!RNA, Antisense/*genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!*Transcription, Genetic!",scholar,2004,Mol Biochem Parasitol,136,1,35
15140830,A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling.,http://intl.genome.org/cgi/content/abstract/14/6/1052,"Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene family in Plasmodium falciparum that encodes 11 transmembrane proteins localized to the Maurer's clefts. Using coimmunoprecipitation and shotgun proteomics, we were able to enrich specifically for these proteins and detect distinct peptides, allowing us to conclude that four to 10 products were present at a given time. Nearly all of the Pfmc-2tm genes are transcribed during the trophozoite stage; this narrow time frame of transcription overlaps with the specific stevor and rif genes that are differentially expressed during the erythrocyte cycle. The description of the structural properties of the proteins led us to manually reannotate published sequences, and to detect potentially homologous gene families in both P. falciparum and Plasmodium yoelii yoelii, where no orthologs were predicted uniquely based on sequence similarity. These basic proteins with two transmembrane domains belong to a larger superfamily, which includes STEVORs and RIFINs. State University, Cleveland, Ohio 44115, USA. ilibot@hotmail.com","Amino Acid Sequence!Animals!Antibodies, Monoclonal/metabolism!DNA, Protozoan/genetics!Erythrocytes/chemistry/parasitology!Gene Expression Profiling/methods!Gene Expression Regulation/genetics!Genes, Protozoan/genetics!Humans!Membrane Proteins/chemistry/*genetics/immunology!Molecular Sequence Data!Multigene Family/genetics!Plasmodium falciparum/*genetics!Plasmodium yoelii/*genetics!Precipitin Tests/methods!Protein Transport/physiology!Protozoan Proteins/chemistry/genetics/immunology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Homology, Amino Acid!Telomere/genetics!",scholar,2004,Genome Research,14,6,1052
15186492,START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors.,http://genomebiology.com/2004/5/6/R41,"BACKGROUND: In animals, steroid hormones regulate gene expression by binding to nuclear receptors. Plants lack genes for nuclear receptors, yet genetic evidence from Arabidopsis suggests developmental roles for lipids/sterols analogous to those in animals. In contrast to nuclear receptors, the lipid/sterol-binding StAR-related lipid transfer (START) protein domains are conserved, making them candidates for involvement in both animal and plant lipid/sterol signal transduction. RESULTS: We surveyed putative START domains from the genomes of Arabidopsis, rice, animals, protists and bacteria. START domains are more common in plants than in animals and in plants are primarily found within homeodomain (HD) transcription factors. The largest subfamily of HD-START proteins is characterized by an HD amino-terminal to a plant-specific leucine zipper with an internal loop, whereas in a smaller subfamily the HD precedes a classic leucine zipper. The START domains in plant HD-START proteins are not closely related to those of animals, implying collateral evolution to accommodate organism-specific lipids/sterols. Using crystal structures of mammalian START proteins, we show structural conservation of the mammalian phosphatidylcholine transfer protein (PCTP) START domain in plants, consistent with a common role in lipid transport and metabolism. We also describe putative START-domain proteins from bacteria and unicellular protists. CONCLUSIONS: The majority of START domains in plants belong to a novel class of putative lipid/sterol-binding transcription factors, the HD-START family, which is conserved across the plant kingdom. HD-START proteins are confined to plants, suggesting a mechanism by which lipid/sterol ligands can directly modulate transcription in plants. Claremont, CA 91711, USA. Kathrin_Schrick@kgi.edu","Animals!Arabidopsis/genetics/growth & development!Arabidopsis Proteins/*genetics/physiology!Bacterial Proteins/genetics/physiology!Caenorhabditis elegans Proteins/genetics/physiology!Cell Differentiation/genetics/physiology!Comparative Study!Drosophila Proteins/genetics/physiology!Evolution, Molecular!Gene Amplification/*genetics/physiology!Homeodomain Proteins/*genetics/physiology!Humans!Leucine Zippers/genetics/physiology!Ligands!*Lipid Metabolism!Peptides/*genetics/physiology!Phylogeny!Protein Structure, Tertiary/genetics/physiology!Protozoan Proteins/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Saccharomyces cerevisiae Proteins/genetics/metabolism!Species Specificity!Sterols/*metabolism!Transcription Factors/*genetics/physiology!",scirus,2004,Genome Biology,5,6,41
15222903,The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains.,http://www.biomedcentral.com/content/pdf/1471-2105-5-83.pdf,"BACKGROUND: Identification and characterization of novel Plasmodium gene families is necessary for developing new anti-malarial therapeutics. The products of the Plasmodium falciparum gene, MB2, were shown previously to have a stage-specific pattern of subcellular localization and proteolytic processing. RESULTS: Genes homologous to MB2 were identified in five additional parasite species, P. knowlesi, P. gallinaceum, P. berghei, P. yoelii, and P. chabaudi. Sequence comparisons among the MB2 gene products reveal amino acid conservation of structural features, including putative S1 and GTP-binding domains, and putative signal peptides and nuclear localization signals. CONCLUSIONS: The combination of domains is unique to this gene family and indicates that MB2 genes comprise a novel family and therefore may be a good target for drug development. California, Irvine, CA 92697-3900, USA. lopie@uci.edu","Amino Acid Sequence!Animals!Conserved Sequence/genetics!DNA, Protozoan/genetics!GTP-Binding Proteins/*genetics!Genome, Protozoan!Molecular Sequence Data!Multigene Family/genetics!Open Reading Frames/genetics!Peptides/*genetics!Plasmodium/*genetics!Plasmodium berghei/genetics!Plasmodium falciparum/genetics!Plasmodium gallinaceum/genetics!Plasmodium knowlesi/genetics!Plasmodium yoelii/genetics!Protein Sorting Signals/genetics!Protein Structure, Tertiary/genetics!Protozoan Proteins/*genetics!Repetitive Sequences, Amino Acid/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scholar,2004,BMC Bioinformatics,5,,83
15228526,Identification of a 67-amino-acid region of the Plasmodium falciparum variant surface antigen that binds chondroitin sulphate A and elicits antibodies reactive with the surface of placental isolates.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04145.x/abs/,"The complications of malaria in pregnancy are caused by the massive sequestration of parasitized erythrocytes (PE) in the placenta. Placental isolates of Plasmodium falciparum are unusual in that they do not bind the primary microvasculature receptor CD36 but instead bind chondroitin sulphate A (CSA). Pregnant mothers develop antibodies that recognize placental variants worldwide, suggesting that a vaccine against malaria in pregnancy is possible. Some members of the Duffy binding-like gamma (DBL-gamma) domain of the large and diverse P. falciparum erythrocyte membrane protein-1 (PfEMP-1) family, when expressed on Chinese hamster ovary (CHO) cells, bind CSA. To characterize better the molecular requirements for DBL-gamma adhesion to CSA, we determined the binding of various DBL-gamma domains. Most DBL-gamma did not bind CSA, and no conserved region was identified that strictly differentiated binders from non-binders. Structure-function analysis of the FCR3-CSA DBL-gamma domain localized the minimal CSA binding region to a 67-residue fragment. This region was partially conserved among some binding sequences. Serum from a rabbit immunized with the minimal domain reacted with CSA-binding parasite lines, but not with non-CSA-adherent PE lines that adhered to CD36 and other receptors. The identification of a minimal binding region from a highly variable cytoadherent family may have application for a vaccine against malaria in pregnancy. 20892-0425, USA. bgamain@pasteur.fr","Amino Acid Sequence!Animals!Antibodies, Protozoan/blood/*immunology!Antigens, CD36/metabolism!Antigens, Protozoan/chemistry/genetics/immunology/metabolism!Cell Adhesion!Cell Line!Chondroitin Sulfates/*metabolism!Conserved Sequence!Cricetinae!Membrane Proteins/chemistry/genetics/immunology/metabolism!Phylogeny!Plasmodium falciparum/*immunology/pathogenicity!Protein Binding!Protein Structure, Tertiary!Protozoan Proteins/chemistry/genetics/*immunology/*metabolism!Rabbits!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Homology!Structure-Activity Relationship!",scholar,2004,Molecular Microbiology,53,2,445
15230980,"Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.",http://www.biomedcentral.com/1471-2199/5/6,"BACKGROUND: Although the complete genome sequences of a large number of organisms have been determined, the exact proteomes need to be characterized. More specifically, the extent to which post-translational processes such as proteolysis affect the synthesized proteins has remained unappreciated. We examined this issue in selected protein phosphatases of the protease-rich malaria parasite, Plasmodium falciparum. RESULTS: P. falciparum encodes a number of Ser/Thr protein phosphatases (PP) whose catalytic subunits are composed of a catalytic core and accessory domains essential for regulation of the catalytic activity. Two examples of such regulatory domains are found in the Ca+2-regulated phosphatases, PP7 and PP2B (calcineurin). The EF-hand domains of PP7 and the calmodulin-binding domain of PP2B are essential for stimulation of the phosphatase activity by Ca+2. We present biochemical evidence that P. falciparum generates these full-length phosphatases as well as their catalytic cores, most likely as intermediates of a proteolytic degradation pathway. While the full-length phosphatases are activated by Ca+2, the processed cores are constitutively active and either less responsive or unresponsive to Ca+2. The processing is extremely rapid, specific, and occurs in vivo. CONCLUSIONS: Post-translational cleavage efficiently degrades complex full-length phosphatases in P. falciparum. In the course of such degradation, enzymatically active catalytic cores are produced as relatively stable intermediates. The universality of such proteolysis in other phosphatases or other multi-domain proteins and its potential impact on the overall proteome of a cell merits further investigation. Alabama, College of Medicine, Mobile, USA 36688-0002. rkumar@usamail.usouthal.edu","Animals!Calcineurin/*biosynthesis/chemistry/metabolism!Gene Expression Regulation, Enzymologic/genetics!Humans!Malaria!Malaria, Falciparum/*enzymology!Molecular Sequence Data!Parasites/*enzymology!Peptide Hydrolases/metabolism!Phosphoprotein Phosphatase/*biosynthesis/chemistry!Plasmodium falciparum/*enzymology/*metabolism!Protein Processing, Post-Translational/*physiology!Protein-Serine-Threonine Kinases/*biosynthesis/chemistry!*Proteomics!Protozoan Proteins/metabolism!Recombinant Proteins/biosynthesis/chemistry!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment/methods!",scholar,2004,BMC Molecular Biology,2004,5,6
15245577,Antioxidant defense in Plasmodium falciparum--data mining of the transcriptome.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D514526,"The intraerythrocytic malaria parasite is under constant oxidative stress originating both from endogenous and exogenous processes. The parasite is endowed with a complete network of enzymes and proteins that protect it from those threats, but also uses redox activities to regulate enzyme activities. In the present analysis, the transcription of the genes coding for the antioxidant defense elements are viewed in the time-frame of the intraerythrocytic cycle. Time-dependent transcription data were taken from the transcriptome of the human malaria parasite Plasmodium falciparum. Whereas for several processes the transcription of the many participating genes is coordinated, in the present case there are some outstanding deviations where gene products that utilize glutathione or thioredoxin are transcribed before the genes coding for elements that control the levels of those substrates are transcribed. Such insights may hint to novel, non-classical pathways that necessitate further investigations. Francisco, 600 16th Str, San Francisco, CA 94143-0448, USA. zbynek@derisilab.ucsf.edu","Animals!Erythrocytes/metabolism/*parasitology!Glutathione/biosynthesis/genetics/metabolism!Lactoylglutathione Lyase/genetics/metabolism!Oxidation-Reduction!Oxidative Stress/genetics!Plasmodium falciparum/enzymology/genetics/*metabolism!Protein Folding!Reactive Oxygen Species/metabolism!Superoxide Dismutase/genetics/metabolism!Thiolester Hydrolases/genetics/metabolism!Thioredoxin/genetics/metabolism!*Transcription, Genetic!",scholar,2004,Malaria Journal,3,1,23
15252121,The Plasmodium falciparum Vps4 homolog mediates multivesicular body formation.,http://jcs.biologists.org/cgi/content/abstract/117/17/3831,"Members of the apicomplexan family of parasites contain morphologically unique secretory organelles termed rhoptries that are essential for host cell invasion. Rhoptries contain internal membranes, and thus resemble multivesicular bodies. To determine whether multivesicular body endosomal intermediates are formed in Apicomplexa, we used the Plasmodium falciparum homolog of the class E gene, Vps4, as a probe. Endogenous P. falciparum Vps4 (PfVps4) localized to the cytoplasm of P. falciparum trophozoites, and transgenic PfVps4 localized to the cytosol in P. falciparum, in the related parasite Toxoplasma gondii and in COS cells. When mutated to block ATP hydrolysis, transiently expressed PfVps4 localized instead to large vesicular structures in P. falciparum. The same construct, and another mutant blocked in ATP binding, generated large cholesterol-enriched multivesicular bodies in both COS cells and T. gondii. Mutant PfVps4 structures in T. gondii co-localized with markers for early endosomes. These results demonstrate a conservation of Vps4 function across wide phylogenetic boundaries, and indicate that endosomal multivesicular bodies form in both P. falciparum and T. gondii. Infectious Disease, 333 Cedar Street, PO Box 208022, New Haven, CT 06520-8022, USA.","Adenosine Triphosphate/metabolism!Adenosinetriphosphatase/*metabolism/*physiology!Animals!COS Cells!Cell Proliferation!Cholesterol/metabolism!Cloning, Molecular!Cytoplasm/metabolism!Cytosol/metabolism!DNA/metabolism!Electroporation!Endosomes/metabolism!Fibroblasts/parasitology!Green Fluorescent Proteins/metabolism!Humans!Hydrolysis!Immunoblotting!Lipoproteins, LDL/metabolism!Microscopy, Electron!Mutation!Phylogeny!Plasmodium falciparum/metabolism/*physiology!Protein Structure, Tertiary!Protozoan Proteins!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Subcellular Fractions!Toxoplasma!Transfection!Transgenes!",scholar,2004,Journal of Cell Science,117,,3831
15256513,Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum.,http://intl.genome.org/cgi/content/abstract/14/8/1548,"The life cycle of the parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, requires specialized protein expression for survival in the mammalian host and insect vector. To identify components of processes controlling gene expression during its life cycle, the malarial genome--along with seven crown eukaryote group genomes--was queried with a reference set of transcription-associated proteins (TAPs). Following clustering on the basis of sequence similarity of the TAPs with their homologs, and together with hidden Markov model profile searches, 156 P. falciparum TAPs were identified. This represents about a third of the number of TAPs usually found in the genome of a free-living eukaryote. Furthermore, the P. falciparum genome appears to contain a low number of sequences, which are highly conserved and abundant within the kingdoms of free-living eukaryotes, that contribute to gene-specific transcriptional regulation. However, in comparison with these other eukaryotic genomes, the CCCH-type zinc finger (common in proteins modulating mRNA decay and translation rates) was found to be the most abundant in the P. falciparum genome. This observation, together with the paucity of malarial transcriptional regulators identified, suggests Plasmodium protein levels are primarily determined by posttranscriptional mechanisms. European Molecular Biology Laboratory Cambridge Outstation, Cambridge CB10 1SD, United Kingdom.","Animals!Comparative Study!Conserved Sequence!*Gene Expression Regulation!*Genome!Humans!Phylogeny!Physical Chromosome Mapping!Plasmodium falciparum/*genetics!Research Support, Non-U.S. Gov't!*Transcription, Genetic!",scholar,2004,Genome Research,14,8,1548
15265035,Structural and functional analysis of ataxin-2 and ataxin-3.,http://content.febsjournal.org/cgi/content/abstract/271/15/3155,"Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3) are autosomal-dominantly inherited, neurodegenerative diseases caused by CAG repeat expansions in the coding regions of the genes encoding ataxin-2 and ataxin-3, respectively. To provide a rationale for further functional experiments, we explored the protein architectures of ataxin-2 and ataxin-3. Using structure-based multiple sequence alignments of homologous proteins, we investigated domains, sequence motifs, and interaction partners. Our analyses focused on presumably functional amino acids and the construction of tertiary structure models of the RNA-binding Lsm domain of ataxin-2 and the deubiquitinating Josephin domain of ataxin-3. We also speculate about distant evolutionary relationships of ubiquitin-binding UIM, GAT, UBA and CUE domains and helical ANTH and UBX domain extensions. mario.albrecht@mpi-sb.mpg.de","Amino Acid Sequence!Animals!Humans!Models, Molecular!Molecular Sequence Data!Nerve Tissue Proteins/*chemistry/*metabolism!Peptides/chemistry/metabolism!Protein Binding!Protein Structure, Tertiary!Proteins/*chemistry/*metabolism!RNA/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!Structure-Activity Relationship!Ubiquitin/metabolism!",scholar,2004,FEBS Journal,271,,3155
15286401,Identification of a hypothetical membrane protein interactor of ribosomal phosphoprotein P0.,http://www.ias.ac.in/jbiosci/mar2004/33.pdf,"The ribosomal phosphoprotein P0 of the human malarial parasite Plasmodium falciparum (PfP0) has been identified as a protective surface protein. In Drosophila, P0 protein functions in the nucleus. The ribosomal function of P0 is mediated at the stalk of the large ribosomal subunit at the GTPase centre, where the elongation factor eEF2 binds. The multiple roles of the P0 protein presumably occur through interactions with other proteins. To identify such interacting protein domains, a yeast two-hybrid screen was carried out. Out of a set of sixty clones isolated, twelve clones that interacted strongly with both PfP0 and the Saccharomyces cerevisiae P0 (ScP0) protein were analysed. These belonged to three broad classes: namely (i) ribosomal proteins; (ii) proteins involved in nucleotide binding; and (iii) hypothetical integral membrane proteins. One of the strongest interactors (clone 67B) mapped to the gene YFL034W which codes for a hypothetical integral membrane protein, and is conserved amongst several eukaryotic organisms. The insert of clone 67B was expressed as a recombinant protein, and immunoprecipitaion (IP) reaction with anti-P0 antibodies pulled down this protein along with PfP0 as well as ScP0 protein. Using deletion constructions, the domain of ScP0, which interacted with clone 67B, was mapped to 60-148 amino acids. It is envisaged that the surface localization of P0 protein may be mediated through interactions with putative YFL034W-like proteins in P. falciparum. Homi Bhabha Road, Mumbai 400 005, India.sharma@tifr.res.in",,scholar,2004,J. Biosci,29,1,101
15287581,Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes.,http://www.utsa.edu/mbrs/pages/colloquium/seminar/attach105/wangMBP.pdf,"Proteins on the surface of parasite-infected erythrocytes (PIESPs) have been one of the major focuses of malaria research due to their role in pathogenesis and their potential as targets for immunity and drug intervention. Despite intense scrutiny, only a few surface proteins have been identified and characterized. We report the identification of two novel surface proteins from Plasmodium falciparum-infected erythrocytes. Surface proteins were fractionated through biotin-streptavidin interaction and analyzed by shotgun proteomics. From a list of 36 candidates, two were selected for further characterization. The surface location of both proteins was confirmed by confocal microscopy using specific antibodies. PIESP1 and PIESP2 are unlikely to be associated with knobs, the protrusions on the parasite-infected erythrocyte (PIE) surface. In contrast to other known PIESPs, such as PfEMP1 and Rifin, these novel proteins are encoded by single copy genes, highly conserved across Plasmodium ssp., making them good targets for interventions with a broad specificity to various P. falciparum isolates. Torrey Pines Rd., La Jolla, CA 92037, USA.","Amino Acid Sequence!Animals!Antibodies, Protozoan!Antigens, Protozoan/chemistry/genetics/*isolation & purification!Conserved Sequence!Erythrocyte Membrane/chemistry!Erythrocytes/*chemistry/*parasitology!Genes, Protozoan!Membrane Proteins/chemistry/genetics/*isolation & purification!Microscopy, Fluorescence!Molecular Sequence Data!Plasmodium falciparum/*chemistry/genetics!*Proteomics!Protozoan Proteins/chemistry/genetics/*isolation & purification!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Sequence Homology, Amino Acid!",scholar,2004,Mol. Biochem. Parasitol,135,,1
15287589,Genetic and metabolic analysis of folate salvage in the human malaria parasite Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104000301&_version=1&_returnURL=&md5=fd8bdc39f49301c740d5386d6b2b575a,"Antifolate drugs that target the biosynthesis and processing of essential folate cofactors are widely used for treatment of chloroquine-resistant falciparum malaria. Salvage of pre-formed folate can strongly compromise the efficacy of these drugs in vitro and the availability of folate from the human host in natural infections also influences therapeutic outcomes. To investigate how different parasite lines respond to the presence of exogenous folate, we measured the effect of the latter on the susceptibility of parasites to sulfa-drug blockage of folate biosynthesis, utilising the parents and 22 progeny of the HB3-Dd2 genetic cross of Plasmodium falciparum, together with selected unrelated lines. Complete linkage of the folate utilisation phenotype was observed to a DNA sequence of 48.6 kb lying between nucleotide positions 738,489 and 787,058 of chromosome 4 and encompassing the dihydrofolate reductase-thymidylate synthase (dhfr-ts) gene locus. Examination of the putative ORFs on this fragment upstream (3) and downstream (4) of dhfr-ts revealed no plausible candidate genes for folate processing. Similarly, a marked heterogeneity in the 5'-UTR regions of Dd2 and HB3, manifest as a directly repeated 256 bp sequence in the former, also did not correlate with the folate utilisation phenotype nor apparently influence levels of dhfr-ts transcripts or protein products. By contrast, the nature of the coding sequence of the dhfr domain appeared to play a direct role, with the single mutant (S108N) HB3-type utilising folic acid much less efficiently than other allelic variants. We also compared the processing of exogenous folic acid, folinic acid and p-aminobenzoic acid (pABA) in metabolic labelling studies of HB3 and Dd2. These support the view that DHFR is likely to have a low-level folate reductase activity as well as its normal function of reducing dihydrofolate to tetrahydrofolate, and that a significant hurdle in the utilisation of exogenous folic acid is the initial reduction of fully oxidised folic acid to dihydrofolate, an activity that the single mutant enzyme found in HB3 is postulated to perform particularly poorly. This would mirror earlier studies indicating that the DHFR activity of HB3 is also compromised relative to other variants. Science and Technology, P.O. Box 88, Manchester M60 1QD, UK. development/*metabolism","4-Aminobenzoic Acid/metabolism!5' Untranslated Regions!Amino Acid Substitution!Animals!Antimalarials/pharmacology!Chromosome Mapping!DNA, Protozoan/chemistry/genetics!Folic Acid/*analogs & derivatives/*metabolism!Genes, Protozoan!Leucovorin/metabolism!Multienzyme Complexes/*antagonists & inhibitors/*genetics/metabolism!Phenotype!Plasmodium falciparum/drug effects/*genetics/growth &!Polymorphism, Genetic!Protozoan Proteins/genetics/physiology!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA!Sulfadoxine/*pharmacology!Tetrahydrofolate Dehydrogenase/*genetics/metabolism!Tetrahydrofolates/metabolism!Thymidylate Synthase/*antagonists & inhibitors/*genetics/metabolism!",scirus,2004,Molecular and Biochemical Parasitology,135,1,77
15287595,Plasmodium falciparum genes differentially expressed during merozoite morphogenesis.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104000210&_version=1&_returnURL=&md5=342c04d898e91c43d13f968cbc8df1cf,,"Animals!DNA, Protozoan/chemistry/isolation & purification!Gene Expression Profiling!*Gene Expression Regulation!*Genes, Protozoan!Molecular Sequence Data!Morphogenesis!Nucleic Acid Hybridization!Plasmodium falciparum/*genetics/*growth & development!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA!Sequence Homology!",scirus,2004,Molecular and Biochemical Parasitology,135,1,143
9920046,Plasmodium berghei: identification of an mdr-like gene associated with drug resistance.,,"Amplification, mutations, or overexpression of the pfmdr1 gene have been associated with multiple drug resistance in some strains of Plasmodium falciparum. In order to better understand this potential mechanism of drug resistance, we are currently investigating putative mdr homologues in vivo in the rodent malaria Plasmodium berghei. We have identified and partially sequenced a gene that is amplified in a MFQ-resistant (MFQr) line. Using degenerate primers, a 579-bp fragment was amplified by PCR using P. berghei genomic DNA as template. The predicted amino acid sequence shares 66% identity with the previously reported pfmdr1 gene product (Pgh1) of P. falciparum. Southern blots and slot blots of genomic DNA suggest that this gene is amplified two- to threefold in a MFQr line (N/1100), as has been previously reported in some MFQr strains of P. falciparum. The P. berghei gene was mapped to chromosome 12 in all of the lines analyzed. Furthermore, the cloned PCR product also hybridizes to chromosome 5 of the MFQr strain.","Gene Amplification,Antimalarials,Amino Acid Sequence,Genes, Protozoan,Sequence Alignment,Gene Dosage,Plasmodium berghei,Mefloquine,Cloning, Molecular,Chromosome Mapping,Molecular Sequence Data,Drug Resistance, Multiple,Polymerase Chain Reaction,Animals,ATP-Binding Cassette Transporters,Protozoan Proteins",NCBI,1999,Experimental parasitology,91,1,86-92
15296759,High coding density on the largest Paramecium tetraurelia somatic chromosome.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0960982204005330&_version=1&_returnURL=&md5=c3cfea8e2a289b8e89f1ab7a83317763,"Paramecium, like other ciliates, remodels its entire germline genome at each sexual generation to produce a somatic genome stripped of transposons and other multicopy elements. The germline chromosomes are fragmented by a DNA elimination process that targets heterochromatin to give a reproducible set of some 200 linear molecules 50 kb to 1 Mb in size. These chromosomes are maintained at a ploidy of 800n in the somatic macronucleus and assure all gene expression. We isolated and sequenced the largest megabase somatic chromosome in order to explore its organization and gene content. The AT-rich (72%) chromosome is compact, with very small introns (average size 25 nt), short intergenic regions (median size 202 nt), and a coding density of at least 74%, higher than that reported for budding yeast (70%) or any other free-living eukaryote. Similarity to known proteins could be detected for 57% of the 460 potential protein coding genes. Thirty-two of the proteins are shared with vertebrates but absent from yeast, consistent with the morphogenetic complexity of Paramecium, a long-standing model for differentiated functions shared with metazoans but often absent from simpler eukaryotes. Extrapolation to the whole genome suggests that Paramecium has at least 30,000 genes. Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.","Animals!Base Composition!Base Sequence!Chromosome Mapping!Chromosomes/*genetics!Comparative Study!Gene Components!Gene Library!Genes, Protozoan/*genetics!*Genome, Protozoan!Molecular Sequence Data!Open Reading Frames/genetics!Paramecium tetraurelia/*genetics!Repetitive Sequences, Nucleic Acid/genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA!Sequence Homology!",scirus,2004,Current Biology,14,15,1397
15304495,A Plasmodium falciparum dipeptidyl aminopeptidase I participates in vacuolar hemoglobin degradation.,http://www.jbc.org/cgi/content/abstract/279/41/43000,"Intraerythrocytic growth of the human malaria parasite Plasmodium falciparum requires the catabolism of large amounts of host cell hemoglobin. Endoproteolytic digestion of hemoglobin to short oligopeptides occurs in an acidic organelle called the food vacuole. How amino acids are generated from these peptides is not well understood. To gain insight into this process, we have studied a plasmodial ortholog of the lysosomal exopeptidase cathepsin C. The plasmodial enzyme dipeptidyl aminopeptidase 1 (DPAP1) was enriched from parasite extract by two different approaches and was shown to possess hydrolytic activity against fluorogenic dipeptide substrates. To localize DPAP1 we created a transgenic parasite line expressing a chromosomally encoded DPAP1-green fluorescent protein fusion. Green fluorescent protein fluorescence was observed in the food vacuole of live transgenic parasites, and anti-DPAP1 antibody labeled the food vacuole in parasite cryosections. Together these data implicate DPAP1 in the generation of dipeptides from hemoglobin-derived oligopeptides. To assess the significance of DPAP1, we attempted to ablate DPAP1 activity from blood stage parasites by truncating the chromosomal DPAP1-coding sequence. The inability to disrupt the coding sequence indicates that DPAP1 is important for asexual proliferation. The proenzyme form of DPAP1 was found to accumulate in the parasitophorous vacuole of mature parasites. This observation suggests a trafficking route for DPAP1 through the parasitophorous vacuole to the food vacuole. University School of Medicine, St. Louis, Missouri 63110, USA.","Amino Acid Sequence!Animals!Blotting, Southern!Cell Division!Chromosomes/metabolism!Cloning, Molecular!Dipeptidyl Peptidase I/chemistry/metabolism/*physiology!Erythrocytes/metabolism!Hemoglobins/*metabolism!Humans!Hydrolysis!Immunoblotting!Immunoprecipitation!Microscopy, Fluorescence!Microscopy, Immunoelectron!Models, Biological!Models, Genetic!Molecular Sequence Data!Peptides/chemistry!Plasmodium falciparum/*metabolism!Proteins/chemistry!Recombinant Fusion Proteins/chemistry!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Homology, Amino Acid!Subcellular Fractions!Time Factors!Vacuoles/*metabolism!",scholar,,Journal of Biological Chemistry,,,
15315475,'FAS't inhibition of malaria.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1133732,"Malaria, a tropical disease caused by Plasmodium sp., has been haunting mankind for ages. Unsuccessful attempts to develop a vaccine, the emergence of resistance against the existing drugs and the increasing mortality rate all call for immediate strategies to treat it. Intense attempts are underway to develop potent analogues of the current antimalarials, as well as a search for novel drug targets in the parasite. The indispensability of apicoplast (plastid) to the survival of the parasite has attracted a lot of attention in the recent past. The present review describes the origin and the essentiality of this relict organelle to the parasite. We also show that among the apicoplast specific pathways, the fatty acid biosynthesis system is an attractive target, because its inhibition decimates the parasite swiftly unlike the 'delayed death' phenotype exhibited by the inhibition of the other apicoplast processes. As the enzymes of the fatty acid biosynthesis system are present as discrete entities, unlike those of the host, they are amenable to inhibition without impairing the operation of the host-specific pathway. The present review describes the role of these enzymes, the status of their molecular characterization and the current advancements in the area of developing inhibitors against each of the enzymes of the pathway. India. surolia@mbu.iisc.ernet.in or surolia@jncasr.ac.in","Animals!Enzyme Inhibitors/pharmacology!Fatty Acid Synthetase Complex/antagonists & inhibitors/*metabolism!Fatty Acids/antagonists & inhibitors/biosynthesis!Humans!Malaria/*enzymology!Plasmodium/drug effects/enzymology/pathogenicity!Research Support, Non-U.S. Gov't!",scholar,2004,Biochem. J,383,,401
15317584,An alpha-proteobacterial type malate dehydrogenase may complement LDH function in Plasmodium falciparum. Cloning and biochemical characterization of the enzyme.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1432-1033.2004.04281.x/pdf,"Malate dehydrogenase (MDH) may be important in carbohydrate and energy metabolism in malarial parasites. The cDNA corresponding to the MDH gene, identified on chromosome 6 of the Plasmodium falciparum genome, was amplified by RT-PCR, cloned and overexpressed in Escherichia coli. The recombinant Pf MDH was purified to homogeneity and biochemically characterized as an NAD(+)(H)-specific MDH, which catalysed reversible interconversion of malate to oxaloacetate. Pf MDH could not use NADP/NADPH as a cofactor, but used acetylpyridine adenine dinucleoide, an analogue of NAD. The enzyme exhibited strict substrate and cofactor specificity. The highest levels of Pf MDH transcripts were detected in trophozoites while the Pf MDH protein level remained high in trophozoites as well as schizonts. A highly refined model of Pf MDH revealed distinct structural characteristics of substrate and cofactor binding sites and important amino acid residues lining these pockets. The active site amino acid residues involved in substrate binding were conserved in Pf MDH but the N-terminal glycine motif, which is involved in nucleotide binding, was similar to the GXGXXG signature sequence found in Pf LDH and also in alpha-proteobacterial MDHs. Oxamic acid did not inhibit Pf MDH, while gossypol, which interacts at the nucleotide binding site of oxidoreductases and shows antimalarial activity, inhibited Pf MDH also. Treatment of a synchronized culture of P. falciparum trophozoites with gossypol caused induction in expression of Pf MDH, while expression of Pf LDH was reduced and expression of malate:quinone oxidoreductase remained unchanged. Pf MDH may complement Pf LDH function of NAD/NADH coupling in malaria parasites. Thus, dual inhibitors of Pf MDH and Pf LDH may be required to target this pathway and to develop potential new antimalarial drugs. Pharmacological Sciences, University of Mississippi, MS 38677, USA.","Amino Acid Sequence!Animals!Cloning, Molecular!Enzyme Inhibitors/metabolism!Gossypol/metabolism!Humans!L-Lactate Dehydrogenase/chemistry/classification/genetics/*metabolism!Malate Dehydrogenase/chemistry/classification/genetics/*metabolism!Models, Molecular!Molecular Sequence Data!Molecular Structure!Oxamic Acid/metabolism!Oxidation-Reduction!Oxidoreductases/chemistry/genetics/metabolism!Phylogeny!Plasmodium falciparum/*enzymology!Protozoan Proteins/genetics/*metabolism!Recombinant Proteins/genetics/metabolism!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!",scholar,2004,Eur. J. Biochem,271,,3488
15356386,Diversification of genes encoding mei2 -like RNA binding proteins in plants.,http://www.springerlink.com/index/P75W2751761X47G6.pdf,"A predominantly plant-based family of genes encoding RNA binding proteins is defined by the presence of a highly conserved RNA binding motif first described in the mei2 gene of the fission yeast Schizosaccharomyces pombe. In silico analyses reveal nine mei2 -like genes in Arabidopsis thaliana and six in Oryza sativa. These predicted genes group into four distinct clades, based on overall sequence similarity and subfamily-specific sequence elements. In situ analysis show that Arabidopsis genes from one of these clades, TEL1 and TEL2, are specifically expressed in central zone of the shoot apical meristem and the quiescent center of the root apical meristem, suggesting that they may somehow function to maintain indeterminacy in these tissues. By contrast, members of two sister clades, AML1 through AML5, are expressed more broadly, a trend that was confirmed by Q-PCR analysis. mei2 -like transcripts with similar sequences showed similar expression patterns, suggesting functional redundancy within the four clades. Phenotypic analyses of lines that contain T-DNA insertions to individual mei2 -like genes reveal no obvious phenotypes, further suggesting redundant activities for these gene products. NY, 14853, USA.","Alternative Splicing!Amino Acid Motifs/genetics!Amino Acid Sequence!Arabidopsis/embryology/genetics/growth & development!Comparative Study!Conserved Sequence/genetics!DNA, Complementary/chemistry/genetics!DNA, Plant/chemistry/genetics!Gene Duplication!Gene Expression Regulation, Developmental!Gene Expression Regulation, Plant!Genes, Plant/genetics!In Situ Hybridization!Molecular Sequence Data!Oryza sativa/genetics!Phylogeny!Plant Proteins/*genetics!Plants/*genetics!RNA-Binding Proteins/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Sequence Alignment!Sequence Analysis, DNA!Sequence Deletion!Sequence Homology, Amino Acid!Variation (Genetics)!",scholar,2004,Plant Molecular Biology,54,5,653
15358235,Plasmodium falciparum expresses a multidrug resistance-associated protein.,http://www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26list_uids%3D15358235%26dopt%3DCitation,"Plasmodium falciparum proteins that efflux toxic metabolic products such as oxidised glutathione (GSSG) are possible targets for anti-malarial drug development. Proteins capable of transporting GSSG and glutathione conjugates include the multidrug resistance-associated transporters (MRPs). A gene, PFA0590w, encoding a MRP homologue, has been identified in P. falciparum. Here we show the presence of full-length mRNA (5.5 kb) of this PfMRP in trophozoites by RT-PCR and Northern blotting. A polyclonal anti-PfMRP antibody generated against two unique, hydrophilic peptides in the predicted sequence produced a strong immunoreactive protein band of 210-215 kDa on Western blots of schizonts of chloroquine-sensitive and chloroquine-resistant strains, confirming expression of PfMRP protein. Using confocal microscopy the protein was seen to be localised at the edge of the schizonts with no obvious staining of the food vacuole. We suggest that PfMRP may act as the GSSG transporter in the parasite plasma membrane. UK.","Amino Acid Sequence!Animals!Base Sequence!DNA Primers!Drug Resistance, Multiple/*genetics!Glutathione Disulfide!Molecular Sequence Data!Plasmodium falciparum/*genetics!Protozoan Proteins/genetics!RNA, Messenger/genetics!",scholar,2004,Biochem Biophys Res Commun,321,1,197
15358256,Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1369527404000803&_version=1&_returnURL=&md5=b1c503ddbe5e17dd2aa8dbb574605345,"The asexual intraerythrocytic developmental cycle (IDC) of Plasmodium falciparum is responsible for the majority of the clinical manifestations of malaria in humans. Although malaria has been studied for over a century, the elucidation of the full genome sequence of P. falciparum has now allowed for in-depth studies of gene expression throughout the entire intraerythrocytic stage. As the mainstays of anti-malarial chemotherapy become increasingly ineffective, we need a deeper understanding of fundamental plasmodial bioregulatory mechanisms to successfully subvert them. Recent gene expression studies have begun to examine different aspects of the IDC and are providing key insights into the basic mechanisms of Plasmodium gene regulation and are helping to define gene functions. However, to date, no transcription factor has been fully characterized from Plasmodium and the definitive identification of cis-acting regulatory elements along with their corresponding trans-acting partners is still lacking. The characterization of the transcriptome of P. falciparum is the first major step towards the understanding of the genome wide regulation of gene expression in this parasite. IDC expression data for almost every gene in the P. falciparum genome can now be publicly queried at and. The results of these studies suggest promising leads for identifying novel targets for anti-malarial therapeutics and vaccines in addition to providing a solid foundation for the ongoing elucidation of plasmodial gene expression. Street, BOX 2240, San Francisco, California 94143-2240, USA. manuel@derisilab.ucsf.edu","Animals!Erythrocytes/*parasitology!Gene Expression Profiling/methods!*Gene Expression Regulation!*Genome, Protozoan!Humans!Malaria, Falciparum/parasitology!Plasmodium falciparum/*growth & development!*Proteome!Protozoan Proteins/genetics/*metabolism!",scirus,2004,Current Opinion in Microbiology,7,4,382
15385514,Correct promoter control is needed for trafficking of the ring-infected erythrocyte surface antigen to the host cytosol in transfected malaria parasites.,http://iai.asm.org/cgi/content/abstract/72/10/6095,"Following invasion of human erythrocytes, the malaria parasite, Plasmodium falciparum, exports proteins beyond the confines of its own plasma membrane to modify the properties of the host red cell membrane. These modifications are critical to the pathogenesis of malaria. Analysis of the P. falciparum genome sequence has identified a large number of molecules with putative atypical signal sequences. The signals remain poorly characterized; however, a number of molecules with these motifs localize to the host erythrocyte. To examine the role of these atypical signal sequences in the export of parasite proteins, we have generated transfected parasites expressing a chimeric protein comprising the N-terminal region of the P. falciparum ring-infected erythrocyte surface antigen (RESA) appended to green fluorescent protein (GFP). This N-terminal region contains a hydrophobic stretch of amino acids that is presumed to act as a noncanonical secretory signal sequence. Modulation of the timing of transgene expression demonstrates that trafficking of malaria proteins into the host erythrocyte is dependent on both the presence of an appropriate transport signal and the timing of expression. Transgene expression under the control of a trophozoite-specific promoter mistargets the chimeric molecule to the parasitophorous vacuole surrounding the parasite. However, expression of RESA-GFP in schizont stages, under the control of the RESA promoter, enables correct trafficking of a population of the chimeric protein to the host erythrocyte. Australia. falciparum)","Amino Acid Sequence!Animals!Cytosol/*metabolism!Erythrocytes/*parasitology/pathology!Fluorescent Antibody Technique!Green Fluorescent Proteins!Humans!Luminescent Proteins/analysis/genetics/metabolism!Malaria, Falciparum/parasitology!Molecular Sequence Data!Plasmodium falciparum/*genetics/*metabolism!Promoter Regions (Genetics)/*genetics!Protein Transport!Protozoan Proteins/chemistry/*genetics/*metabolism/ultrastructure!Recombinant Fusion Proteins/chemistry/genetics/metabolism/ultrastructure!Research Support, Non-U.S. Gov't!Subcellular Fractions/metabolism!Time Factors!Transfection!",scholar,,Infection and Immunity,,,
15451420,Isolation of a dinoflagellate mitotic cyclin by functional complementation in yeast.,http://www.bio.umontreal.ca/profs/Morse/images/Bertomeu.BBRC.04.pdf,"Dinoflagellates are protists with permanently condensed chromosomes that lack histones and whose nuclear membrane remains intact during mitosis. These unusual nuclear characters have suggested that the typical cell cycle regulators might be slightly different than those in more typical eukaryotes. To test this, a cyclin has been isolated from the dinoflagellate Gonyaulax polyedra by functional complementation in cln123 mutant yeast. This GpCyc1 sequence contains two cyclin domains in its C-terminal region and a degradation box typical of mitotic cyclins. Similar to other dinoflagellate genes, GpCyc1 has a high copy number, with approximately 5000 copies found in the Gonyaulax genome. An antibody raised against the N-terminal region of the GpCYC1 reacts with a 68kDa protein on Western blots that is more abundant in cell cultures enriched for G2-phase cells than in those containing primarily G1-phase cells, indicating its cellular level follows a pattern expected for a mitotic cyclin. This is the first report of a cell cycle regulator cloned and sequenced from a dinoflagellate, and our results suggest control of the dinoflagellate cell cycle will be very similar to that of other organisms. Vegetale, Universite de Montreal, 4101 Sherbrooke est, Montreal, Quebec, Canada H1X 2B2. purification/*metabolism purification/metabolism","Amino Acid Sequence!Animals!Cell Cycle Proteins/*chemistry/genetics/isolation &!Cells, Cultured!Cloning, Molecular/methods!Comparative Study!Cyclins/*chemistry/genetics/isolation & purification/*metabolism!Dinoflagellida/genetics/*metabolism!Mitosis/*physiology!Molecular Sequence Data!Recombinant Proteins/chemistry/genetics/isolation &!Research Support, Non-U.S. Gov't!Saccharomyces cerevisiae/genetics/metabolism!*Sequence Analysis, Protein!Sequence Homology, Amino Acid!",scholar,2004,Biochemical and Biophysical Research Communications,323,,1172
15452112,The methylerythritol phosphate pathway is functionally active in all intraerythrocytic stages of Plasmodium falciparum.,http://www.jbc.org/cgi/content/abstract/279/50/51749,"Two genes encoding the enzymes 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase have been recently identified, suggesting that isoprenoid biosynthesis in Plasmodium falciparum depends on the methylerythritol phosphate (MEP) pathway, and that fosmidomycin could inhibit the activity of 1-deoxy-D-xylulose-5-phosphate reductoisomerase. The metabolite 1-deoxy-D-xylulose-5-phosphate is not only an intermediate of the MEP pathway for the biosynthesis of isopentenyl diphosphate but is also involved in the biosynthesis of thiamin (vitamin B1) and pyridoxal (vitamin B6) in plants and many microorganisms. Herein we report the first isolation and characterization of most downstream intermediates of the MEP pathway in the three intraerythrocytic stages of P. falciparum. These include, 1-deoxy-D-xylulose-5-phosphate, 2-C-methyl-D-erythritol-4-phosphate, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol-2-phosphate, and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. These intermediates were purified by HPLC and structurally characterized via biochemical and electrospray mass spectrometric analyses. We have also investigated the effect of fosmidomycin on the biosynthesis of each intermediate of this pathway and isoprenoid biosynthesis (dolichols and ubiquinones). For the first time, therefore, it is demonstrated that the MEP pathway is functionally active in all intraerythrocytic forms of P. falciparum, and de novo biosynthesis of pyridoxal in a protozoan is reported. Its absence in the human host makes both pathways very attractive as potential new targets for antimalarial drug development. of Sao Paulo, 05508-900 Sao Paulo, Brazil. development/*metabolism","Animals!Antimalarials/pharmacology!Dolichol/biosynthesis!Erythritol/*analogs & derivatives/*metabolism!Erythrocytes/parasitology!Fosfomycin/*analogs & derivatives/pharmacology!Genes, Protozoan!Humans!Malaria, Falciparum/drug therapy/parasitology!Molecular Structure!Pentosephosphates/biosynthesis!Plasmodium falciparum/drug effects/genetics/growth &!Pyridoxal Phosphate/*analogs & derivatives/biosynthesis!Research Support, Non-U.S. Gov't!Spectrometry, Mass, Electrospray Ionization!Sugar Phosphates/*metabolism!Ubiquinone/biosynthesis!",scholar,2004,Journal of Biological Chemistry,279,50,51749
15474309,"Transcriptome of 3D7 and its gametocyte-less derivative F12 Plasmodium falciparum clones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0378111904004184&_version=1&_returnURL=&md5=70110a63f09933b36d0c33636e4ef072,"During the complex life cycle of Plasmodium falciparum, through mosquito and human, the erythrocytic cycle is responsible for malarial disease and transmission. The regulation of events that occur during parasite development, such as proliferation and differentiation, implies a fine control of transcriptional activities that in turn governs the expression profiles of sets of genes. Pathways that underline gametocyte commitment are yet poorly understood even though kinases and transcription factors have been assumed to play a crucial role in this event. In order to understand the molecular mechanisms controlling the variation of gene expression profiles that might participate in early gametocytogenesis, the transcriptome of two clones, 3D7 and its gametocyte-less derivative F12, was compared at five time points of the erythrocytic asexual development. We have used a thematic DNA microarray containing 150 PCR fragments, representative of P. falciparum genes involved in signal transduction, cell cycle and transcriptional regulation. We identified several genes eliciting different expression profiles among which some implicated in gene regulation or encoding putative transcription factors. The differential expression of transcription factor and kinase transcripts observed in the two clones may enlighten genes that might have a role in impairment of the early gametocytogenesis of the F12 clone. l'Hopital, 75013 Paris, France.","Animals!Cell Cycle Proteins/genetics!Comparative Study!Erythrocytes/*parasitology!*Gene Expression Profiling!Gene Expression Regulation, Developmental!Genes, Protozoan/*genetics!Humans!Oligonucleotide Array Sequence Analysis/*methods!Plasmodium falciparum/*genetics/growth & development!Reproducibility of Results!Research Support, Non-U.S. Gov't!Transcription Factors/genetics!Transcription, Genetic/*genetics!",scirus,2004,Gene,341,.,267
15476558,"Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data.",http://www.biomedcentral.com/content/pdf/1471-2105-5-178.pdf,"BACKGROUND: A key step in the analysis of microarray expression profiling data is the identification of genes that display statistically significant changes in expression signals between two biological conditions. RESULTS: We describe a new method, Rank Difference Analysis of Microarrays (RDAM), which estimates the total number of truly varying genes and assigns a p-value to each signal variation. Information on a group of differentially expressed genes includes the sensitivity and the false discovery rate. We demonstrate the feasibility and efficiency of our approach by applying it to a large synthetic expression data set and to a biological data set obtained by comparing vegetatively-growing wild type and tor2-mutant yeast strains. In both cases we observed a significant improvement of the power of analysis when our method is compared to another popular nonparametric method. CONCLUSIONS: This study provided a valuable new statistical method to analyze microarray data. We conclude that the good quality of the results obtained by RDAM is mainly due to the quasi-perfect equalization of variation distribution, which is related to the standardization procedure used and to the measurement of variation by rank difference. dietmar.martin@unibas.ch <dietmar.martin@unibas.ch> numerical data/*trends","Comparative Study!Gene Expression Profiling/standards/*statistics & numerical data/*trends!Oligonucleotide Array Sequence Analysis/*methods/standards/statistics &!Research Support, Non-U.S. Gov't!",scholar,2004,BMC Bioinformatics,5,,148
15477199,Myosin-like sequences in the malaria parasite Plasmodium falciparum bind human erythrocyte membrane protein 4.1.,http://www.haematologica.org/journal/2004/891168.pdf,"BACKGROUND AND OBJECTIVES: Plasmodium falciparum malaria is one of the most lethal infectious diseases afflicting humanity. During development within the erythrocyte, P. falciparum induces significant modifications to the structure and function of the human erythrocyte membrane. This study focused on the identification of new protein-protein interactions between host and parasite. DESIGN AND METHODS: A novel application of in vitro display technology was used: P. falciparum phage display expression libraries were screened against purified human erythrocyte protein 4.1. DNA sequencing and bioinformatic analyses were used to identify parasite proteins that bind protein 4.1. RESULTS: P. falciparum proteins displaying strong binding specificity toward protein 4.1 included five hypothetical proteins, erythrocyte binding antigen-175, erythrocyte binding ligand-1 like protein and a putative serine/threonine kinase. A common binding motif displaying homology to muscle myosin and neurofilament sequences was also identified in four of the eight proteins. INTERPRETATION AND CONCLUSIONS: These proteins are potentially involved in the invasion and/or release, as well as the growth and survival of malaria parasites during development with the red blood cell. The characterization of novel protein interactions between P. falciparum and erythrocyte membrane protein 4.1 will lead to a better understanding of malaria pathogenesis and parasite biology. Laboratory Service, School of Pathology, University of the Witwatersrand, Parktown, Johannesburg 2193, South Africa.",,scholar,2004,Haematologica(Roma),89,10,1168
15479470,Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.,http://www.biomedcentral.com/1471-2164/5/79,"BACKGROUND: Malaria, caused by the parasitic protist Plasmodium falciparum, represents a major public health problem in the developing world. The P. falciparum genome has been sequenced, which provides new opportunities for the identification of novel drug targets. Eukaryotic protein kinases (ePKs) form a large family of enzymes with crucial roles in most cellular processes; hence malarial ePKS represent potential drug targets. We report an exhaustive analysis of the P. falciparum genomic database (PlasmoDB) aimed at identifying and classifying all ePKs in this organism. RESULTS: Using a variety of bioinformatics tools, we identified 65 malarial ePK sequences and constructed a phylogenetic tree to position these sequences relative to the seven established ePK groups. Predominant features of the tree were: (i) that several malarial sequences did not cluster within any of the known ePK groups; (ii) that the CMGC group, whose members are usually involved in the control of cell proliferation, had the highest number of malarial ePKs; and (iii) that no malarial ePK clustered with the tyrosine kinase (TyrK) or STE groups, pointing to the absence of three-component MAPK modules in the parasite. A novel family of 20 ePK-related sequences was identified and called FIKK, on the basis of a conserved amino acid motif. The FIKK family seems restricted to Apicomplexa, with 20 members in P. falciparum and just one member in some other Apicomplexan species. CONCLUSION: The considerable phylogenetic distance between Apicomplexa and other Eukaryotes is reflected by profound divergences between the kinome of malaria parasites and that of yeast or mammalian cells. Dumbarton Road, Glasgow G11 6NU, Scotland, UK. info@paulineward.me.uk","Animals!Eukaryotic Cells/enzymology!Humans!Malaria, Falciparum/enzymology!Phylogeny!Plasmodium falciparum/*enzymology!Protein Kinases/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Variation (Genetics)/*genetics!",scholar,2004,BMC Genomics,5,1,79
15481109,"A novel Plasmodium falciparum ring stage protein, REX, is located in Maurer's clefts.",http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104001070&_version=1&_returnURL=&md5=7e1de1b2df9088982e8c7daf287aa419,"The asexual stages of the malaria parasite Plasmodium falciparum develop inside erythrocytes of the human host. Erythrocytes are highly specialized cells lacking organelles and trafficking machinery. The parasite must therefore establish its own transport system to export proteins and waste and import nutrients. A number of parasite-derived structures, implicated in trafficking, appear in the infected red blood cell at the late ring stage. We have identified a novel gene transcribed in ring stage parasites coding for a protein designated the ring exported protein, REX. REX is located in a red cell modification known as the Maurer's clefts, which are parasite induced structures implicated in trafficking of parasite proteins to the red blood cell surface. REX contains predicted coiled-coil regions and a region with similarity to a domain in vesicle-tethering proteins. REX persists in Maurer's clefts throughout the infection of the erythrocyte, where it may play a role in the biogenesis and/or function of this organelle.","Animals!Antibodies, Protozoan!Base Sequence!DNA, Protozoan/genetics!Erythrocytes/parasitology!Gene Expression Regulation, Developmental!Genes, Protozoan!Humans!Malaria, Falciparum/parasitology!Organelles/parasitology!Plasmodium falciparum/genetics/growth & development/immunology/*metabolism!Protozoan Proteins/genetics/immunology/*metabolism!RNA, Messenger/genetics/metabolism!RNA, Protozoan/genetics/metabolism!Research Support, Non-U.S. Gov't!",scirus,2004,Molecular and Biochemical Parasitology,136,2,181
15489329,High-throughput generation of P. falciparum functional molecules by recombinational cloning.,http://intl.genome.org/cgi/content/full/14/10b/2076,"Large-scale functional genomics studies for malaria vaccine and drug development will depend on the generation of molecular tools to study protein expression. We examined the feasibility of a high-throughput cloning approach using the Gateway system to create a large set of expression clones encoding Plasmodium falciparum single-exon genes. Master clones and their ORFs were transferred en masse to multiple expression vectors. Target genes (n = 303) were selected using specific sets of criteria, including stage expression and secondary structure. Upon screening four colonies per capture reaction, we achieved 84% cloning efficiency. The genes were subcloned in parallel into three expression vectors: a DNA vaccine vector and two protein expression vectors. These transfers yielded a 100% success rate without any observed recombination based on single colony screening. The functional expression of 95 genes was evaluated in mice with DNA vaccine constructs to generate antibody against various stages of the parasite. From these, 19 induced antibody titers against the erythrocytic stages and three against sporozoite stages. We have overcome the potential limitation of producing large P. falciparum clone sets in multiple expression vectors. This approach represents a powerful technique for the production of molecular reagents for genome-wide functional analysis of the P. falciparum genome and will provide for a resource for the malaria resource community distributed through public repositories. 20910, USA. aguiarj@nmrc.navy.mil","Animals!Antibodies, Protozoan/blood!Antigens, Protozoan/*genetics!Cloning, Molecular/*methods!DNA, Protozoan/genetics!Genome, Protozoan!Liver/parasitology!Malaria/immunology/parasitology/prevention & control!Malaria Vaccines/administration & dosage/*genetics/pharmacology!Mice!Plasmids/genetics!Plasmodium falciparum/*genetics/growth & development/*immunology!Polymerase Chain Reaction!Recombinant Proteins/genetics/isolation & purification/metabolism!*Recombination, Genetic!Research Support, U.S. Gov't, Non-P.H.S.!Vaccines, DNA/administration & dosage/genetics/pharmacology!",scholar,2004,Genome Research,14,10 b,2076
15491999,Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy.,http://www.jbc.org/cgi/content/abstract/279/52/54088,"The digestive vacuole plasmepsins PfPM1, PfPM2, PfPM4, and PfHAP (a histoaspartic proteinase) are 4 aspartic proteinases among 10 encoded in the Plasmodium falciparum malarial genome. These have been hypothesized to initiate and contribute significantly to hemoglobin degradation, a catabolic function essential to the survival of this intraerythrocytic parasite. Because of their perceived significance, these plasmepsins have been proposed as potential targets for antimalarial drug development. To test their essentiality, knockout constructs were prepared for each corresponding gene such that homologous recombination would result in two partial, nonfunctional gene copies. Disruption of each gene was achieved, as confirmed by PCR, Southern, and Northern blot analyses. Western and two-dimensional gel analyses revealed the absence of mature or even truncated plasmepsins corresponding to the disrupted gene. Reduced growth rates were observed with PfPM1 and PfPM4 knockouts, indicating that although these plasmepsins are not essential, they are important for parasite development. Abnormal mitochondrial morphology also appeared to accompany loss of PfPM2, and an abundant accumulation of electron-dense vesicles in the digestive vacuole was observed upon disruption of PfPM4; however, those phenotypes only manifested in about a third of the disrupted cells. The ability to compensate for loss of individual plasmepsin function may be explained by close similarity in the structure and active site of these four vacuolar enzymes. Our data imply that drug discovery efforts focused on vacuolar plasmepsins must incorporate measures to develop compounds that can inhibit two or more of this enzyme family. 32611-0880, USA.","Animals!Aspartic Endopeptidases/*genetics/*physiology!Blotting, Northern!Blotting, Southern!Blotting, Western!Cloning, Molecular!Electrophoresis, Gel, Two-Dimensional!Enzyme Inhibitors!Erythrocytes/parasitology!Genetic Engineering!Hemoglobins/metabolism!Microscopy, Electron!Plasmodium falciparum/enzymology/*genetics/growth & development!Research Support, U.S. Gov't, P.H.S.!Transfection!Vacuoles/enzymology!",scholar,2004,Journal of Biological Chemistry,279,52,54088
15515182,A genomic perspective of protein kinases in Plasmodium falciparum.,http://doi.wiley.com/10.1002/prot.20278,"Protein kinases are central to regulation of cellular signaling in the eukaryotes. Well-conserved and lineage-specific protein kinases have previously been identified from various completely sequenced genomes of eukaryotes. The current work describes a genome-wide analysis for protein kinases encoded in the Plasmodium falciparum genome. Using a few different profile matching methods, we have identified 99 protein kinases or related proteins in the parasite genome. We have classified these kinases into subfamilies and analyzed them in the context of noncatalytic domains that occur in these catalytic kinase domain-containing proteins. Compared to most eukaryotic protein kinases, these sequences vary significantly in terms of their lengths, inserts in catalytic domains, and co-occurring domains. Catalytic and noncatalytic domains contain long stretches of repeats of positively charged and other polar amino acids. Various components of the cell cycle, including 4 cyclin-dependent kinase (CDK) homologues, 2 cyclins, 1 CDK regulatory subunit, and 1 kinase-associated phosphatase, are identified. Identification of putative mitogen-activated protein (MAP) Kinase and MAP Kinase Kinase of P. falciparum suggests a new paradigm in the highly conserved signaling pathway of eukaryotes. The calcium-dependent kinase family, well represented in P. falciparum, shows varying domain combinations with EF-hands and pleckstrin homology domains. The analysis reveals a new subfamily of protein kinases having limited sequence similarity with previously known subfamilies. A new transmembrane kinase with 6 membrane-spanning regions is identified. Putative apicoplast targeting sequences have been detected in some of these protein kinases, suggesting their export to the apicoplast.","Animals!Genes, Protozoan/genetics!*Genome, Protozoan!Genomics/*methods!Plasmodium falciparum/*enzymology/*genetics!Protein Kinases/*genetics!Protozoan Proteins/genetics!Research Support, Non-U.S. Gov't!",scholar,2005,"PROTEINS: Structure, Function, and Bioinformatics""""",58,,180
15520249,Evidence for the involvement of VAR2CSA in pregnancy-associated malaria.,http://www.jem.org/cgi/content/abstract/200/9/1197,"In Plasmodium falciparum-endemic areas, pregnancy-associated malaria (PAM) is an important health problem. The condition is precipitated by accumulation of parasite-infected erythrocytes (IEs) in the placenta, and this process is mediated by parasite-encoded variant surface antigens (VSA) binding to chondroitin sulfate A (CSA). Parasites causing PAM express unique VSA types, VSAPAM, which can be serologically classified as sex specific and parity dependent. It is sex specific because men from malaria-endemic areas do not develop VSAPAM antibodies; it is parity dependent because women acquire anti-VSAPAM immunoglobulin (Ig) G as a function of parity. Previously, it was shown that transcription of var2csa is up-regulated in placental parasites and parasites selected for CSA binding. Here, we show the following: (a) that VAR2CSA is expressed on the surface of CSA-selected IEs; (b) that VAR2CSA is recognized by endemic plasma in a sex-specific and parity-dependent manner; (c) that high anti-VAR2CSA IgG levels can be found in pregnant women from both West and East Africa; and (d) that women with high plasma levels of anti-VAR2CSA IgG give birth to markedly heavier babies and have a much lower risk of delivering low birth weight children than women with low levels. Immunology, Panum Institute 24-2, Blegdamsvej 3, 2200 Copenhagen, Denmark. salanti@cmp.dk.","Africa!Birth Weight/*immunology!Chondroitin Sulfates/*metabolism!Comparative Study!DNA Primers!Enzyme-Linked Immunosorbent Assay!Erythrocytes/metabolism/*parasitology!Female!Humans!Immunoglobulin G/blood/immunology!Malaria, Falciparum/*immunology/metabolism!Male!Microscopy, Confocal!Placenta/*parasitology!Pregnancy!Protozoan Proteins/*metabolism!Recombinant Proteins/metabolism!Research Support, Non-U.S. Gov't!Sex Factors!",scholar,,Journal of Experimental Medicine,200,9,1197
9747969,A Plasmodium chabaudi protein contains a repetitive region with a predicted spectrin-like structure.,,"cDNA and genomic DNA clones covering the entire open reading frame (ORF) for a Plasmodium chabaudi 96V protein were isolated. From the first ATG codon the intronless gene codes for a 229-kDa protein. Antisera raised against recombinant polypeptides coded by two different regions of the gene reacted with a 240/225-kDa doublet on Western blots of parasite extracts. In immunofluorescence studies the same sera detected the antigen at the apical end of the merozoite, possibly in rhoptry organelles. In Western blotting experiments the recombinant polypeptides were recognised by antibodies induced by natural infection. A 364-amino acid residue repetitive region, based on 32 11-mer repeats divided by two 6-mer repeats into three blocks, is located in the centre of the protein. Analysis of this repetitive region led us to propose a model in which each of the three units forms an alpha-helical coiled-coil triple-helix containing a possible leucine-histidine zipper. Each unit resembles in structure the units present in spectrin. The repeat region is flanked by predicted heptad based alpha-helical coiled-coil regions, and we propose that the protein forms a dimer. The 229-kDa protein has the overall character of a cytoskeletal protein. We have named the 229-kDa protein repetitive organellar protein (ROPE) and suggest that ROPE may be involved in the process of invasion, possibly by interacting with the erythrocyte cytoskeleton, and that the leucine histidine-zipper may be involved in molecular mimicry of spectrin.","Spectrin,Mice, Inbred BALB C,Fluorescent Antibody Technique,Erythrocytes,Dimerization,Amino Acid Sequence,Genes, Protozoan,Malaria,Plasmodium chabaudi,Cloning, Molecular,DNA, Protozoan,Leucine Zippers,Molecular Sequence Data,DNA, Complementary,Mice,Rats, Inbred F344,Rats,Repetitive Sequences, Amino Acid,Protein Structure, Secondary,Animals,Protozoan Proteins",NCBI,1998,Molecular and biochemical parasitology,94,2,185-96
15522671,Malaria vaccines: if at first you don't succeed...,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492204002508&_version=1&_returnURL=&md5=847974a8bd3f0b60ddfde84a502fdbc6,"The Roll Back Malaria campaign vowed to halve the global burden of malaria in ten years but, midway into that campaign, few new malaria control tools have been introduced, and many established methods appear to be failing with effective chemotherapy being perhaps the most problematic. It has been repeatedly argued that the discovery and implementation of a safe and effective vaccine against malaria is a major priority in the control of the disease. Indeed, many malaria control experts believe that sustainable reductions in malaria control will be nigh on impossible in the absence of such a vaccine. While most would agree that we are still some way from being able to introduce a vaccine, steady progress is being made. We review here some new approaches and developments in vaccine research that were discussed at the Molecular Approaches to Malaria conference held 1-5 February 2004 in Lorne, Australia. and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.","Animals!Antigens, Protozoan/immunology!Humans!Immunologic Memory!Malaria/*immunology/prevention & control!Malaria Vaccines/*immunology/therapeutic use!Plasmodium/*immunology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scirus,2004,Trends in Parasitology,20,12,604
12169096,"Critical role of amino acid 23 in mediating activity and specificity of vinckepain-2, a papain-family cysteine protease of rodent malaria parasites.",http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1222974,"Cysteine proteases of Plasmodium falciparum, known as falcipains, have been identified as haemoglobinases and potential drug targets. As anti-malarial drug discovery requires the analysis of non-primate malaria, genes encoding related cysteine proteases of the rodent malaria parasites P. vinckei (vinckepain-2) and P. berghei (berghepain-2) were characterized. These genes encoded fairly typical papain-family proteases, but they contained an unusual substitution of Gly23 with Ala (papain numbering system). Vinckepain-2 was expressed in Escherichia coli, solubilized, refolded and autoprocessed to an active enzyme. The protease shared important features with the falcipains, including an acidic pH optimum, preference for reducing conditions, optimal cleavage of peptide substrates with P2 Leu and ready hydrolysis of haemoglobin. However, key differences between the plasmodial proteases were identified. In particular, vinckepain-2 showed very different kinetics against many substrates and an unusual preference for peptide substrates with P1 Gly. Replacement of Ala23 with Gly remarkably altered vinckepain-2, including loss of the P1 Gly substrate preference, markedly increased catalytic activity ( k cat/ K m increased approx. 100-fold) and more rapid autohydrolysis. The present study identifies key animal-model parasite targets. It indicates that drug discovery studies must take into account important differences between plasmodial proteases and sheds light on the critical role of amino acid 23 in catalysis by papain-family proteases.","Plasmodium falciparum,Peptide Library,Rodentia,Amino Acid Sequence,Malaria,Recombinant Proteins,Amino Acid Substitution,Mutation,Substrate Specificity,Rodent Diseases,Molecular Sequence Data,Sequence Homology, Amino Acid,Base Sequence,Helminth Proteins,Cysteine Endopeptidases,Protein Folding,Papain,Animals,Protozoan Proteins",NCBI,2002,The Biochemical journal,368,Pt 1,273-81
15550167,GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.,http://www.biomedcentral.com/1471-2105/5/178,"BACKGROUND: The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation. RESULTS: The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned GO terms against direct transitive assignment from the highest scoring annotated BLAST search hit (TOPBLAST). GOtcha exploits information deep into the 'twilight zone' of similarity search matches, making use of much information that is otherwise discarded by more simplistic approaches.At a P-score cutoff of 50%, GOtcha provided 60% better recovery of annotation terms and 20% higher selectivity than annotation with TOPBLAST at an E-value cutoff of 10(-4). CONCLUSIONS: The GOtcha method is a useful tool for genome annotators. It has identified both errors and omissions in the original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects. University of Dundee, Dow Street, Dundee DD1 5EH, UK. d.m.a.martin@dundee.ac.uk","Animals!Arabidopsis/*genetics!Caenorhabditis elegans/*genetics!Drosophila melanogaster/*genetics!*Genome!Genome, Fungal!Genome, Human!Genome, Plant!Genome, Protozoan!Humans!Plasmodium falciparum/*genetics!Predictive Value of Tests!Proteins/*physiology!Research Support, Non-U.S. Gov't!Saccharomyces cerevisiae/*genetics!*Software!",scholar,2004,BMC Bioinformatics,5,1,178
15562607,Functional characterization of an LCCL-lectin domain containing protein family in Plasmodium berghei.,http://www.bioone.org/bioone/%3Frequest%3Dget-abstract%26issn%3D0022-3395%26volume%3D090%26issue%3D05%26page%3D1062,"Using bioinformatic, proteomic, immunofluorescence, and genetic cross methods, we have functionally characterized a family of putative parasite ligands as potential mediators of cell-cell interactions. We name these proteins the Limulus clotting factor C, Coch-5b2, and Lgl1 (LCCL)-lectin adhesive-like protein (LAP) family. We demonstrate that this family is conserved amongst Plasmodium spp. It possesses a unique arrangement of adhesive protein domains normally associated with extracellular proteins. The proteins are expressed predominantly, though not exclusively, in the mosquito stages of the life cycle. We test the hypothesis that these proteins are surface proteins with 1 member of this gene family, lap1, and provide evidence that it is expressed on the surface of Plasmodium berghei sporozoites. Finally, through genetic crosses of wild-type Pblap1+ and transgenic Pblap1- parasites, we show that the N phenotype previously reported for sporozoite development in a Pblap1- mutant can be rescued within a heterokaryotic oocyst and that infectious Pblap1 sporozoites can be formed. The mutant is not rescued by coparasitization of mosquitoes with a mixture Pblap1+ and Pblap1- homokaryotic oocysts. Imperial College London, South Kensington, London SW7 2AZ, UK.","Amino Acid Sequence!Animals!Anopheles!Blotting, Western!Female!Fluorescent Antibody Technique, Indirect!Gene Expression!Lectins/chemistry/*genetics!Mice!Microscopy, Phase-Contrast!Molecular Sequence Data!*Multigene Family!Plasmodium berghei/chemistry/*genetics!Polymerase Chain Reaction!Protozoan Proteins/chemistry/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!",scholar,,Journal of Parasitology,90,5,1062
15577928,Survival of protozoan intracellular parasites in host cells.,,"The most common human diseases are caused by pathogens. Several of these microorganisms have developed efficient ways in which to exploit host molecules, along with molecular pathways to ensure their survival, differentiation and replication in host cells. Although the contribution of the host cell to the development of many intracellular pathogens (particularly viruses and bacteria) has been unequivocally established, the study of host-cell requirements during the life cycle of protozoan parasites is still in its infancy. In this review, we aim to provide some insight into the manipulation of the host cell by parasites through discussing the hurdles that are faced by the latter during infection. Portugal.","Animals!Cytoplasm/*parasitology!Host-Parasite Relations/physiology!Humans!Protozoa/*pathogenicity!Research Support, Non-U.S. Gov't!Vacuoles/*parasitology!",scholar,,,,,
15580261,Genetically modified Plasmodium parasites as a protective experimental malaria vaccine.,http://neuron.montana.edu/courses/BIOL451M/DynaPage.pdf,"Malaria is a mosquito-borne disease that is transmitted by inoculation of the Plasmodium parasite sporozoite stage. Sporozoites invade hepatocytes, transform into liver stages, and subsequent liver-stage development ultimately results in release of pathogenic merozoites. Liver stages of the parasite are a prime target for malaria vaccines because they can be completely eliminated by sterilizing immune responses, thereby preventing malarial infection. Using expression profiling, we previously identified genes that are only expressed in the pre-erythrocytic stages of the parasite. Here, we show by reverse genetics that one identified gene, UIS3 (upregulated in infective sporozoites gene 3), is essential for early liver-stage development. uis3-deficient sporozoites infect hepatocytes but are unable to establish blood-stage infections in vivo, and thus do not lead to disease. Immunization with uis3-deficient sporozoites confers complete protection against infectious sporozoite challenge in a rodent malaria model. This protection is sustained and stage specific. Our findings demonstrate that a safe and effective, genetically attenuated whole-organism malaria vaccine is possible. Heidelberg 69120, Germany. development/*immunology/pathogenicity","Animals!Female!Gene Deletion!Gene Targeting!Liver/parasitology!Malaria/immunology/*parasitology/*prevention & control!Malaria Vaccines/*genetics/*immunology!Mice!Mice, Inbred C57BL!Phenotype!Plasmodium berghei/*genetics/growth &!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Vaccines, Attenuated/genetics/immunology!",scholar,2005,Nature,433,7022,164
15582520,Gene expression in Plasmodium: from gametocytes to sporozoites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751904002127&_version=1&_returnURL=&md5=1fca83361c115d1945b1e73ba216d678,"Completion of the complex developmental program of Plasmodium in the mosquito is essential for parasite transmission, yet this part of its life cycle is still poorly understood. In recent years, considerable progress has been made in the identification and characterization of genes expressed during parasite development in the mosquito. This line of investigation was greatly facilitated by the availability of the genome sequence of several Plasmodium, and by the application of approaches such as proteomics, microarrays, gene disruption by homologous recombination (gene knockout) and by use of subtraction libraries. Here, we review what is presently known about genes expressed in gametocytes and during the Plasmodium life cycle in the mosquito. Public Health, Malaria Research Institute, The Johns Hopkins University, 615 N Wolfe St., Baltimore, MD 21205, USA.","Animals!Gene Expression!*Genes, Protozoan!Life Cycle Stages/genetics!Plasmodium/*genetics/growth & development!Research Support, U.S. Gov't, P.H.S.!Sporozoites/genetics/growth & development!",scirus,2004,International Journal for Parasitology,34,13,1431
15582523,The role of programmed cell death in Plasmodium-mosquito interactions.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751904002073&_version=1&_returnURL=&md5=298d7de18dc6acce7191b948b9e080ec,"Many host-parasite interactions are regulated in part by the programmed cell death of host cells or the parasite. Here we review evidence suggesting that programmed cell death occurs during the early stages of the development of the malaria parasite in its vector. Zygotes and ookinetes of Plasmodium berghei have been shown to die by programmed cell death (apoptosis) in the midgut lumen of the vector Anopheles stephensi, or whilst developing in vitro. Several morphological markers, indicative of apoptosis, are described and evidence for the involvement of a biochemical pathway involving cysteine proteases discussed in relationship to other protozoan parasites. Malaria infection induces apoptosis in the cells of two mosquito tissues, the midgut and the follicular epithelium. Observations on cell death in both these tissues are reviewed including the role of caspases as effector molecules and the rescue of resorbing follicles resulting from inhibition of caspases. Putative signal molecules that might induce parasite and vector apoptosis are suggested including nitric oxide, reactive nitrogen intermediates, oxygen radicals and endocrine balances. Finally, we suggest that programmed cell death may play a critical role in regulation of infection by the parasite and the host, and contribute to the success or not of parasite establishment and host survival. Keele University, Staffordshire ST5 5BG, UK. h.hurd@keele.ac.uk",Animals!*Apoptosis!Culicidae/*parasitology!Host-Parasite Relations!Insect Vectors/*parasitology!Malaria/*parasitology/transmission!Plasmodium/cytology/*physiology!,scirus,2004,International Journal for Parasitology,34,13,1459
15582526,Cysteine proteases of malaria parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751904002085&_version=1&_returnURL=&md5=eceab3b0feb898edc1addff6b62a5bf2,"A number of cysteine proteases of malaria parasites have been described, and many more putative cysteine proteases are suggested by analysis of the Plasmodium falciparum genome sequence. Studies with protease inhibitors have suggested roles for cysteine proteases in hemoglobin hydrolysis, erythrocyte rupture, and erythrocyte invasion by erythrocytic malaria parasites. The best characterised Plasmodium cysteine proteases are the falcipains, a family of papain-family (clan CA) enzymes. Falcipain-2 and falcipain-3 are hemoglobinases that appear to hydrolyse host erythrocyte hemoglobin in the parasite food vacuole. This function was recently confirmed for falcipain-2, with the demonstration that disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis. A role for falcipain-1 in erythrocyte invasion was recently suggested, but disruption of the falcipain-1 gene did not alter parasite development. Other papain-family proteases predicted by the genome sequence include dipeptidyl peptidases, a calpain homolog, and serine-repeat antigens. The serine-repeat antigens have cysteine protease motifs, but in some the active site Cys is replaced by a Ser. One of these proteins, SERA-5, was recently shown to have serine protease activity. As SERA-5 and some other serine-repeat antigens localise to the parasitophorous vacuole in mature parasites, they may play a role in erythrocyte rupture. The P. falciparum genome sequence also predicts more distantly related (clan CD and CE) cysteine proteases, but biochemical characterisation of these proteins has not been done. New drugs for malaria are greatly needed, and cysteine proteases may provide useful new drug targets. Cysteine protease inhibitors have demonstrated potent antimalarial effects, and the optimisation and testing of falcipain inhibitor antimalarials is underway. California, San Francisco, Box 0811, San Francisco, CA 94143, USA. rosnthl@itsa.ucsf.edu","Animals!Antimalarials/therapeutic use!Cysteine Endopeptidases/genetics/*physiology!Cysteine Proteinase Inhibitors/therapeutic use!Erythrocytes/parasitology!Genes, Protozoan!Malaria/*parasitology!Plasmodium/*enzymology/genetics!Plasmodium falciparum/enzymology/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scirus,2004,International Journal for Parasitology,34,13,1489
15591057,Histone acetylase GCN5 enters the nucleus via importin-alpha in protozoan parasite Toxoplasma gondii.,http://www.jbc.org/cgi/content/abstract/280/7/5902,"The histone acetyltransferase GCN5 acetylates nucleosomal histones to alter gene expression. How GCN5 gains entry into the nucleus of the cell has not been determined. We have mapped a six-amino acid motif (RKRVKR) that serves as a necessary and sufficient nuclear localization signal (NLS) for GCN5 in the protozoan pathogen Toxoplasma gondii (TgGCN5). Virtually nothing is known about nucleocytoplasmic transport in these parasites (phylum Apicomplexa), and this study marks the first demonstrated NLS delineated for members of the phylum. The TgGCN5 NLS has predictive value because it successfully identifies other nuclear proteins in three different apicomplexan genomic databases. Given the basic composition of the T. gondii NLS, we hypothesized that TgGCN5 physically interacts with importin-alpha, the main transport receptor in the importin/karyopherin nuclear import pathway. We cloned the importin-alpha gene from T. gondii (TgIMPalpha), which encodes a protein of 545 amino acids that possesses an importin-beta-binding domain and armadillo/beta-catenin-like repeats. In vitro co-immunoprecipitation experiments confirm that TgIMPalpha directly interacts with TgGCN5, but this interaction is abolished if the TgGCN5 NLS is deleted. Taken together, these data argue that TgGCN5 gains access to the parasite nucleus by interacting with TgIMPalpha. Bioinformatics analysis of the T. gondii genome reveals that other components of the importin pathway are present in the organism. This study demonstrates the utility of T. gondii as a model for the study of nucleocytoplasmic trafficking in early eukaryotic cells. Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.","Acetyltransferases/chemistry/genetics/*metabolism!Active Transport, Cell Nucleus!Amino Acid Motifs!Amino Acid Sequence!Animals!Binding Sites!Cell Nucleus/*metabolism!Cloning, Molecular!Computational Biology!Fibroblasts/parasitology!Histone Acetyltransferases!Humans!Immunoprecipitation!Molecular Sequence Data!Nuclear Localization Signals/chemistry/genetics/*physiology!Protein Binding!Protozoan Proteins/chemistry/genetics/*metabolism!RNA, Messenger/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Toxoplasma/*cytology/enzymology/genetics/*metabolism!alpha Karyopherins/chemistry/genetics/*metabolism!",scholar,2005,Journal of Biological Chemistry,280,7,5902
15591202,Targeting malaria virulence and remodeling proteins to the host erythrocyte.,http://171.66.122.53/cgi/content/abstract/sci%3B306/5703/1930,"To establish infection in the host, malaria parasites export remodeling and virulence proteins into the erythrocyte. These proteins can traverse a series of membranes, including the parasite membrane, the parasitophorous vacuole membrane, and the erythrocyte membrane. We show that a conserved pentameric sequence plays a central role in protein export into the host cell and predict the exported proteome in Plasmodium falciparum. We identified 400 putative erythrocyte-targeted proteins corresponding to approximately 8% of all predicted genes, with 225 virulence proteins and a further 160 proteins likely to be involved in remodeling of the host erythrocyte. The conservation of this signal across Plasmodium species has implications for the development of new antimalarials. 3050, Australia. development/*metabolism/*pathogenicity","*Amino Acid Motifs!Amino Acid Sequence!Animals!Computational Biology!Cytoplasm/metabolism!Erythrocyte Membrane/metabolism!Gene Expression Profiling!Genes, Protozoan!Humans!Hydrophobicity!Malaria, Falciparum/parasitology!Membrane Proteins/chemistry/metabolism!Molecular Sequence Data!Oligonucleotide Array Sequence Analysis!Plasmodium/chemistry/genetics/metabolism!Plasmodium falciparum/genetics/growth &!*Protein Sorting Signals!Protein Transport!Protozoan Proteins/chemistry/genetics/*metabolism!Recombinant Fusion Proteins/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!Vacuoles/metabolism/parasitology!Virulence!Virulence Factors/chemistry/genetics/*metabolism!",scholar,2004,Science,306,5703,1930
15591203,A host-targeting signal in virulence proteins reveals a secretome in malarial infection.,http://171.66.122.53/cgi/content/abstract/306/5703/1934,"Malaria parasites secrete proteins across the vacuolar membrane into the erythrocyte, inducing modifications linked to disease and parasite survival. We identified an 11-amino acid signal required for the secretion of proteins from the Plasmodium falciparum vacuole to the human erythrocyte. Bioinformatics predicted a secretome of >320 proteins and conservation of the signal across parasite species. Functional studies indicated the predictive value of the signal and its role in targeting virulence proteins to the erythrocyte and implicated its recognition by a receptor/transporter. Erythrocyte modification by the parasite may involve plasmodial heat shock proteins and be vastly more complex than hitherto realized. Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA. development/*metabolism/*pathogenicity","*Amino Acid Motifs!Amino Acid Sequence!Animals!Computational Biology!Cytosol/metabolism!Erythrocytes/*metabolism/parasitology!Genes, Protozoan!Humans!Malaria, Falciparum/parasitology!Membrane Proteins/chemistry/metabolism!Molecular Sequence Data!Plasmodium falciparum/genetics/growth &!*Protein Sorting Signals!Protein Structure, Tertiary!Protein Transport!Protozoan Proteins/chemistry/genetics/*metabolism!Recombinant Fusion Proteins/chemistry/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Transgenes!Vacuoles/metabolism/parasitology!Virulence Factors/chemistry/genetics/*metabolism!",scholar,2004,Science,306,5703,1934
15610814,Gene expression in Plasmodium berghei ookinetes and early oocysts in a co-culture system with mosquito cells.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104000623&_version=1&_returnURL=&md5=4e1a49236ac644e0c690fa2cc9170729,"Using an in vitro development system for Plasmodium berghei sporogonic stages and microarray technology we examined parasite gene expression during ookinete invasion of Aedes cells and the ensuing oocyst development. A number of genes were found to be differentially expressed. The most prominent class of up-regulated elements corresponded to products involved in protein synthesis and metabolism. Furthermore, several previously studied genes with a known in vivo developmental profile matched published data. A large number of genes with a hitherto unknown function during the life cycle stages studied also show a differential pattern of expression, indicating the involvement of their products in control and execution of active developmental processes. and Technology Hellas, Vassilika Vouton, Box 1527, 711 10 Heraklion, Crete, Greece.","Animals!Cells, Cultured!Cluster Analysis!Coculture Techniques!Culicidae/cytology/*parasitology!Energy Metabolism!Epithelial Cells/parasitology!*Gene Expression!*Gene Expression Profiling!*Genes, Protozoan!Life Cycle Stages!Oligonucleotide Array Sequence Analysis!Plasmodium berghei/*genetics/growth & development!Protein Biosynthesis/genetics!Research Support, Non-U.S. Gov't!",scirus,2005,Molecular and Biochemical Parasitology,139,1,1
15612915,"The malaria parasite Plasmodium falciparum has only one pyruvate dehydrogenase complex, which is located in the apicoplast.",http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04407.x/abs/,"The relict plastid (apicoplast) of apicomplexan parasites synthesizes fatty acids and is a promising drug target. In plant plastids, a pyruvate dehydrogenase complex (PDH) converts pyruvate into acetyl-CoA, the major fatty acid precursor, whereas a second, distinct PDH fuels the tricarboxylic acid cycle in the mitochondria. In contrast, the presence of genes encoding PDH and related enzyme complexes in the genomes of five Plasmodium species and of Toxoplasma gondii indicate that these parasites contain only one single PDH. PDH complexes are comprised of four subunits (E1alpha, E1beta, E2, E3), and we confirmed four genes encoding a complete PDH in Plasmodium falciparum through sequencing of cDNA clones. In apicomplexan parasites, many nuclear-encoded proteins are targeted to the apicoplast courtesy of two-part N-terminal leader sequences, and the presence of such N-terminal sequences on all four PDH subunits as well as phylogenetic analyses strongly suggest that the P. falciparum PDH is located in the apicoplast. Fusion of the two-part leader sequences from the E1alpha and E2 genes to green fluorescent protein experimentally confirmed apicoplast targeting. Western blot analysis provided evidence for the expression of the E1alpha and E1beta PDH subunits in blood-stage malaria parasites. The recombinantly expressed catalytic domain of the PDH subunit E2 showed high enzymatic activity in vitro indicating that pyruvate is converted to acetyl-CoA in the apicoplast, possibly for use in fatty acid biosynthesis. Melbourne, Parkville, VIC 3010, Australia.","Acetyl Coenzyme A/metabolism!Animals!Blotting, Western!DNA, Complementary/chemistry!DNA, Protozoan/chemistry!Erythrocytes/parasitology!Genes, Reporter!Green Fluorescent Proteins/genetics!Introns!Molecular Sequence Data!Plasmodium falciparum/*enzymology/genetics!Plastids/*enzymology!Protein Subunits/genetics/metabolism!Pyruvate Dehydrogenase Complex/genetics/*metabolism!Pyruvic Acid/metabolism!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA!Sequence Homology!Toxoplasma/enzymology/genetics!",scholar,2005,Molecular Microbiology,55,1,39
15612927,"PfPK7, an atypical MEK-related protein kinase, reflects the absence of classical three-component MAPK pathways in the human malaria parasite Plasmodium falciparum.",http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04393.x/abs/,"Two members of the mitogen-activated protein kinase (MAPK) family have been previously characterized in Plasmodium falciparum, but in vitro attempts at identifying MAP kinase kinase (MAPKK) homologues have failed. Here we report the characterization of a novel plasmodial protein kinase, PfPK7, whose top scores in blastp analysis belong to the MAPKK3/6 subgroup of MAPKKs. However, homology to MAPKKs is restricted to regions of the C-terminal lobe of the kinase domain, whereas the N-terminal region is closer to fungal protein kinase A enzymes (PKA, members of the AGC group of protein kinases). Hence, PfPK7 is a 'composite' enzyme displaying regions of similarity to more than one protein kinase family, similar to a few other plasmodial protein kinases. PfPK7 is expressed in several developmental stages of the parasite, both in the mosquito vector and in the human host. Recombinant PfPK7 displayed kinase activity towards a variety of substrates, but was unable to phosphorylate the two P. falciparum MAPK homologues in vitro, and was insensitive to PKA and MEK inhibitors. Together with the absence of a typical MAPKK activation site in its T-loop, this suggests that PfPK7 is not a MAPKK orthologue, despite the fact that this enzyme is the most 'MAPKK-like' enzyme encoded in the P. falciparum genome. This is consistent with recent observations that the plasmodial MAPKs are not true orthologues of the ERK1/2, p38 or JNK MAPKs, and strengthens the evidence that classical three-component module-dependent MAPK signalling pathways do not operate in malaria parasites, a feature that has not been described in any other eukaryote. 56 Dumbarton Road, Glasgow G11 6NU, Scotland, UK. inhibitors/chemistry/genetics/*metabolism","Amino Acid Sequence!Animals!Conserved Sequence!Cyclic AMP-Dependent Protein Kinases/genetics/*metabolism!Enzyme Inhibitors/pharmacology!Fungal Proteins/chemistry!Gene Expression!In Vitro!MAP Kinase Signaling System!Mitogen-Activated Protein Kinase Kinases/antagonists &!Molecular Sequence Data!Plasmodium falciparum/*enzymology/genetics!Protein Structure, Tertiary!Protozoan Proteins/genetics/*metabolism!Recombinant Fusion Proteins/genetics/metabolism!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Substrate Specificity!",scholar,2005,Molecular Microbiology,55,1,184
2601715,Antifolate drug selection results in duplication and rearrangement of chromosome 7 in Plasmodium chabaudi.,http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=363670,"We selected lines of Plasmodium chabaudi that are resistant to high levels of the antifolate drug pyrimethamine and have shown that rearrangement and duplication of a portion of chromosome 7 has occurred in the resistant lines. This chromosomal duplication results in an increase in the chromosome number from 14 to 15: two derived chromosomes (450 kilobases and 1.1 megabases) were smaller than the original chromosome 7 (1.3 megabases), so that essentially only a 200-kilobase region was duplicated. This region contained the DHFR-TS gene and the closely linked Hsp70 gene. We have macrorestriction mapped chromosome 7 from the pyrimethamine-susceptible line (DS) and also the duplicated chromosome 7s in the resistant line. From these maps, we have proposed a process for the karyotype changes. Sequencing of the DHFR gene from the parent and derived chromosomes showed that there were no mutations in the coding sequence. As a result of the duplication of the DHFR-TS gene, there is at least a twofold increase in expression of the DHFR-TS gene, and this may explain the ability of the pyrimethamine-resistant lines to grow in increased amounts of the drug.","Karyotyping,Genes,Amino Acid Sequence,Restriction Mapping,Pyrimethamine,Sequence Homology, Nucleic Acid,Molecular Sequence Data,Gene Rearrangement,Heat-Shock Proteins,Multigene Family,Base Sequence,Linkage (Genetics),Drug Resistance,Animals,Chromosomes,Plasmodium",NCBI,1989,Molecular and cellular biology,9,11,5182-8
15659064,A Plasmodium sporozoite protein with a membrane attack complex domain is required for breaching the liver sinusoidal cell layer prior to hepatocyte infection.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1462-5822.2004.00447.x/full/,"Plasmodium sporozoites are injected into the mammalian host during mosquito blood feeding and carried by the blood stream to the liver, where they infect hepatocytes and develop into erythrocyte-invasive forms. To reach the hepatocytes, sporozoites must cross the liver sinusoidal cell layer, which separates the hepatocytes from the circulatory system. Little is known about the molecular mechanisms by which sporozoites breach this cellular barrier. Here we report that a protein with a membrane attack complex/perforin (MACPF)-related domain is involved in this step. This molecule is specifically expressed in liver-infective sporozoites and localized in micronemes, organelles engaged in host cell invasion. Gene disruption experiments revealed that this protein is essential for the membrane-wounding activity of the sporozoite and is involved in its traversal of the sinusoidal cell layer prior to hepatocyte-infection. Disruptants failed to leave the circulation, and most of them were eliminated from the blood by liver perfusion. Our results suggest that rupture of the host plasma membrane by the pore-forming activity of this molecule is essential for cell passage of the sporozoite. This report is the first to demonstrate an important role of a MACPF-related protein in host cell invasion by a pathogenic microorganism.","Amino Acid Sequence!Animals!Cell Membrane/parasitology!Complement Membrane Attack Complex/*chemistry!Expressed Sequence Tags!Gene Targeting!Hepatocytes/*parasitology!Humans!Kupffer Cells/parasitology!Liver/*parasitology!Membrane Glycoproteins/genetics/physiology!Molecular Sequence Data!Mutagenesis, Insertional!Plasmodium berghei/genetics/*physiology!Protein Structure, Tertiary/physiology!Protozoan Proteins/chemistry/genetics/*physiology!Rats!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!",scholar,2004,Cell Microbiol,2,,
15659354,A selenocysteine tRNA and SECIS element in Plasmodium falciparum.,http://www.rnajournal.org/cgi/content/abstract/11/2/119,"The molecular machinery for incorporating selenocysteine into proteins is present in both prokaryotes and eukaryotes. Although selenocysteine insertion has been reported in animals, plants, and protozoans, known eukaryotic selenocysteine tRNA sequences and selenocysteine insertion sequences are limited to animals and plants. Here we present clear indications of the presence of selenocysteine-tRNA and a selenocysteine insertion sequence in Plasmodium falciparum. To our knowledge, this is the first report of an identification of protozoan selenocysteine insertion machinery at the sequence level.","Amino Acid Sequence!Animals!Base Sequence!DNA Transposable Elements/*genetics!DNA, Protozoan/*genetics!Molecular Sequence Data!Nucleic Acid Conformation!Plasmodium/genetics!Plasmodium falciparum/*genetics/metabolism!Protozoan Proteins/biosynthesis/chemistry!RNA, Protozoan/chemistry/*genetics!RNA, Transfer, Amino Acyl/chemistry/*genetics!Research Support, Non-U.S. Gov't!Selenocysteine/metabolism!Sequence Homology, Amino Acid!",scholar,2005,RNA,11,,119
15659379,Identifying Plasmodium falciparum cytoadherence-linked asexual protein 3 (CLAG 3) sequences that specifically bind to C32 cells and erythrocytes.,http://protsci.highwire.org/cgi/content/abstract/14/2/504,"Adhesion of mature asexual stage Plasmodium falciparum parasite-infected erythrocytes (iRBC) to the vascular endothelium is a critical event in the pathology of Plasmodium falciparum malaria. It has been suggested that the clag gene family is essential in cytoadherence to endothelial receptors. Primers used in PCR and RT-PCR assays allowed us to determine that the gene encoding CLAG 3 (GenBank accession no. NP_473155) is transcribed in the Plasmodium falciparum FCB2 strain. Western blot showed that antisera produced against polymerized synthetic peptides from this protein recognized a 142-kDa band in P. falciparum schizont lysate. Seventy-one 20-amino-acid-long nonoverlapping peptides, spanning the CLAG 3 (cytoadherence-linked asexual protein on chromosome 3) sequence were tested in C32 cell and erythrocyte binding assays. Twelve CLAG peptides specifically bound to C32 cells (which mainly express CD36) with high affinity, hereafter referred to as high-affinity binding peptides (HABPs). Five of them also bound to erythrocytes. HABP binding to C32 cells and erythrocytes was independent of peptide charge or peptide structure. Affinity constants were between 100 nM and 800 nM. Cross-linking and SDS-PAGE analysis allowed two erythrocyte binding proteins of around 26 kDa and 59 kDa to be identified, while proteins of around 53 kDa were identified as possible receptor sites for C-32 cells. The HABPs' role in Plasmodium falciparum invasion inhibition was determined. Such an approach analyzing various CLAG 3 regions may elucidate their functions and may help in the search for new antigens important for developing antimalarial vaccines. Colombia, Avda. Calle 26 No. 50-00, Bogota, Colombia. marisol_ocampo@fidic.org.co","Amino Acid Sequence!Animals!Antibodies/chemistry!Antigens, CD36/chemistry!Base Sequence!Blotting, Western!Cell Adhesion Molecules/*chemistry!Circular Dichroism!Cross-Linking Reagents/chemistry!DNA Primers/chemistry!DNA, Complementary/metabolism!Electrophoresis, Polyacrylamide Gel!Erythrocytes/*metabolism/*parasitology!Humans!Immunoblotting!Molecular Sequence Data!Peptides/chemistry!Plasmodium falciparum/*metabolism!Polymerase Chain Reaction!Polymers/chemistry!Protein Binding!Protein Conformation!Protein Structure, Tertiary!Protozoan Proteins/*chemistry/*physiology!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Sequence Homology, Amino Acid!",scholar,2005,Protein Science,14,,504
15661734,Resistance to a protein farnesyltransferase inhibitor in Plasmodium falciparum.,http://www.jbc.org/cgi/content/abstract/280/14/13554,"The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. Inhibition of protein farnesyltransferase (PFT) is lethal to the pathogenic protozoa Plasmodium falciparum. Parasites were isolated that were resistant to BMS-388891, a tetrahydroquinoline (THQ) PFT inhibitor. Resistance was associated with a 12-fold decrease in drug susceptibility. Genotypic analysis revealed a single point mutation in the beta subunit in resistant parasites. The resultant tyrosine 837 to cysteine alteration in the beta subunit corresponded to the binding site for the THQ and peptide substrate. Biochemical analysis of Y837C-PFT demonstrated a 13-fold increase in BMS-388891 concentration necessary for inhibiting 50% of the enzyme activity. These data are consistent with PFT as the target of BMS-388891 in P. falciparum and suggest that PFT inhibitors should be combined with other antimalarial agents for effective therapy. 98195, USA.","Alkyl and Aryl Transferases/*antagonists & inhibitors/genetics/*metabolism!Amino Acid Sequence!Animals!Binding Sites!Drug Resistance/genetics/*physiology!Humans!Imidazoles/chemistry/metabolism/therapeutic use!Malaria/drug therapy/parasitology!Models, Molecular!Molecular Sequence Data!Molecular Structure!Plasmodium falciparum/genetics/*metabolism!Point Mutation!Protein Processing, Post-Translational!Protein Subunits/genetics/metabolism!Protozoan Proteins/*antagonists & inhibitors/genetics/*metabolism!Quinolines/chemistry/metabolism/therapeutic use!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!",scholar,2005,Journal of Biological Chemistry,280,14,13554
15664648,Identification of putative Plasmodium falciparum mefloquine resistance genes.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104002828&_version=1&_returnURL=&md5=50a32719b900479bd7373189429c3ccb,"Mefloquine is an effective antimalarial drug; however, resistant strains of the human malarial pathogen, Plasmodium falciparum, are beginning to arise. The yeast Saccharomyces cerevisiae is sensitive to mefloquine, enabling a screen for P. falciparum genes involved in resistance. Yeast were transformed with a P. falciparum expression library, followed by selection on mefloquine plates and sequencing of plasmids that conferred resistance. We characterized the four genes that conferred the strongest mefloquine-resistant phenotype in yeast. All four (PFD0090c, PFI0195c, PF10_0372 and PF14_0649) are uncharacterized P. falciparum genes from distinct chromosomes (4, 9, 10 and 14, respectively). The mefloquine-resistant phenotype was dependent on induction of the P. falciparum gene and independent of vector context. PFI0195c, which likely encodes a small GTPase activator (GAP), also conferred resistance to cycloheximide and halofantrine in yeast. Immunolocalization of the encoded protein to the Golgi complex in yeast is consistent with potential GAP function. The other three candidate proteins localized to the cytoplasm and plasma membrane (PF14_0649), nuclear envelope/ER (PF10_0372) and Golgi (PFD0090c) of yeast. Analysis of mefloquine-resistant P. falciparum strains and the mefloquine-sensitive strain, W2, by sequencing and semi-quantitative RT-PCR identified no relevant mutations in the resistant strains but showed that PFI0195c was upregulated in two out of three resistant strains and PF14_0649 was upregulated in all resistant strains tested. 98195, USA.","Animals!Antimalarials/*pharmacology!Drug Resistance/*genetics!Gene Expression Regulation!Mefloquine/*pharmacology!Parasitic Sensitivity Tests/methods!Plasmodium falciparum/*drug effects/genetics!Protozoan Proteins/*genetics!Saccharomyces cerevisiae/genetics/metabolism!Transformation, Genetic!",scirus,2005,Molecular and Biochemical Parasitology,139,2,133
15664653,A Plasmodium falciparum FK506-binding protein (FKBP) with peptidyl-prolyl cis-trans isomerase and chaperone activities.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104003093&_version=1&_returnURL=&md5=a42aba7a691470da55b8f51fdd0d730a,"The immunosuppressive drugs FK506 and rapamycin have anti-malarial properties but their mechanisms of action against malaria parasites remain unknown. The pathway by which these drugs cause immunosuppression in humans is known to involve an FK506-binding protein (FKBP). Homologues of FKBPs have been identified in almost every organism in which they have been sought. Here, we describe the characterisation of the first member of the FKBP family identified in the human malarial parasite, Plasmodium falciparum. This 35-kDa protein, PfFKBP35, comprises a single, N-terminal, FKBP domain and a C-terminal tripartite tetratricopeptide repeat domain. A recombinant form of PfFKBP35, like most other FKBPs, displayed peptidyl-prolyl cis-trans isomerase activity that was inhibitable by FK506 and rapamycin. Unusually the phosphatase activity of calcineurin, the target of the FK506-FKBP complex in T-lymphocytes, was inhibited by PfFKBP35 independently of FK506 binding. PfFKBP35 also inhibited the thermal aggregation in vitro of two model substrates, suggesting that it has general chaperone properties. Analysis of the P. falciparum genome database suggested this to be the only FKBP present in the parasite. The function of this protein remains unknown but the presence of tetratricopeptide repeat motifs suggests a role in intracellular protein transport or modulation of protein function. Trinity College, Dublin 2, Ireland.","Amino Acid Sequence!Animals!Immunosuppressive Agents/*metabolism!Molecular Chaperones/*metabolism!Molecular Sequence Data!Peptidylprolyl Isomerase/*metabolism!Plasmodium falciparum/genetics/*metabolism!Protein Folding!Protozoan Proteins/*metabolism!Recombinant Proteins/metabolism!Research Support, Non-U.S. Gov't!Tacrolimus/*metabolism!Tacrolimus Binding Proteins/chemistry/genetics/*metabolism!",scirus,2005,Molecular and Biochemical Parasitology,139,2,185
15665330,Maize phosphoenolpyruvate carboxylase. Mutations at the putative binding site for glucose 6-phosphate caused desensitization and abolished responsiveness to regulatory phosphorylation.,http://www.jbc.org/cgi/content/abstract/280/12/11798,"Phosphoenolpyruvate carboxylases (PEPC, EC 4.1.1.31) from higher plants are regulated by both allosteric effects and reversible phosphorylation. Previous x-ray crystallographic analysis of Zea mays PEPC has revealed a binding site for sulfate ion, speculated to be the site for an allosteric activator, glucose 6-phosphate (Glc-6-P) (Matsumura, H., Xie, Y., Shirakata, S., Inoue, T., Yoshinaga, T., Ueno, Y., Izui, K., and Kai, Y. (2002) Structure (Lond.) 10, 1721-1730). Because kinetic experiments have also supported this notion, each of the four basic residues (Arg-183, -184, -231, and -372' on the adjacent subunit) located at or near the binding site was replaced by Gln, and the kinetic properties of recombinant mutant enzymes were investigated. Complete desensitization to Glc-6-P was observed for R183Q, R184Q, R183Q/R184Q (double mutant), and R372Q, as was a marked decrease in the sensitivity for R231Q. The heterotropic effect of Glc-6-P on an allosteric inhibitor, l-malate, was also abolished, but sensitivity to Gly, another allosteric activator of monocot PEPC, was essentially not affected, suggesting the distinctness of their binding sites. Considering the kinetic and structural data, Arg-183 and Arg-231 were suggested to be involved directly in the binding with phosphate group of Glc-6-P, and the residues Arg-184 and Arg-372 were thought to be involved in making up the site for Glc-6-P and/or in the transmission of an allosteric regulatory signal. Most unexpectedly, the mutant enzymes had almost lost responsiveness to regulatory phosphorylation at Ser-15. An apparent lack of kinetic competition between the phosphate groups of Glc-6-P and of phospho-Ser at 15 suggested the distinctness of their binding sites. The possible roles of these Arg residues are discussed. Kyoto 606-8502, Japan.","Amino Acid Sequence!Binding Sites!Enzyme Activation!Glucose-6-Phosphate/*metabolism!Molecular Sequence Data!Mutation!Phosphoenolpyruvate Carboxylase/*chemistry!Phosphorylation!Protein Structure, Secondary!Research Support, Non-U.S. Gov't!Sulfates/metabolism!Zea mays/*enzymology!",scholar,2005,Journal of Biological Chemistry,280,12,11798
15670824,Unusual properties of Plasmodium falciparum actin: new insights into microfilament dynamics of apicomplexan parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0014579304015753&_version=1&_returnURL=&md5=975b07955613f3e9143df44ef4f65de7,"Plasmodium falciparum, the etiologic agent of malaria, is a facultative intracellular parasite of the phylum Apicomplexa. A limited turnover of microfilaments takes place beneath the parasite plasma membrane, but the cytoplasm of apicomplexans is virtually devoid of F-actin. We produced Plasmodium actin in yeast. Purified recombinant Plasmodium actin polymerized inefficiently unless both gelsolin and phalloidin were added. The resulting actin polymers appeared fragmented in the fluorescence microscope. Plasmodium actin bound DNaseI about 200 times weaker than bovine non-muscle actin. Our findings suggest that the unique properties of Plasmodium actin can explain some of the unusual features of apicomplexan parasite microfilaments. Roslagstullsbacken 15, 11421 Stockholm, Sweden. herwig@dbb.su.se","Actins/chemistry/genetics/*metabolism!Amino Acid Sequence!Animals!Cloning, Molecular!DNA, Complementary!Models, Molecular!Molecular Sequence Data!Plasmodium falciparum/*metabolism!Protein Conformation!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!",scirus,2005,FEBS Letters,579,3,655
15671043,"Proteomic analysis identifies novel proteins of the Maurer's clefts, a secretory compartment delivering Plasmodium falciparum proteins to the surface of its host cell.",http://www.mcponline.org/cgi/content/abstract/4/4/582%3Fetoc,"A novel method was validated for the efficient distinction between malaria parasite-derived and host cell proteins in mass spectrometry analyses. This method was applied to a ghost fraction from Plasmodium falciparum-infected erythrocytes containing the red blood cell plasma membrane, the erythrocyte submembrane skeleton, and the Maurer's clefts, a Golgi-like apparatus linked to and addressing parasite proteins to the host cell surface. This method allowed the identification of 78 parasite proteins. Among these we identified seven novel proteins of the Maurer's clefts based on immunofluorescence studies and proteinase K digestion assays. The products of six contiguous genes located on chromosome 5 were identified, and the location within the Maurer's clefts was established for two of them. This suggests a clustering of genes encoding Maurer's cleft proteins. Our study sheds new light on the biological function of the Maurer's clefts, which are central to the pathogenesis and to the intraerythrocytic development of P. falciparum. Pasteur, 25-28 Rue du Dr Roux, 75724 Paris Cedex 15, France.","Animals!Blotting, Western!DNA Primers!DNA, Protozoan/chemistry!Deuterium/metabolism!Endopeptidase K/metabolism!Erythrocyte Membrane/*chemistry/drug effects/metabolism/*parasitology!Glutathione Transferase/metabolism!Host-Parasite Relations!Humans!Life Cycle Stages!Malaria, Falciparum/parasitology!Membrane Proteins/*analysis/chemistry/isolation & purification/metabolism!Microscopy, Fluorescence!Models, Biological!Nucleic Acid Amplification Techniques!Octoxynol/pharmacology!Peptide Fragments/chemistry/metabolism!Plasmodium falciparum/growth & development/*physiology!Polymerase Chain Reaction!Protozoan Proteins/*analysis/chemistry/isolation & purification/metabolism!Recombinant Fusion Proteins/chemistry/metabolism!Reproducibility of Results!Research Support, Non-U.S. Gov't!Spectrum Analysis, Mass!",scholar,2005,Molecular & Cellular Proteomics,4,,582
15681372,Parasitology. Malaria vaccines: back to the future?,http://www.sciencemag.org/cgi/content/summary/307/5709/528,,"Animals!Apoptosis!Genes, Protozoan!Genetic Engineering!Hepatocytes/parasitology/physiology!Humans!Immunization Schedule!Immunization, Secondary!Malaria/*immunology/prevention & control!*Malaria Vaccines/immunology!Malaria, Falciparum/immunology/prevention & control!Mice!Plasmodium berghei/genetics/growth & development/*immunology!Plasmodium falciparum/genetics/immunology!Protozoan Proteins/genetics/physiology!Sporozoites/genetics/growth & development/*immunology!Vaccination!Vaccines, Attenuated/immunology!",scholar,2005,Science,307,5709,528
15694486,A novel 'DEAD-box' DNA helicase from Plasmodium falciparum is homologous to p68.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685104003354&_version=1&_returnURL=&md5=9738e5d74d250fa31d675859f0e34971,,"Adenosine Triphosphate/metabolism!Adenosinetriphosphatase/analysis!Amino Acid Sequence!Animals!Comparative Study!DNA Helicases/chemistry/genetics/*metabolism!Escherichia coli/genetics/metabolism!Isopropyl Thiogalactoside!Molecular Sequence Data!Molecular Weight!Plasmodium falciparum/*enzymology/genetics!*Protein Kinases/chemistry/genetics!*RNA Helicases/chemistry/genetics!Recombinant Proteins/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!Sequence Homology, Amino Acid!",scirus,2005,Molecular and Biochemical Parasitology,140,1,55
15694487,A novel Sushi domain-containing protein of Plasmodium falciparum.,http://www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26list_uids%3D15694487%26dopt%3DCitation,"Using bioinformatics analyses of the completed malaria genome sequence, we have identified a novel protein with a potential role in erythrocyte invasion. The protein (PFD0295c, ) has a predicted signal sequence and transmembrane domain and a sequence near the C-terminus of the protein shows significant similarity with Sushi domains. These domains, which exist in a wide variety of complement and adhesion proteins, have previously been shown to be involved in protein-protein and protein-ligand interactions. Orthologous genes have also been identified in the genomes of several other Plasmodium species, suggesting a conserved function for this protein in Plasmodium. Our results show that this protein is located in apical organelles and we have therefore designated the protein apical Sushi protein (ASP). We show that the expression of ASP is tightly regulated in the intraerythrocytic stages of the parasite and that it undergoes post-translational proteolytic processing. Based on our observations of timing of expression, location and proteolytic processing, we propose a role for ASP in erythrocyte invasion. NW71AA, UK. aokeeff@nimr.mrc.ac.uk","Amino Acid Sequence!Animals!Comparative Study!Fluorescent Antibody Technique!Immunoblotting!Molecular Sequence Data!Plasmodium falciparum/*genetics/metabolism!Protein Structure, Tertiary!Protozoan Proteins/*genetics/isolation & purification/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!Virulence!",scholar,2005,Mol Biochem Parasitol,140,1,61
15699336,Plasmodium liver stage developmental arrest by depletion of a protein at the parasite-host interface.,http://www.pnas.org/cgi/content/abstract/102/8/3022,"Plasmodium parasites of mammals, including the species that cause malaria in humans, infect the liver first and develop there into clinically silent liver stages. Liver stages grow and ultimately produce thousands of first-generation merozoites, which initiate the erythrocytic cycles causing malaria pathology. Here, we present a Plasmodium protein with a critical function for complete liver stage development. UIS4 (up-regulated in infective sporozoites gene 4) is expressed exclusively in infective sporozoites and developing liver stages, where it localizes to the parasitophorous vacuole membrane. Targeted gene disruption of UIS4 in the rodent model malaria parasite Plasmodium berghei generated knockout parasites that progress through the malaria life cycle until after hepatocyte invasion but are severely impaired in further liver stage development. Immunization with UIS4 knockout sporozoites completely protects mice against subsequent infectious WT sporozoite challenge. Genetically attenuated liver stages may thus induce immune responses, which inhibit subsequent infection of the liver with WT parasites. 69120 Heidelberg, Germany. America.","Animals!Female!Immunization!Liver/*parasitology!Mice!Mice, Inbred C57BL!Plasmodium berghei/*growth & development/immunology!Protozoan Proteins/*physiology!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sporozoites/immunology/physiology!Vacuoles/parasitology!",scholar,2005,Proceedings of the National Academy of Sciences,102,8,3022
15703443,RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum.,http://www.rnajournal.org/cgi/content/abstract/11/4/365,"The recent identification of antisense RNA in the transcriptomes of many eukaryotes has generated enormous interest. The presence of antisense RNA in Plasmodium falciparum, the causative agent of severe malaria, remains controversial. Elucidation of the mechanism of antisense RNA in P. falciparum synthesis is critical in order to demonstrate the origin and function of these transcripts. Therefore, a systematic analysis of antisense and sense RNA synthesis was performed using direct labeling experiments. Nuclear run on experiments with single-stranded DNA probes demonstrated that antisense RNA is synthesized in the nucleus at several genomic loci. Antisense RNA synthesis is sensitive to the potent RNA polymerase II inhibitor alpha-amanitin. Antisense and sense transcription was also detected in nuclei isolated from synchronized parasites, suggesting concurrent synthesis. In summary, our experiments directly demonstrate that antisense RNA synthesis is a common transcriptional phenomenon in P. falciparum, and is catalyzed by RNA polymerase II. Diseases, 665 Huntington Avenue, Building I, Room 705, Boston, MA 02115, USA.","Animals!Blotting, Southern!DNA, Single-Stranded!Plasmodium falciparum/*genetics/metabolism!RNA Polymerase II/genetics/*metabolism!RNA, Antisense/*biosynthesis/genetics!RNA, Protozoan/*biosynthesis/genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Transcription, Genetic!",scholar,2005,RNA,11,,365
15710548,Expression of mRNAs and proteins for peroxiredoxins in Plasmodium falciparum erythrocytic stage.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1383576904000716&_version=1&_returnURL=&md5=1e003ee6cb7f0c27fd645abdfa9f93fb,"mRNA and protein expression profiles for three peroxiredoxins (PfTPx-1, PfTPx-2 and Pf1-Cys-Prx) and a thioredoxin (PfTrx-1) of Plasmodium falciparum during the erythrocytic stage were examined by real-time quantitative reverse transcription-PCR (RT-PCR), Western blotting and confocal laser scanning microscopy. PfTPx-1 was expressed constitutively in the parasite cytoplasm throughout the erythrocytic stage, suggesting a housekeeping role of this enzyme for control of intercellular reactive oxygen species (ROS) in the parasite. Pf1-Cys-Prx showed elevated expression during the trophozoite and early schizont stages in the parasite cytoplasm, and this profile suggested that this peroxiredoxin (Prx) detoxifies metabolism-derived ROS such as those released from heme iron. The other 2-Cys Prx, PfTPx-2, was detected in mitochondria and was expressed in both the trophozoite and schizont stages. Detection of the Prx in mitochondria is consistent with recent reports of the existence of a respiratory chain, which produces ROS, in the mitochondria of P. falciparum. PfTrx-1 showed elevated expression during the trophozoite and schizont stages in the parasite cytoplasm. Finally, expression of these antioxidant protein genes is most likely regulated at the transcriptional level because their mRNA and protein expression profiles overlapped. Shinjuku-ku, Tokyo 162-8655, Japan.","Animals!Blotting, Western!Erythrocytes/*parasitology!*Gene Expression Regulation!Microscopy, Fluorescence!Peroxidases/genetics/*metabolism!Plasmodium falciparum/genetics/growth & development/*metabolism!Protozoan Proteins/metabolism!RNA, Messenger/*metabolism!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Subcellular Fractions/metabolism!Thioredoxin/genetics/*metabolism!",scirus,2005,Parasitology International,54,1,35
15717280,Identification of multiple chondroitin sulfate A (CSA)-binding domains in the var2CSA gene transcribed in CSA-binding parasites.,http://www.journals.uchicago.edu/cgi-bin/resolve%3Fid%3Ddoi:10.1086/428137,"Malaria in pregnancy is a serious complication associated with parasitized erythrocyte (PE) sequestration in the placenta. Recent work suggests that var genes could play an important role in PE binding to chondroitin sulfate A (CSA), a primary placental adherence receptor. Here, we confirm that var2CSA is transcriptionally up-regulated in CSA-binding parasites and define CSA-binding domains in var2CSA. The identification of multiple binding domains in var2CSA strengthens the evidence for their involvement in malaria during pregnancy and may have applications for the development of a vaccine against malaria in pregnancy. Pasteur, Paris, France. bgamain@pasteur.fr","Amino Acid Sequence!Animals!Antigens, Protozoan/*chemistry/genetics/metabolism!CHO Cells!Cattle!Chondroitin Sulfates/*metabolism!Cricetinae!Molecular Sequence Data!Plasmodium falciparum/*metabolism!Protozoan Proteins/*chemistry/genetics/metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Transcription, Genetic!*Up-Regulation!",scholar,2005,J Infect Dis,191,6,1010
11163248,A central role for P48/45 in malaria parasite male gamete fertility.,,"Fertilization and zygote development are obligate features of the malaria parasite life cycle and occur during parasite transmission to mosquitoes. The surface protein PFS48/45 is expressed by male and female gametes of Plasmodium falciparum and PFS48/45 antibodies prevent zygote development and transmission. Here, gene disruption was used to show that Pfs48/45 and the ortholog Pbs48/45 from a rodent malaria parasite P. berghei play a conserved and important role in fertilization. p48/45- parasites had a reduced capacity to produce oocysts in mosquitoes due to greatly reduced zygote formation. Unexpectedly, only male gamete fertility of p48/45- parasites was affected, failing to penetrate otherwise fertile female gametes. P48/45 is shown to be a surface protein of malaria parasites with a demonstrable role in fertilization.","Plasmodium falciparum,Amino Acid Sequence,Malaria,Plasmodium berghei,Female,Male,Molecular Sequence Data,Antibodies,Zygote,Gametogenesis,Genome, Protozoan,Fertility,Malaria Vaccines,Culicidae,Animals,Protozoan Proteins",NCBI,2001,Cell,104,1,153-64
15723602,Using expression information to discover new drug and vaccine targets in the malaria parasite Plasmodium falciparum.,http://www.futuremedicine.com/doi/full/10.1517/14622416.6.1.17,"The recent completion of the malaria parasite Plasmodium falciparum genome has opened the door for applying a variety of genomic-based systems biology approaches that complement existing gene-by-gene methods of investigation. Transcriptomic analyses of P.falciparum using DNA microarrays has allowed for the rapid elucidation of gene function, parasite drug response, and invivo expression profiles, as well as general mechanisms guiding the parasite life cycle that are vital to disease pathogenesis. The results of these studies have identified promising novel gene targets for the development of new drug and vaccine therapies. 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.",,scholar,2005,Pharmacogenomics,6,1,17
15727041,Parasite plastids: approaching the endgame.,http://www.journals.cambridge.org/abstract_S1464793104006591,"Considerable work still needs to be done to understand more fully the basic processes going on inside the non-photosynthetic plastid organelle of Plasmodium spp., the causative agent of malaria. Following an explosion of genomic and transcriptional information in recent years, research workers are still analysing these data looking for new material relevant to the plastid. Several metabolic and housekeeping functions based on bacterial biochemistry have been elucidated and this has given impetus to finding lead inhibitors based on established anti-microbials. Structural investigations of plastid-associated enzymes identified as potential targets have begun. This review gives a perspective on the research to date and hopes to emphasize that a practical outcome for the clinic should be an important focus of future efforts. Malaria parasites have become resistant to front-line anti-malarials that are widely used and were formerly dependable. This has become a worrying problem in many regions where malaria is endemic. The time lag between hunting for new inhibitors and their application as pharmaceuticals is so long and costly that a steady stream of new ventures has to be undertaken to give a reasonable chance of finding affordable and appropriate anti-malarials for the future. Attempts to find inhibitors of the plastid organelle of the malaria parasite should be intensified in such programmes. rwilson@nimr.mrc.ac.uk","Animals!Antimalarials/pharmacology!Evolution!Genome, Protozoan!Humans!Intracellular Membranes/metabolism!Malaria/*drug therapy/metabolism/prevention & control!Organelles/metabolism!Parasitic Sensitivity Tests!Phylogeny!Plasmodium/classification/drug effects/*metabolism/*ultrastructure!Plastids/*metabolism!",scholar,2005,Biological Reviews,80,1,129
15729590,Identification of proteins interacting with Toxoplasma SRCAP by yeast two-hybrid screening.,http://www.springerlink.com/index/G7PR145YK9RLPRPP.pdf,"Toxoplasma gondii is an opportunistic protozoan parasite that differentiates into latent cysts (bradyzoite) that can be reactivated during immunosuppression. TgSRCAP (Toxoplasma gondii Snf2-related CBP activator protein) is a SWI2/SNF2 family chromatin remodeler whose expression increases during cyst development. Identifying the proteins associating with TgSRCAP during the pre-cyst stage (tachyzoite) will increase our understanding of how parasite differentiation is initiated. We employed the yeast two-hybrid system to identify proteins that may interact directly with TgSRCAP. A stretch of 1,060 amino acids between ATPase subdomains IV and V of TgSRCAP was chosen as "bait" since the corresponding region in human SRCAP interacts with other proteins, including CREB binding protein. We have identified several novel parasite-specific transcription factors predicted to be in the T. gondii genome. Metabolic enzymes that may participate in cyst development were also identified as interacting with TgSRCAP. Medicine, Medical Sciences Building Room A-525, 635 Barnhill Drive, Indianapolis, IN 46202, USA.","Animals!Computational Biology!Enzymes/genetics/isolation & purification/metabolism!Humans!Immunoprecipitation!Plasmids!Protein Binding!Protozoan Proteins/genetics/*metabolism!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Toxoplasma/genetics/growth & development/*metabolism!Transcription Factors/genetics/isolation & purification/*metabolism!Two-Hybrid System Techniques!",scholar,2005,Parasitology Research,95,4,236
15741555,Analysis of the genetic diversity of the Plasmodium falciparum multidrug resistance gene 5' upstream region.,http://www.ajtmh.org/cgi/content/abstract/72/2/182,"Recent findings indicating a low level of polymorphism in the Plasmodium falciparum genome have led to the hypothesis that existent polymorphisms are likely to have functional significance. We tested this hypothesis by developing a map of the polymorphism in the P. falciparum multidrug resistance 1 (pfmdr1) gene 5' upstream region and assaying its correlation with drug resistance in a sample of field isolates from Dakar, Senegal. A comparison of six geographically diverse laboratory strains showed that the 1.94-kb 5'-untranslated region is highly monomorphic, with a total of four unique single nucleotide polymorphisms (SNPs) being identified. All of the mutations were localized to a 462-basepair region proximal to the transcription start point. Analysis of this region in field isolates shows the prevalence of one SNP throughout the entire population of parasites, irrespective of drug resistance status. The SNP frequency of the pfmdr1 upstream region is lower than that found in the noncoding region of other genes. California at San Francisco, 94110, USA.","ATP-Binding Cassette Transporters/*genetics!Animals!Antimalarials/therapeutic use!DNA Primers!DNA, Protozoan/analysis!Genes, MDR/*genetics!Humans!Malaria, Falciparum/drug therapy/epidemiology!Plasmodium falciparum/*genetics!Polymerase Chain Reaction!Polymorphism, Single Nucleotide!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Senegal/epidemiology!Variation (Genetics)!",scholar,2005,The American Journal of Tropical Medicine and Hygiene,72,2,182
15745999,metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.,http://nar.oupjournals.org/cgi/content/abstract/33/4/1399,"The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux system and requires only a set of raw DNA sequences (genomic, expressed sequence tag and/or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10(-20), our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5x to 7.5x. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella. john@bioinformatics.leeds.ac.uk","Animals!Coenzyme A/biosynthesis!Eimeria tenella/enzymology/genetics!Enzymes/*genetics!*Genome, Protozoan!Genomics/*methods!Plasmodium falciparum/enzymology/genetics!Research Support, Non-U.S. Gov't!Sequence Analysis, DNA/*methods!*Software!",scholar,2005,Nucleic Acids Research,33,4,1399
3556207,Plasmodium berghei: cloning of the circumsporozoite protein gene.,,"A DNA fragment encoding the carboxy terminal 80% of the Plasmodium berghei circumsporozoite protein was selected from a genomic DNA expression library. Sequencing revealed that the P. berghei circumsporozoite protein was similar in overall structure to circumsporozoite proteins from other malaria species, although the central repeat region was unique in comprising two different blocks of tandem peptide repeats: 11 eight amino acid repeats with predominant sequence DPAPPNAN were followed by 16 two amino repeats, predominantly PQ. The P. berghei circumsporozoite protein exhibited limited, but about equal amino acid homology to circumsporozoite proteins from P. knowlesi, P. vivax, and P. falciparum, indicating that P. berghei is not closely related to any of these other malaria species. Cloning of the P. berghei circumsporozoite protein gene will allow direct testing of sporozoite vaccines in mice.","Plasmodium falciparum,Amino Acid Sequence,Plasmodium berghei,Cloning, Molecular,Antigens, Protozoan,Antigens, Surface,Base Sequence,Plasmodium vivax,Animals,Protozoan Proteins,Plasmodium,Evolution",NCBI,1987,Experimental parasitology,63,3,295-300
2432395,Circumsporozoite protein of Plasmodium berghei: gene cloning and identification of the immunodominant epitopes.,http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=367160,"The gene encoding the circumsporozoite (CS) protein of the rodent malaria parasite Plasmodium berghei was cloned and characterized. A cDNA library made from P. berghei sporozoite RNA was screened with a monoclonal antibody for expression of CS protein epitopes. The resulting cDNA clone was used to isolate the CS protein gene from a lambda library containing parasite blood-stage DNA. The CS protein gene contains a central region encoding two types of tandemly repeated amino acid units, flanked by nonrepeated regions encoding amino- and carboxy-terminal signal and anchorlike sequences, respectively. One of the central repeated amino acid unit types contains the immunodominant epitopes.","Oligodeoxyribonucleotides,Genes,Amino Acid Sequence,Plasmodium berghei,Radioimmunoassay,Cloning, Molecular,DNA Restriction Enzymes,Antigens, Protozoan,Genes, Dominant,Epitopes,Antigens, Surface,Animals,Protozoan Proteins",NCBI,1986,Molecular and cellular biology,6,11,3965-72
15752424,"A new Apicomplexa-specific protein kinase family: multiple members in Plasmodium falciparum, all with an export signature.",http://www.biomedcentral.com/1471-2164/6/30,"BACKGROUND: Malaria caused by protozoan parasites of the genus Plasmodium spp. is a major health burden in tropical countries. The development of new control tools, including vaccines and drugs, is urgently needed. The availability of genome sequences from several malaria parasite species provides a basis on which to identify new potential intervention targets. Database mining for orthologs to the Plasmodium falciparum trophozoite protein R45, a vaccine candidate, led us identify a new gene family. RESULTS: Orthologs to the P. falciparum trophozoite protein R45 were detected exclusively in protozoan parasites of the phylum Apicomplexa, including several Plasmodium spp., Toxoplasma gondii and Cryptosporidium parvum. All family members are hybrid genes with a conserved C-terminal protein kinase domain of a novel type, recently called FIKK kinase, associated with a non conserved N-terminal region without any known functional signature. While a single copy gene was detected in most species, considerable gene expansion was observed in P. falciparum and its closest phylogenic relative P. reichenowi, with 20 and six copies, respectively, each with a distinct N-terminal domain. Based on full length protein sequence, pairs of orthologs were observed in closely related species, such as P. berghei and P.y. yoelii, P. vivax and P. knowlesi, or P. reichenowi and P. falciparum. All 20 P. falciparum paralogs possess a canonical Plasmodium export element downstream of a signal / anchor sequence required for exportation outside the parasitophorous vacuole. This is consistent with the reported association of the trophozoite protein R45, the only paralog characterised to date, with the infected red blood cell membrane. Interestingly, most genes are located in the subtelomeric region of chromosomes, in association with other multigene families contributing to the remodelling of the infected red blood cell membrane, in particular the ring erythrocyte surface antigen multigene family. CONCLUSION: This Apicomplexan-specific gene family was called R45-FIKK kinase. The family hallmark is a kinase domain with unusual characteristics, raising the possibility of designing drug or vaccine strategies targeting this domain. The characteristics of the P. falciparum family suggest a role in remodelling the infected cell and as such possibly contribute to the particular virulence of this species. Pasteur, Paris, France. Achim_Schneider1@gmx.net","Animals!Antigenic Variation!Antigens, Protozoan/chemistry/*physiology!Apicomplexa/*metabolism!Catalytic Domain!Chromosome Mapping!Conserved Sequence!Erythrocyte Membrane/metabolism!Erythrocytes/*parasitology!Humans!Models, Biological!Molecular Sequence Data!Multigene Family!Phylogeny!Plasmodium!Plasmodium falciparum/*metabolism!Plasmodium vivax/metabolism!Plasmodium yoelii/metabolism!Protein Kinases/*chemistry!Protein Structure, Tertiary!Protozoan Proteins/chemistry!Research Support, Non-U.S. Gov't!",scholar,2005,BMC Genomics,6,1,30
15760655,Implication of a Plasmodium falciparum gene in the switch between asexual reproduction and gametocytogenesis.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105000022&_version=1&_returnURL=&md5=5ef744c3fa735388521eea010cf1594a,"Gametocytogenesis is fundamental for transmission of the malaria parasite Plasmodium falciparum from the human host to the mosquito vector, yet very little is understood about what triggers the switch between asexual reproduction and gametocytogenesis. Arresting the progression through the sexual cycle would block transmission of this disease. Here we identify a novel gene in P. falciparum that when genetically silenced reduces gametocyte production by a factor of 6, and when complemented up-regulates gametocyte-specific gene transcription. Tropical Health and Nutrition, The Queensland Institute of Medical Research, 300 Herston Road, Herston, Qld 4006, Australia. dong@qimr.edu.au","Animals!Antigens, Protozoan/biosynthesis/metabolism!Blotting, Northern!Gametogenesis/genetics!*Genes, Protozoan!Genetic Complementation Test!Membrane Proteins/biosynthesis/metabolism!Plasmodium falciparum/genetics/*physiology!Reproduction, Asexual/genetics!Research Support, Non-U.S. Gov't!",scirus,2005,Molecular & Biochemical Parasitology,140,2,153
15763561,Variation and evolution of biomolecular systems: searching for functional relevance.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0014579305001699&_version=1&_returnURL=&md5=8548322a0c925949961e2d1e2801e003,"The availability of genome sequences and functional genomics data from multiple species enables us to compare the composition of biomolecular systems like biochemical pathways and protein complexes between species. Here, we review small- and large-scale, "genomics-based" approaches to biomolecular systems variation. In general, caution is required when comparing the results of bioinformatics analyses of genomes or of functional genomics data between species. Limitations to the sensitivity of sequence analysis tools and the noisy nature of genomics data tend to lead to systematic overestimates of the amount of variation. Nevertheless, the results from detailed manual analyses, and of large-scale analyses that filter out systematic biases, point to a large amount of variation in the composition of biomolecular systems. Such observations challenge our understanding of the function of the systems and their individual components and can potentially facilitate the identification and functional characterization of sub-systems within a system. Mapping the inter-species variation of complex biomolecular systems on a phylogenetic species tree allows one to reconstruct their evolution. Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9010, 6500 GL Nijmegen, The Netherlands. m.huynen@cmbi.kun.nl","*Evolution, Molecular!Multiprotein Complexes/*genetics!Phylogeny!Protein Binding/genetics!Variation (Genetics)!",scirus,2005,FEBS Letters,579,8,1839
15774020,Data mining of the transcriptome of Plasmodium falciparum: the pentose phosphate pathway and ancillary processes.,http://www.malariajournal.com/content/4/1/17,"The general paradigm that emerges from the analysis of the transcriptome of the malaria parasite Plasmodium falciparum is that the expression clusters of genes that code for enzymes engaged in the same cellular function is coordinated. Here the consistency of this perception is examined by analysing specific pathways that metabolically-linked. The pentose phosphate pathway (PPP) is a fundamental element of cell biochemistry since it is the major pathway for the recycling of NADP+ to NADPH and for the production of ribose-5-phosphate that is needed for the synthesis of nucleotides. The function of PPP depends on the synthesis of NADP+ and thiamine pyrophosphate, a co-enzyme of the PPP enzyme transketolase. In this essay, the transcription of gene coding for enzymes involved in the PPP, thiamine and NAD(P)+ syntheses are analysed. The genes coding for two essential enzymes in these pathways, transaldolase and NAD+ kinase could not be found in the genome of P. falciparum. It is found that the transcription of the genes of each pathway is not always coordinated and there is usually a gene whose transcription sets the latest time for the full deployment of the pathway's activity. The activity of PPP seems to involve only the oxidative arm of PPP that is geared for maximal NADP+ reduction and ribose-5-phosphate production during the early stages of parasite development. The synthesis of thiamine diphosphate is predicted to occur much later than the expression of transketolase. Later in the parasite cycle, the non-oxidative arm of PPP that can use fructose-6-phosphate and glyceraldehyde-3-phosphate supplied by glycolysis, becomes fully deployed allowing to maximize the production of ribose-5-phosphate. These discrepancies require direct biochemical investigations to test the activities of the various enzymes in the developing parasite. Notably, several transcripts of PPP enzyme-coding genes display biphasic pattern of transcription unlike most transcripts that peak only once during the parasite cycle. The physiological meaning of this pattern requires further investigation. Singapore. ZBozdech@ntu.edu.sg",,scirus,2005,Malaria Journal,4,1,17
15774027,The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1088945,"BACKGROUND: The uptake of nutrients, expulsion of metabolic wastes and maintenance of ion homeostasis by the intraerythrocytic malaria parasite is mediated by membrane transport proteins. Proteins of this type are also implicated in the phenomenon of antimalarial drug resistance. However, the initial annotation of the genome of the human malaria parasite Plasmodium falciparum identified only a limited number of transporters, and no channels. In this study we have used a combination of bioinformatic approaches to identify and attribute putative functions to transporters and channels encoded by the malaria parasite, as well as comparing expression patterns for a subset of these. RESULTS: A computer program that searches a genome database on the basis of the hydropathy plots of the corresponding proteins was used to identify more than 100 transport proteins encoded by P. falciparum. These include all the transporters previously annotated as such, as well as a similar number of candidate transport proteins that had escaped detection. Detailed sequence analysis enabled the assignment of putative substrate specificities and/or transport mechanisms to all those putative transport proteins previously without. The newly-identified transport proteins include candidate transporters for a range of organic and inorganic nutrients (including sugars, amino acids, nucleosides and vitamins), and several putative ion channels. The stage-dependent expression of RNAs for 34 candidate transport proteins of particular interest are compared. CONCLUSION: The malaria parasite possesses substantially more membrane transport proteins than was originally thought, and the analyses presented here provide a range of novel insights into the physiology of this important human pathogen. Australian National University, Canberra, ACT 0200, Australia. Rowena.Martin@anu.edu.au","Amino Acid Sequence!Amino Acid Transport Systems/genetics/metabolism!Animals!Computational Biology/methods!Equilibrative Nucleoside Transport Proteins/genetics/metabolism!Erythrocytes/parasitology!Genomics!Humans!Hydrophobicity!Ion Channels/genetics/metabolism!Malaria, Falciparum/parasitology!Membrane Transport Proteins/chemistry/*genetics/physiology!Molecular Sequence Data!Multigene Family/genetics/physiology!Plasmodium falciparum/*genetics/growth & development/metabolism!Protein Structure, Tertiary!Protozoan Proteins/chemistry/*genetics/physiology!RNA, Protozoan/metabolism!Research Support, Non-U.S. Gov't!Sequence Alignment!",scholar,2005,Genome Biology,2005,6,R26
15778902,"Structure and the evolutionary implication of the triplicated complement factor B genes of a urochordate ascidian, Ciona intestinalis.",http://www.springerlink.com/index/P96GKD54P7T51AJ1.pdf,"To elucidate the evolution of the complement system and MHC class III region, we analyzed the complement factor B (Bf) genes of a urochordate ascidian, Ciona intestinalis. Three different cDNA species, termed CiBf-1, CiBf-2 and CiBf-3, were identified. The deduced amino-acid sequences all contained the usual domains of vertebrate Bf and, in addition, three extra domains at the N-terminus. Furthermore, the serine protease domain of these CiBfs shared unique features with vertebrate complement components C1r/s and mannose-binding lectin-associated serine protease (MASP)-2/3, the absence of the disulfide bond designated histidine loop, and the usage of the AGY codon for the catalytic serine residue. These results indicate that complement genes have evolved through extensive exon shuffling events in the early stage of chordate evolution. Overall deduced amino-acid identity between CiBf-1 and -2 was 88%, whereas CiBf-3 showed 49% identity to both CiBf-1 and CiBf-2. These three CiBf genes were located within an approximately 50-kb genomic region, and exons 3 and 5 of all the three Bf genes showed an extremely high degree of nucleotide identity, indicating that the CiBf genes experienced extensive reorganization, such as duplication and gene conversion, since its divergence from the vertebrate Bf/C2 gene. Fluorescent in situ hybridization (FISH) to the chromosomes showed that genetic loci for the CiBfs, CiC3-1 and CiC3-2 genes are present on three different chromosomes, suggesting the possibility that the linkage among the MHC class III complement genes was established in the vertebrate lineage after its divergence from urochordates. University of Tokyo, Tokyo 113-0033, Japan.","Amino Acid Sequence!Animals!Base Sequence!Chromosome Mapping!Ciona intestinalis/*genetics/*immunology!Cloning, Molecular!Comparative Study!Complement Factor B/chemistry/*genetics!DNA, Complementary/genetics!*Evolution, Molecular!Exons!Female!Gene Conversion!*Gene Duplication!Gene Expression!Genome!In Situ Hybridization, Fluorescence!Linkage (Genetics)!Male!Molecular Sequence Data!Phylogeny!Protein Structure, Tertiary!RNA, Messenger/genetics/metabolism!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Species Specificity!Vertebrates/genetics/immunology!",scholar,2005,Immunogenetics,56,12,930
15792953,Cyanobacterial non-mevalonate pathway: (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase interacts with ferredoxin in Thermosynechococcus elongatus BP-1.,http://www.jbc.org/cgi/content/abstract/280/21/20672%3Fct,"(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE), which catalyzes the conversion of 2-C-methyl-D-erythritol cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP), is an essential enzyme of the non-mevalonate (2-C-methyl-D-erythritol-4-phosphate (MEP)) pathway for isoprenoid biosynthesis. The terminal steps of the MEP pathway are still not fully understood, although this pathway is necessary for survival in various organisms such as cyanobacteria, plastids of algae and higher plants, and the apicoplast of human malaria parasites. To determine the efficient redox partner for thermophilic cyanobacterial GcpE, We have expressed the gcpE and petF genes in Escherichia coli and studied the protein-protein interaction of GcpE protein with ferredoxin I (PetF) from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Recombinant GcpE protein was purified by an N-terminal His(6) tag and reconstituted as a [4Fe-4S](2+) metalloprotein. GcpE was shown to interact strongly with PetF via the bacterial two-hybrid system designed to detect protein-protein interactions. Moreover, a direct protein-protein interaction between PetF and GcpE was confirmed in an in vitro glutathione S-transferase (GST) pull-down assay. To investigate electron transfer activity from PetF to GcpE, we also constructed a NADPH-dependent reducing shuttle system with purified recombinant ferredoxin-NADP(+) oxidoreductase (PetH) and PetF. The result demonstrated that PetF has the ability to transfer electrons to GcpE. Thus, the combined data provide the first evidence that GcpE is a ferredoxin-dependent enzyme in T. elongatus BP-1. 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. okadak@protein.osaka-u.ac.jp","Alkyl and Aryl Transferases/*metabolism!Amino Acid Sequence!Animals!Arabidopsis/enzymology!Cloning, Molecular!Comparative Study!Cyanobacteria/*enzymology/metabolism!Electron Transport!Enzymes/chemistry/genetics/*metabolism!Escherichia coli/genetics!Ferredoxins/genetics/*metabolism!Gene Expression!Glutathione Transferase/genetics!Iron-Sulfur Proteins!Mevalonic Acid/metabolism!Molecular Sequence Data!NADP/metabolism!Plasmodium falciparum/enzymology!Recombinant Proteins!Sequence Alignment!Transformation, Bacterial!",scholar,2005,Journal of Biological Chemistry,280,21,20672
15797990,Antigenic variation in Plasmodium falciparum is associated with movement of var loci between subnuclear locations.,http://www.pnas.org/cgi/content/abstract/102/15/5414,"Much of the success of Plasmodium falciparum in establishing persistent infections is attributed to immune evasion through antigenic variation. This process involves periodically exchanging variants of the major surface antigen PfEMP1, a protein also responsible for parasite cytoadherence. PfEMP1 is encoded by genes of the 60-member var family, located at subtelomeric and internal chromosome loci. The active or silenced state of var genes is heritable, and its control by nonsequence information remains puzzling. Using FISH analysis, we demonstrate that both internal and subtelomeric var genes are positioned at the nuclear periphery in their repressed state. Upon activation, the same var genes are still found in the periphery, indicating that this zone can be transcriptionally competent, rather than uniformly silenced. However, activation of a var gene is linked with altered positioning at the nuclear periphery, with subtelomeric var loci exiting chromosome end clusters and being relocated to distinct nuclear sites. Serial sectioning of parasite nuclei reveals areas of both condensed and noncondensed chromatin at the nuclear periphery. Our results demonstrate that regulation of antigenic variation is associated with subnuclear position effects and point to the existence of transcriptionally permissive perinuclear zones for var genes. Recherche Associee 2581, 25 Rue du Docteur Roux, F-75724 Paris Cedex 15, France. America.","Animals!Antigenic Variation/*genetics!Cell Nucleus/*genetics/metabolism/ultrastructure!Gene Expression Regulation/*genetics!Gene Silencing!Genes, Protozoan/*genetics!In Situ Hybridization, Fluorescence!Models, Genetic!Plasmodium falciparum/cytology/*genetics/*immunology/ultrastructure!Protozoan Proteins/genetics!Research Support, Non-U.S. Gov't!Telomere/*genetics/metabolism!Transcription, Genetic/genetics!",scholar,2005,Proceedings of the National Academy of Sciences,102,15,5414
15819631,Broad analysis reveals a consistent pattern of var gene transcription in Plasmodium falciparum repeatedly selected for a defined adhesion phenotype.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2005.04577.x/abs/,"Transcription of the majority of the members of the Plasmodium falciparum var multigene family were analysed in two isolates by a quantitative approach. Both of these isolates had been repeatedly selected for adhesion to chondroitin sulphate A (CSA) and one had also been selected for adhesion to hyaluronic acid (HA). These adhesion phenotypes are expressed by many parasites isolated from placentae and are associated with malaria disease in pregnancy. Increased transcription of the var gene var2csa, or its homologue IT4 var4, was associated with the CSA and HA adhesion phenotypes in all parasites suggesting that it was the dominant, if not the only, var gene that encoded adhesion to CSA in these allogeneic isolates. Some var genes were consistently transcribed at higher levels than others regardless of expressed adhesion phenotypes suggesting a transcriptional hierarchy. Unspliced or partial transcripts were detected for most var genes tested. These atypical var gene transcripts may have implications for the regulation of var gene transcription. Parkville, Victoria, Australia. mduffy@unimelb.edu.au","Alternative Splicing!Animals!Cattle!Cell Adhesion!Chondroitin Sulfates/metabolism!Female!Gene Expression Regulation!Genes, Dominant!Hyaluronic Acid/metabolism!Malaria, Falciparum/parasitology!Multigene Family!Oligonucleotide Array Sequence Analysis/methods!Phenotype!Placenta/parasitology!Plasmodium falciparum/*cytology/*genetics!Pregnancy!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction/methods!Transcription, Genetic!*Variation (Genetics)!",scholar,2005,Molecular Microbiology,56,3,774
15820675,Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum.,http://www.biologie.uni-erlangen.de/bc/ckoch/SeminarSS2005/malaria2.pdf,"The malaria parasite Plasmodium falciparum undergoes antigenic variation to evade host immune responses through switching expression of variant surface proteins encoded by the var gene family. We demonstrate that both a subtelomeric transgene and var genes are subject to reversible gene silencing. Var gene silencing involves the SIR complex as gene disruption of PfSIR2 results in activation of this gene family. We also demonstrate that perinuclear gene activation involves chromatin alterations and repositioning into a location that may be permissive for transcription. Together, this implies that locus repositioning and heterochromatic silencing play important roles in the epigenetic regulation of virulence genes in P. falciparum. Australia.","Animals!Antigenic Variation/*genetics/immunology!Cell Compartmentation/*genetics/immunology!Cell Nucleus/genetics/immunology!Chromatin Assembly and Disassembly/*genetics!Chromosomes/genetics/immunology!Gene Silencing/*immunology!Genes, Protozoan/genetics/immunology!Heterochromatin/*genetics/immunology!Humans!In Situ Hybridization, Fluorescence!Malaria, Falciparum/genetics/*parasitology!Microarray Analysis!Plasmids/genetics/immunology!Plasmodium falciparum/*genetics/immunology/*pathogenicity!Research Support, Non-U.S. Gov't!Telomere/genetics!Tetrahydrofolate Dehydrogenase/genetics!Virulence/genetics!",scholar,2005,Cell,121,,13
15820676,Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites.,http://students.washington.edu/mdminer/pabio_551/campbell11.pdf,"Malaria parasites use antigenic variation to avoid immune clearance and increase the duration of infection in the human host. Variation at the surface of P. falciparum-infected erythrocytes is mediated by the differential control of a family of surface antigens encoded by var genes. Switching of var gene expression occurs in situ, mostly from telomere-associated loci, without detectable DNA alterations, suggesting that it is controlled by chromatin structure. We have identified chromatin modifications at telomeres that spread far into telomere-proximal regions, including var gene loci (>50 kb). One type of modification is mediated by a protein homologous to yeast Sir2 called PfSir2, which forms a chromosomal gradient of heterochromatin structure and histone hypoacetylation. Upon activation of a specific telomere-associated var gene, PfSir2 is removed from the promoter region and acetylation of histone occurs. Our data demonstrate that mutually exclusive transcription of var genes is linked to the dynamic remodeling of chromatin. 25, rue du Dr. Roux, 75724 Paris, France.","Animals!Antigenic Variation/*genetics!Cell Nucleolus/*genetics!Chromatin Immunoprecipitation!*Gene Silencing!Genes, Protozoan/genetics!Heterochromatin/*genetics!Histone Deacetylases/genetics!In Situ Hybridization, Fluorescence!Microscopy, Immunoelectron!Plasmodium falciparum/*genetics!Promoter Regions (Genetics)/genetics!Research Support, Non-U.S. Gov't!Saccharomyces cerevisiae/genetics!Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics!Sirtuins/genetics!Telomere/genetics!",scholar,2005,Cell,121,,25
15826641,Integration of tools and resources for display and analysis of genomic data for protozoan parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751905000500&_version=1&_returnURL=&md5=d401ce5fa367f8eb9499bf9bc6bb8143,"Centralisation of tools for analysis of genomic data is paramount in ensuring that research is always carried out on the latest currently available data. As such, World Wide Web sites providing a range of online analyses and displays of data can play a crucial role in guaranteeing consistency of in silico work. In this respect, the protozoan parasite research community is served by several resources, either focussing on data and tools for one species or taking a broader view and providing tools for analysis of data from many species, thereby facilitating comparative studies. In this paper, we give a broad overview of the online resources available. We then focus on the GeneDB project, detailing the features and tools currently available through it. Finally, we discuss data curation and its importance in keeping genomic data 'relevant' to the research community. Cambridge CB10 1SA, UK. maa@sanger.ac.uk","Animals!Computational Biology!*Databases, Genetic!*Genome, Protozoan!*Genomics!Information Storage and Retrieval!Online Systems!Research Support, Non-U.S. Gov't!",scirus,2005,International Journal for Parasitology,35,5,481
17253978,Plasmodium cysteine repeat modular proteins 1-4: complex proteins with roles throughout the malaria parasite life cycle.,,"The Cysteine Repeat Modular Proteins (PCRMP1-4) of Plasmodium, are encoded by a small gene family that is conserved in malaria and other Apicomplexan parasites. They are very large, predicted surface proteins with multipass transmembrane domains containing motifs that are conserved within families of cysteine-rich, predicted surface proteins in a range of unicellular eukaryotes, and a unique combination of protein-binding motifs, including a > 100 kDa cysteine-rich modular region, an epidermal growth factor-like domain and a Kringle domain. PCRMP1 and 2 are expressed in life cycle stages in both the mosquito and vertebrate. They colocalize with PfEMP1 (P. falciparum Erythrocyte Membrane Antigen-1) during its export from P. falciparum blood-stage parasites and are exposed on the surface of haemolymph- and salivary gland-sporozoites in the mosquito, consistent with a role in host tissue targeting and invasion. Gene disruption of pcrmp1 and 2 in the rodent malaria model, P. berghei, demonstrated that both are essential for transmission of the parasite from the mosquito to the mouse and has established their discrete and important roles in sporozoite targeting to the mosquito salivary gland. The unprecedented expression pattern and structural features of the PCRMPs thus suggest a variety of roles mediating host-parasite interactions throughout the parasite life cycle.",,NCBI,2007,,,,
15843145,Plasmodium falciparum glutaredoxin-like proteins.,http://www.extenza-eps.com/WDG/doi/ref/10.1515/BC.2005.005,"Glutaredoxin-like proteins form a new subgroup of glutaredoxins with a serine replacing the second cysteine in the CxxC-motif of the active site. Yeast Grx5 is the only glutaredoxin-like protein studied biochemically so far. We identified and cloned three genes encoding glutaredoxin-like proteins from the malaria parasite Plasmodium falciparum (Pf Glp1, Pf Glp2, and Pf Glp3) containing a conserved cysteine in the CGFS-, CKFS-, and CKYS-motif, respectively. Here, we describe biochemical properties of Pf Glp1 and Pf Glp2. Cys 99, the only cysteine residue in Pf Glp1, has a pK(a) value as low as 5.5 and is able to mediate covalent homodimerization. Monomeric and dimeric Pf Glp1 react with GSSG and GSH, respectively. Pf Glp2 is monomeric and both of its cysteine residues can be glutathionylated. Molecular models reveal a thioredoxin fold for the putative C-terminal domain of Pf Glp1, Pf Glp2, and Pf Glp3, as well as conserved residues presumably required for glutathione binding. However, Pf Glp1 and Pf Glp2 neither possess activity in a classical glutaredoxin assay nor display activity as glutathione peroxidase or glutathione S-transferase. Mutation of Ser 102 in the CGFS-motif of Pf Glp1 to cysteine did not generate glutaredoxin activity either. We conclude that, despite their ability to react with glutathione, glutaredoxin-like proteins are a mechanistically and functionally heterogeneous group with only little similarities to canonical glutaredoxins. Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.","Amino Acid Sequence!Animals!Comparative Study!Gene Expression Regulation!Models, Molecular!Molecular Sequence Data!Oxidoreductases/chemistry!Plasmodium falciparum/*enzymology!Protein Conformation!Protein Folding!Protein Structure, Tertiary!Proteins/*chemistry/genetics/isolation & purification!Recombinant Proteins/chemistry/genetics/isolation & purification!Research Support, Non-U.S. Gov't!Saccharomyces cerevisiae/genetics!Thioredoxin/chemistry!",scholar,2005,Biol. Chem,386,,33
15850701,A role for poly(dA)poly(dT) tracts in directing activity of the Plasmodium falciparum calmodulin gene promoter.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105000812&_version=1&_returnURL=&md5=15452c731c624dde5534cd004e07088f,"Expression of the Plasmodium falciparum calmodulin gene (pfcam) is developmentally regulated throughout the blood-stage cycle. The promoter lies within approximately 1 kb of intergenic sequence that separates the pfcam open reading frame (ORF) from an upstream inverted ORF encoding a product homologous to the co-chaperone STI1. Using the oligo-capping method, which selectively reverse-transcribes cDNA from only full-length, capped transcript, we have mapped multiple transcription-initiation sites for both genes. Transcription of the pfSTI1 gene initiates over a 150 bp region centred approximately 350 bp upstream of the ORF. The pfcam transcription start sites cluster into four approximately 30 bp regions lying within 180 bp upstream of the pfcam ORF, generating transcripts with 5' untranslated regions (UTR) of 3-173 nucleotides in length. Remarkably, splicing was found to be related to UTR length, with apparent preferential splicing of longer transcripts. Activity of the pfcam promoter diminished in a linear fashion to undetectable levels upon step-wise removal of sequence between 625 and 230 bp upstream of the start ATG. Electromobility-shift assays demonstrated nuclear factor binding to eight oligonucleotide probes spanning 657 bp of the pfcam ORF proximal upstream sequence. The degree of binding correlated with the density of poly(dA)poly(dT) tracts within the probes, and in all cases could be inhibited by excess synthetic poly(dA)poly(dT), but not by poly(dAdT)poly(dAdT). The multiple transcription-initiation sites of both pfSTI1 and pfcam genes lie just downstream of 25 bp-long poly(dA)poly(dT) tracts, and the intergenic region contains over 20 poly(dA)poly(dT) tracts of 4 bp or more. Our results suggest that the basal pfcam promoter is situated between approximately -300 and -230 bp upstream of the pfcam ORF and that the P. falciparum transcription-initiation complex has a low degree of sequence-specificity for the sites of initiation but preferentially acts downstream of long poly(dA)poly(dT) tracts. Hill, London NW7 1AA, UK.","5' Untranslated Regions!Animals!Calmodulin/*genetics!DNA, Intergenic!*Gene Expression Regulation!Plasmodium falciparum/*genetics/metabolism!Polydeoxyribonucleotides/*metabolism!Promoter Regions (Genetics)/*physiology!Protozoan Proteins/genetics!RNA Processing, Post-Transcriptional!Research Support, Non-U.S. Gov't!Sequence Deletion!Transcription Initiation Site!",scirus,2005,Molecular & Biochemical Parasitology,141,2,179
15853885,A role for the Plasmodium falciparum RESA protein in resistance against heat shock demonstrated using gene disruption.,http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2005.04603.x,"During erythrocyte invasion, the Plasmodium falciparum Ring-infected erythrocyte surface antigen (RESA) establishes specific interactions with spectrin. Based on analysis of strains with a large chromosome 1 deletion, RESA has been assigned several functions, none of which is firmly established. Analysis of parasites with a disrupted resa1 gene and isogenic parental or resa3-disrupted controls confirmed the critical role of RESA in the surface reactivity of immune adult sera on glutaraldehyde-fixed ring stages. Absence of RESA did not influence merozoite invasion or erythrocyte membrane rigidity, was associated with a modest increase of cytoadhesion to CD36 under conditions of flow, but resulted in marked susceptibility to heat shock. resa1-KO-infected erythrocytes were prone to heat-induced vesiculation like uninfected erythrocytes, whereas parental or resa3-KO infected erythrocytes remained undamaged. Furthermore, a 6 h exposure of ring stages at 41 degrees C resulted in 33% culture inhibition of resa1-KO parasites while marginally impacting parental and resa3-KO parasite growth. This points to a role for RESA in protecting the infected erythrocyte cytoskeleton during febrile episodes. Infection patterns of resa1-KO and parental parasites in Saimiri sciureus indicated that RESA does not, at least on its own, modulate virulence in the squirrel monkey, as had been previously suggested. de Parasitologie, Institut Pasteur, Paris, France. falciparum)","Animals!Animals, Genetically Modified!Antigens, CD36/metabolism!Antigens, Protozoan/genetics/metabolism!Cell Shape!Cytoskeleton/metabolism!Erythrocytes/cytology/parasitology!*Heat!Humans!Malaria, Falciparum!*Mutation!Plasmodium falciparum/genetics/*metabolism!Protozoan Proteins/*genetics/*metabolism!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Saimiri/parasitology!",scholar,2005,Molecular Microbiology,56,4,990
15857512,Expression of Plasmodium falciparum erythrocyte membrane protein 1 in experimentally infected humans.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1112614,"BACKGROUND: Parasites causing severe malaria in non-immune patients express a restricted subset of variant surface antigens (VSA), which are better recognized by immune sera than VSA expressed during non-severe disease in semi-immune individuals. The most prominent VSA are the var gene-encoded Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family, which is expressed on the surface of infected erythrocytes where it mediates binding to endothelial receptors. Thus, severe malaria may be caused by parasites expressing PfEMP1 variants that afford parasites optimal sequestration in immunologically naive individuals and high effective multiplication rates. METHODS: var gene transcription was analysed using real time PCR and PfEMP1 expression by western blots as well as immune plasma recognition of parasite cultures established from non-immune volunteers shortly after infection with NF54 sporozoites. RESULTS: In cultures representing the first generation of parasites after hepatic release, all var genes were transcribed, but Group A var genes were transcribed at the lowest levels. In cultures established from second or third generation blood stage parasites of volunteers with high in vivo parasite multiplication rates, the var gene transcription pattern differed markedly from the transcription pattern of the cultures representing first generation parasites. This indicated that parasites expressing specific var genes, mainly belonging to group A and B, had expanded more effectively in vivo compared to parasites expressing other var genes. The differential expression of PfEMP1 was confirmed at the protein level by immunoblot analysis. In addition, serological typing showed that immune sera more often recognized second and third generation parasites than first generation parasites. CONCLUSION: In conclusion, the results presented here support the hypothesis that parasites causing severe malaria express a subset of PfEMP1, which bestows high parasite growth rates in individuals with limited pre-existing immunity. Immunology, University of Copenhagen, Panum Institute 24-2, Blegdamsvej 3, 2200 Copenhagen N, Denmark. thomaslavstsen@vip.cybercity.dk",,scholar,2005,Malaria Journal,2005,4,21
15864297,A mitogen-activated protein kinase regulates male gametogenesis and transmission of the malaria parasite Plasmodium berghei.,,"Differentiation of malaria parasites into sexual forms (gametocytes) in the vertebrate host and their subsequent development into gametes in the mosquito vector are crucial steps in the completion of the parasite's life cycle and transmission of the disease. The molecular mechanisms that regulate the sexual cycle are poorly understood. Although several signal transduction pathways have been implicated, a clear understanding of the pathways involved has yet to emerge. Here, we show that a Plasmodium berghei homologue of Plasmodium falciparum mitogen-activated kinase-2 (Pfmap-2), a gametocyte-specific mitogen-activated protein kinase (MAPK), is required for male gamete formation. Parasites lacking Pbmap-2 are competent for gametocytogenesis, but exflagellation of male gametocytes, the process that leads to male gamete formation, is almost entirely abolished in mutant parasites. Consistent with this result, transmission of mutant parasites to mosquitoes is grossly impaired. This finding identifies a crucial role for a MAPK pathway in malaria transmission. Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.","Animals!Anopheles/parasitology!Cloning, Molecular!Female!Flagella/physiology!Gametogenesis/genetics/*physiology!Host-Parasite Relations!Insect Vectors!MAP Kinase Signaling System/*physiology!Malaria/parasitology/transmission!Male!Mice!Mitogen-Activated Protein Kinase 1/genetics/*physiology!Plasmodium berghei/genetics/metabolism/*physiology!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scholar,,,,,
15895988,2.3 A crystal structure of tetanus neurotoxin light chain.,http://atb.slac.stanford.edu/public/papers.php%3Fsendfile%3D177,"TeNT is the causative agent of the neuroparalytic disease tetanus. A key component of TeNT is its light chain, a Zn(2+) endopeptidase that targets SNAREs. Recent structural studies of closely related BoNT endopeptidases indicate that substrate-binding exosites remote from a conserved active site are the primary determinants of substrate specificity. Here we report the 2.3 A X-ray crystal structure of TeNT-LC, determined by combined molecular replacement and MAD phasing. As expected, the overall structure of TeNT-LC is similar to the other known CNT light chain structures, including a conserved thermolysin-like core inserted between structurally distinct amino- and carboxy-terminal regions. Differences between TeNT-LC and the other CNT light chains are mainly limited to surface features such as unique electrostatic potential profiles. An analysis of surface residue conservation reveals a pattern of relatively high variability matching the path of substrate binding around BoNT/A, possibly serving to accommodate the variations in different SNARE targets of the CNT group. Stanford, California 94305, USA.","Amino Acid Sequence!Comparative Study!Crystallization!Crystallography, X-Ray!Electrostatics!Metalloendopeptidases/*chemistry/metabolism!Models, Molecular!Molecular Sequence Data!Nerve Tissue Proteins/chemistry/metabolism!Protein Binding!Protein Subunits/*chemistry/metabolism!Research Support, N.I.H., Extramural!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!SNARE Proteins!Substrate Specificity!Tetanus Toxin/*chemistry/metabolism!Thermolysin/chemistry!Vesicular Transport Proteins/chemistry/metabolism!",scholar,2005,Biochemistry,44,20,7450
15899528,Biochemical characterization of the two nucleosome assembly proteins from Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001362&_version=1&_returnURL=&md5=b8b1507dd89f78109b2079f51fee4eb2,"The human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins, which we have termed PfNAPS and PfNAPL. We have over-expressed, purified and characterized these proteins using biochemical and biophysical techniques. PfNAPS and PfNAPL exist as dimers in solution and circular dichroism studies suggest that they may have different three-dimensional protein structures. ELISA-based binding data also suggest that PfNAPS and PfNAPL preferentially interact with the H3-H4 tetramer histones over H2A and H2B histones. We show that the parasite lysate phosphorylates only PfNAPL and this phosphorylation can be inhibited by heparin suggesting a potential role of casein kinase II in this process. Immuno-fluorescence experiments revealed that both PfNAPS and PfNAPL were expressed in all erythrocytic stages of the parasite. PfNAPL was predominantly localised in the cytoplasm in asexual and sexual stages of the parasite. PfNAPS did not co-localise with PfNAPL and was more intimately associated with the parasite nucleus, most strikingly in P. falciparum gametocytes. Taken together, our data show that although PfNAPS and PfNAPL share histone chaperone acitivities, they are regulated differently by phosphorylation and are spatially segregated within the parasite. These proteins are therefore likely to play non-redundant roles as nucleosome assembly motors in the parasite. Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.","Animals!Chromatin Assembly and Disassembly!Circular Dichroism!Dimerization!Enzyme-Linked Immunosorbent Assay!Fluorescent Antibody Technique!Gene Expression Regulation!Histones/*metabolism!Humans!Nucleosomes/*metabolism!Phosphorylation!Plasmodium falciparum/genetics/*metabolism/physiology!Protozoan Proteins/*metabolism!Recombinant Proteins/genetics/metabolism!Research Support, Non-U.S. Gov't!",scirus,2005,Molecular & Biochemical Parasitology,142,2,237
15899703,Labelling of four distinct trophozoite falcipains of Plasmodium falciparum by a cystatin-derived probe.,http://www.extenza-eps.com/WDG/doi/ref/10.1515/BC.2005.048,"Trophozoite cysteine protease (TCP) activity, isolated from Plasmodium falciparum soluble 100,000 g extracts, displayed native falcipain-1 kinetic parameters towards peptidyl substrates. The labelling of either isolated TCP or soluble 100,000 g extracts by a cystatin-derived probe (biotinyl-Leu-Val-Gly-CHN2) revealed a single band of ca. 30 kDa by SDS-PAGE, which was resolved into four spots displaying isoelectric points (pI) from 4.7 to 5.3 after two-dimensional separation. The molecular mass and pI correspond to those of falcipain-3, falcipain-2, falcipain-2' and falcipain-1, respectively. The two central spots were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry as falcipain-2 and falcipain-2'. This activity-based probe represents a potential tool for profiling active falcipains in parasites. Developement, Diversite Moleculaire, Museum National d'Histoire Naturelle, 61, rue Buffon, F-75005 Paris, France. florent@mnhn.fr","Animals!Cystatins/analysis/*metabolism!Cysteine Endopeptidases/analysis/*metabolism!Molecular Probes/*metabolism!Peptide Fragments/analysis/metabolism!Plasmodium falciparum/*enzymology/*growth & development!Research Support, Non-U.S. Gov't!",scholar,2005,Biol. Chem,386,,401
15908211,Three-dimensional structure of Plasmodium falciparum Ca2+ -ATPase(PfATP6) and docking of artemisinin derivatives to PfATP6.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0960894X05005238&_version=1&_returnURL=&md5=087ea4eafd3880f49bda74e4bd631dca,Construction of the 3D structure of PfATP6 by homology modeling and docking simulation of artemisinin derivatives to this protein model are reported. Docking and consequent LUDI scores show good relation with in vitro antimalarial activities. The main binding source of artemisinins to the PfATP6 is hydrophobic interaction and biologically important peroxide bonds were exposed to outside of the binding pocket. This study suggests binding of artemisinin to PfATP6 precedes activation of peroxide bond by Fe(2+) species. mjung@yonsei.ac.kr,"Amino Acid Sequence!Animals!Anti-Infective Agents/chemistry/metabolism!Artemisia!Artemisinins/*chemistry/*metabolism!Ca(2+)-Transporting ATPase/*chemistry/*metabolism!Computer Simulation!Hemin/metabolism!Ligands!Models, Molecular!Molecular Sequence Data!Molecular Structure!Peroxides/chemistry/metabolism!Plasmodium falciparum/*enzymology!Protein Binding!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Sesquiterpenes/*chemistry/*metabolism!Structure-Activity Relationship!Thapsigargin/metabolism!",scirus,2005,Bioorganic & Medicinal Chemistry Letters,15,12,2994
15913633,Apicomplexan rhomboids have a potential role in microneme protein cleavage during host cell invasion.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0020751905001268&_version=1&_returnURL=&md5=178985088d6d7a19c6531086d9a025a8,"Apicomplexan parasites secrete transmembrane (TM) adhesive proteins as part of the process leading to host cell attachment and invasion. These microneme proteins are cleaved in their TM domains by an unidentified protease termed microneme protein protease 1 (MPP1). The cleavage site sequence (IA downward arrowGG), mapped in the Toxoplasma gondii microneme proteins TgMIC2 and TgMIC6, is conserved in microneme proteins of other apicomplexans including Plasmodium species. We report here the characterisation of novel T. gondii proteins belonging to the rhomboid family of intramembrane-cleaving serine proteases. T. gondii possesses six genes encoding rhomboid-like proteins. Four are localised along the secretory pathway and therefore constitute possible candidates for MPP1 activity. Toxoplasma rhomboids TgROM1, TgROM2 and TgROM5 cleave the TM domain of Drosophila Spitz, an established substrate for rhomboids from several species, demonstrating that they are active proteases. In addition, TgROM2 cleaves chimeric proteins that contain the TM domains of TgMIC2 and TgMIC12. Fleming Building, South Kensington Campus, London SW7 2AZ, UK.","Animals!Blotting, Western/methods!Cell Adhesion Molecules/genetics/*metabolism!Drosophila Proteins/metabolism!Enzyme Activation!Fluorescent Antibody Technique, Indirect!Membrane Proteins/genetics/metabolism!Microscopy, Confocal!Protozoan Proteins/genetics/*metabolism!Research Support, Non-U.S. Gov't!Serine Endopeptidases/metabolism!Toxoplasma/*metabolism!Toxoplasmosis/*metabolism/transmission!",scirus,2005,International Journal for Parasitology,35,7,747
15913804,The spermidine synthase of the malaria parasite Plasmodium falciparum: molecular and biochemical characterisation of the polyamine synthesis enzyme.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001349&_version=1&_returnURL=&md5=f8f3e34d6052657afa0493e93d2db2a3,"The gene encoding spermidine synthase was cloned from the human malaria parasite Plasmodium falciparum. Northern and Western blot analyses revealed a stage specific expression during the erythrocytic schizogony with the maximal amount of transcript and protein in mature trophozoites. Immunofluorescence assays (IFAs) suggest a cytoplasmatic localisation of the spermidine synthase in P. falciparum. The spermidine synthase polypeptide of 321 amino acids has a molecular mass of 36.6kDa and contains an N-terminal extension of unknown function that, similarly, is also found in certain plants but not in animal or bacterial orthologues. Omitting the first 29 amino acids, a truncated form of P. falciparum spermidine synthase has been recombinantly expressed in Escherichia coli. The enzyme catalyses the transfer of an aminopropyl group from decarboxylated S-adenosylmethionine (dcAdoMet) onto putrescine with Km values of 35 and 52microM, respectively. In contrast to mammalian spermidine synthases, spermidine can replace to some extent putrescine as the aminopropyl acceptor. Hence, P. falciparum spermidine synthase has the capacity to catalyse the formation of spermine that is found in small amounts in the erythrocytic stages of the parasite. Among the spermidine synthase inhibitors tested against P. falciparum spermidine synthase, trans-4-methylcyclohexylamine (4MCHA) was found to be most potent with a Ki value of 0.18microM. In contrast to the situation in mammals, where inhibition of spermidine synthase has no or only little effect on cell proliferation, 4MCHA was an efficient inhibitor of P. falciparum cell growth in vitro with an IC50 of 35microM, indicating that P. falciparum spermidine synthase represents a putative drug target. D-20359 Hamburg, Germany. inhibitors/chemistry/genetics/metabolism","Amino Acid Sequence!Animals!Cloning, Molecular!Erythrocytes/*parasitology!Escherichia coli/enzymology/genetics!Humans!Kinetics!Molecular Sequence Data!Plasmodium falciparum/*enzymology/genetics/*growth & development!Research Support, Non-U.S. Gov't!Spermidine/biosynthesis!*Spermidine Synthase/antagonists &!Spermine/biosynthesis!",scirus,2005,Molecular & Biochemical Parasitology,142,2,224
15924221,Genes coding for tryptophan-rich proteins are transcribed throughout the asexual cycle of Plasmodium falciparum.,http://www.springerlink.com/index/W4R225G2M7X667K1.pdf,"Multigene families are a common feature in Plasmodia spp. and constitute a substantial content of the parasite genome. Here, we analyse the structural organisation and sequence diversity of two further members of the Trp-rich multigene family of P. falciparum. The complete DNA sequence of both genes was determined from a series of laboratory adapted and field isolates. Based on the amino acid sequences, we have termed them tryptophan-rich antigen-3 (TrpA-3) and lysine-tryptophan-rich antigen (LysTrpA). Analysis of the genes using reverse transcriptase-polymerase chain reaction (RT-PCR), showed that both genes are transcribed and that introns are spliced out at predicted positions. Gene expression profiles obtained from microarray analysis indicate that both genes are expressed in the mid-stages of the asexual cycle. In-frame stop codons were detected which interrupted the reading frame of LysTrpA. Whereas the number of the Trp-rich proteins is rather low in P. falciparum, P. chabaudi, P. berghei and P. yoelii, this family seems to have 15 or more members in P. knowlesi and P. vivax. 27, 72074 Tubingen, Germany.","Amino Acid Sequence!Animals!DNA, Protozoan/analysis!Molecular Sequence Data!Nuclear Proteins/*genetics/metabolism!Plasmodium falciparum/*genetics/metabolism!Protozoan Proteins/*genetics!RNA, Protozoan/analysis!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!*Tryptophan!",scholar,2005,Parasitology Research,96,6,347
15926202,Organelle-specific cochaperonins in apicomplexan parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105000435&_version=1&_returnURL=&md5=83425c8d2b5391f8a5774bdaa8cfd81e,"Protein maturation in eukaryotic organelles requires the type I chaperonin system; this comprises chaperonin 60 (Cpn60) and its cochaperonin. We have re-examined and revised the sequence of the nuclear genes specifying organellar cochaperonins in Plasmodium falciparum (Pf). One gene encodes a typical cochaperonin (PfCpn10) whereas the other (encoding PfCpn20) specifies two Cpn10 domains arranged in tandem as in plant chloroplasts. Transfection experiments using fluorescent reporters showed specific localization of PfCpn10 to the mitochondrion and PfCpn20 to the plastid. As P. falciparum also has two Cpn60s, one of which is targeted specifically to the mitochondrion and the other exclusively to the plastid, each organelle has a distinct type I chaperonin system. Comparative sequence analysis extended these findings to several other apicomplexan parasites that have both a mitochondrion and a plastid. Phylogenetic analysis suggests the Cpn10s and Cpn20s of apicomplexans are independently monophyletic. The apicomplexan Cpn10 is phylogenetically related to other mitochondrial versions but a significant relationship between apicomplexan Cpn20s and other cochaperonins was not established. Ridgeway, Mill Hill, London NW7 1AA, UK. ssato@nimr.mrc.ac.uk","Amino Acid Sequence!Animals!Apicomplexa/chemistry/*genetics/metabolism!Chaperonins/*analysis/chemistry/*genetics!Cloning, Molecular!DNA, Protozoan/chemistry!Genes, Protozoan!Green Fluorescent Proteins/analysis/genetics!Mitochondria/chemistry!Molecular Sequence Data!Organelles/*chemistry!Phylogeny!Plasmodium falciparum/chemistry/*genetics/ultrastructure!Protein Structure, Tertiary!Research Support, Non-U.S. Gov't!Sequence Alignment!Sequence Analysis, DNA!Sequence Homology, Amino Acid!",scirus,2005,Molecular & Biochemical Parasitology,141,2,133
15926203,The plastidic DNA replication enzyme complex of Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105000551&_version=1&_returnURL=&md5=303135101a94c254047904d7242e37d0,"The replication and repair of organellar genomes in the malaria parasite Plasmodium falciparum is poorly understood. We have assessed the properties of an open reading frame Pfprex (formerly known as pom1) and confirm that it specifies a multi-domain polypeptide with DNA primase, DNA helicase, DNA polymerase and 3'-5' exonuclease activities. The sequence of the primase/helicase domain is phylogenetically related to the T7-bacteriophage gene 4 product and mammalian mitochondrial helicase, Twinkle. Despite that, the N-terminal sequence of this multi-domain polypeptide directs a green fluorescent protein reporter specifically to the P. falciparum apicoplast and not to the mitochondrion. Phylogenetic analysis placed the DNA polymerase sequence with the family A bacterial polymerases, most closely to those of the thermophilic Aquifex species. Notably, the malarial enzyme was optimally active at 75 degrees C. Pfprex is the first example of a gene encoding contiguous DNA polymerase, DNA primase and DNA helicase components. We propose it has a key role in replication of the malarial plastid genome, a validated drug target. Immunity, University of Glasgow, Glasgow G12 8QQ, UK.","Animals!DNA Helicases/chemistry/genetics/metabolism!DNA Polymerase III/chemistry/genetics/metabolism!DNA Primase/chemistry/genetics/metabolism!*DNA Replication!Exonucleases/chemistry/genetics/metabolism!Genes, Protozoan!Genes, Reporter!Green Fluorescent Proteins/analysis/genetics!Multienzyme Complexes/chemistry/*genetics/metabolism!Organelles/genetics/*metabolism!Phylogeny!Plasmodium falciparum/*enzymology/genetics!Protein Structure, Tertiary!Protein Transport!Protozoan Proteins/chemistry/*genetics/metabolism!Research Support, Non-U.S. Gov't!Sequence Homology!",scirus,2005,Molecular & Biochemical Parasitology,141,2,145
15935755,Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology.,http://www.cmdr.ubc.ca/trainingprogram/papers/jp_Medi_Nov%252021b_05.pdf,"Gametocytes, the precursor cells of malaria-parasite gametes, circulate in the blood and are responsible for transmission from host to mosquito vector. The individual proteomes of male and female gametocytes were analyzed using mass spectrometry, following separation by flow sorting of transgenic parasites expressing green fluorescent protein, in a sex-specific manner. Promoter tagging in transgenic parasites confirmed the designation of stage and sex specificity of the proteins. The male proteome contained 36% (236 of 650) male-specific and the female proteome 19% (101 of 541) female-specific proteins, but they share only 69 proteins, emphasizing the diverged features of the sexes. Of all the malaria life-cycle stages analyzed, the male gametocyte has the most distinct proteome, containing many proteins involved in flagellar-based motility and rapid genome replication. By identification of gender-specific protein kinases and phosphatases and using targeted gene disruption of two kinases, new sex-specific regulatory pathways were defined. Netherlands.","Animals!Chromatography, Liquid!Female!Flow Cytometry!Genes, Reporter!Male!Mitogen-Activated Protein Kinase 1/genetics/metabolism!Plasmodium berghei/enzymology/genetics/*physiology!Promoter Regions (Genetics)!Protein Kinases/genetics/*metabolism!*Proteome!Protozoan Proteins!Research Support, Non-U.S. Gov't!*Sex Determination (Genetics)!Spectrum Analysis, Mass!",scholar,2005,Cell,121,,675
15936248,Comparative folate metabolism in humans and malaria parasites (part II): activities as yet untargeted or specific to Plasmodium.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492205001248&_version=1&_returnURL=&md5=a5160b7b0080aacb1eaff023aa2354d7,"The folate pathway represents a powerful target for combating rapidly dividing systems such as cancer cells, bacteria and malaria parasites. Whereas folate metabolism in mammalian cells and bacteria has been studied extensively, it is understood less well in malaria parasites. In two articles, we attempt to reconstitute the malaria folate pathway based on available information from mammalian and microbial systems, in addition to Plasmodium-genome-sequencing projects. In part I, we focused on folate enzymes that are already used clinically as anticancer drug targets or that are under development in drug-discovery programs. In this article, we discuss mammalian folate enzymes that have not yet been exploited as potential drug targets, and enzymes that function in the de novo folate-synthesis pathway of the parasite--a particularly attractive area of attack because of its absence from the mammalian host. Program, Wellcome Trust Research Laboratories, PO Box 43640, Nairobi GPO 00100, Kenya. anzila@wtnairobi.mimcom.net","Animals!Antimalarials/pharmacokinetics/*pharmacology!Comparative Study!*Drug Design!Folic Acid/*metabolism!Humans!Malaria/drug therapy/*metabolism!Plasmodium/*metabolism!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scirus,2005,Trends in Parasitology,21,7,334
15939796,SURFIN is a polymorphic antigen expressed on Plasmodium falciparum merozoites and infected erythrocytes.,http://www.jem.org/cgi/content/abstract/201/11/1853,"The surfaces of the infected erythrocyte (IE) and the merozoite, two developmental stages of malaria parasites, expose antigenic determinants to the host immune system. We report on surface-associated interspersed genes (surf genes), which encode a novel polymorphic protein family, SURFINs, present on both IEs and merozoites. A SURFIN expressed in 3D7 parasites, SURFIN4.2, was identified by mass spectrometric analysis of peptides cleaved off the surface of live IEs with trypsin. SURFINs are encoded by a family of 10 surf genes, including three predicted pseudogenes, located within or close to the subtelomeres of five of the chromosomes. SURFINs show structural and sequence similarities with exported surface-exposed proteins (PvSTP1, PkSICAvar, PvVIR, Pf332, and PfEMP1) of several Plasmodium species. SURFIN4.2 of a parasite other than 3D7 (FCR3S1.2) showed polymorphisms in the extracellular domain, suggesting sequence variability between genotypes. SURFIN4.2 not only was found cotransported with PfEMP1 and RIFIN to the IE surface, but also accumulated in the parasitophorous vacuole. In released merozoites, SURFIN4.2 was present in an amorphous cap at the parasite apex, where it may be involved in the invasion of erythrocytes. By exposing shared polymorphic antigens on IEs and merozoites, the parasite may coordinate the antigenic composition of these attachment surfaces during growth in the bloodstream. Stockholm, Sweden.","Animals!Antigens, Protozoan/*biosynthesis/genetics/immunology!Cells, Cultured!Erythrocytes/immunology/*metabolism/parasitology!*Gene Expression Regulation/immunology!Genes, Protozoan/genetics/*immunology!Genotype!Host-Parasite Relations/genetics/immunology!Humans!Malaria, Falciparum/genetics/immunology/*metabolism!Membrane Proteins/*biosynthesis/immunology!Plasmodium falciparum/immunology/*metabolism!Polymorphism, Genetic/immunology!Research Support, Non-U.S. Gov't!Vacuoles/genetics/immunology/metabolism!",scholar,,Journal of Experimental Medicine,,,
15950069,Model of the TBP-TFIIB complex from Plasmodium falciparum: interface analysis and perspectives as a new target for antimalarial design.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0188440905000937&_version=1&_returnURL=&md5=eb5c2996b4c3fe0a6b160643cd7ac993,"BACKGROUND: Malaria affects 200-300 million individuals per year worldwide. Plasmodium falciparum is the causative agent of the most severe and mortal type of malaria. The need for new antimalarials comes from the widespread resistance to those in current use. New antimalarial targets are required to increase chemical diversity and effectiveness of the drugs. The research for such new targets and drug chemotypes is aided by structure-based drug design. We present a model of the TBP-TFIIB complex from P. falciparum (pfTBP-pfTFIIB) and a detailed study of the interactions at the TBP-TFIIB interface. METHODS: The model was built using standard methodology, optimized energetically and evaluated structurally. We carried out an analysis of the interface considering its evolution, available experimental data on TBP and TFIIB mutants, and the main conserved and non-conserved interactions. To support the perspective of using this complex as a new target for rational antimalarial design, we present the comparison of the pfTBP-pfTFIIB interface with its human homolog. RESULTS: Despite the high residue conservation at the interface, we identified a potential region, composed of species-specific residues that can be used for rational antimalarial design. CONCLUSIONS: Currently there are no antimalarial drugs targeted to stop the nuclear transcription process, a vital event for all replication stages of P. falciparum. Due to its absolute requirement in transcription initiation, we consider the pfTBP-pfTFIIB interface as a new potential target for novel antimalarial chemotypes. Universidad Autonoma del Estado de Morelos, Morelos, Mexico.","Amino Acid Sequence!Animals!Antimalarials/*pharmacology!Cell Nucleus/metabolism!Crystallography, X-Ray!Evolution, Molecular!Humans!Hydrogen Bonding!Models, Molecular!Molecular Sequence Data!Mutation!Open Reading Frames!Phosphoric Acid Esters/*chemistry!Plasmodium falciparum/*metabolism!Protein Binding!Protein Conformation!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Transcription Factor TFIIB/*chemistry!Transcription, Genetic!",scirus,2005,Archives of Medical Research,36,4,317
15953647,Apical expression of three RhopH1/Clag proteins as components of the Plasmodium falciparum RhopH complex.,http://www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26list_uids%3D15953647%26dopt%3DCitation,"The Plasmodium falciparum high molecular mass rhoptry protein ('PfRhopH') complex is important for parasite growth and comprises three distinct gene products: RhopH1, RhopH2 and RhopH3. We have previously shown that P. falciparum RhopH1 is encoded by either PFC0110w (clag3.2) or PFC0120w (clag3.1), members of the previously-named clag (cytoadherence-linked asexual gene) multigene family. In this report, we have further characterized rhoph1/clag members in terms of gene structure, transcription and protein expression. The cDNA sequences for all five rhoph1/clag members were determined, confirming previous in silico predictions of intron-exon boundaries. All member genes were transcribed in HB3 and 3D7 parasite lines, but clag3.2 was not transcribed in Dd2 parasites. The peak abundance of transcripts for all genes was observed during the late schizont stage. Antisera specific to Clag2 and Clag3.1 localized these proteins to the apical end of merozoites in segmented schizonts, and both proteins are found to be components of the PfRhopH complex. PfRhopH complex that was immunoprecipitated with anti-Clag9 antibody contained neither Clag2 nor Clag3.1, thereby suggesting that PfRhopH complexes contain only individual rhoph1/clag gene products. Since the PfRhopH complex binds the erythrocyte surface, and RhopH2 and RhopH3 are encoded by single copy genes, the RhopH1/Clag proteins may serve to confer some degree of specificity to the roles of the individual complexes. Toon, Shigenobu-cho, Ehime 791-0295, Japan. okaneko@m.ehime-u.ac.jp","Animals!Base Sequence!Chromosome Mapping!Cloning, Molecular!Crosses, Genetic!DNA, Protozoan/genetics!Macromolecular Substances!Plasmodium falciparum/*genetics!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!",scholar,2005,Mol Biochem Parasitol,,,
15960857,AutoFACT: an automatic functional annotation and classification tool.,http://www.biomedcentral.com/1471-2105/6/151,"BACKGROUND: Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. RESULTS: We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1-2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. CONCLUSION: AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm. Montreal, Montreal, Quebec, Canada. lkoski@bch.umontreal.ca","Acanthamoeba castellanii/classification/genetics!Animals!Computational Biology/methods!Contig Mapping/instrumentation/methods!DNA, Complementary/analysis!Databases, Genetic!*Expressed Sequence Tags!Humans!Information Management/*methods!Internet!Phylogeny!Plasmodium falciparum/classification/genetics!Research Support, Non-U.S. Gov't!Rickettsia prowazekii/classification/genetics!Saccharomyces cerevisiae/classification/genetics!Sequence Alignment/methods!Sequence Analysis, DNA/instrumentation/*methods!*Software!Software Validation!",scirus,2005,BMC Bioinformatics,6,1,151
15969766,Molecular analysis of two local falciparum malaria outbreaks on the French Guiana coast confirms the msp1 B-K1/varD genotype association with severe malaria.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1187918,"BACKGROUND: Plasmodium falciparum outbreaks can occur in the coastal area of French Guiana, where the population is essentially non-immune. Two sporadic outbreaks were observed, including one with severe malaria cases. To characterize these outbreaks and verify previous observations of specific genotype characteristics in severe malaria in this area, all cases from each outbreak were studied. METHODS: P. falciparum genotypes for six genetic loci were determined by PCR amplification from peripheral blood parasites. The msp1/block2 and msp2 genotypes were determined by DNA sequencing. Microsatellite and varD genotyping was based on size polymorphism and locus-specific amplification. RESULTS: The outbreak including severe malaria cases was associated with a single genotype. The other mild malaria outbreak was due to at least five distinct genotypes. CONCLUSION: Two distinct types of outbreak occurred despite systematic and sustained deployment of malaria control measures, indicating a need for reinforced vigilance. The varD/B-K1 msp1 linkage and its association with severe malaria in this area was confirmed. region Antilles-Guyane, Institut Pasteur de la Guyane, BP 6010, F-97306 Cayenne-Cedex, France. elegrand@pasteur-cayenne.fr",,scholar,2005,Malaria Journal,2005,4,26
15970588,A NIMA-related protein kinase is essential for completion of the sexual cycle of malaria parasites.,http://www.jbc.org/cgi/content/abstract/280/36/31957,"The molecular mechanisms regulating the sexual development of malaria parasites from gametocytes to oocysts in their mosquito vector are still largely unexplored. In other eukaryotes, NIMA-related kinases (Neks) regulate cell cycle progression and have been implicated in the regulation of meiosis. Here, we demonstrate that Nek-4, a new Plasmodium member of the Nek family, is essential for completion of the sexual cycle of the parasite. Recombinant Plasmodium falciparum Nek-4 possesses protein kinase activity and displays substrate preferences similar to those of other Neks. Nek-4 is highly expressed in gametocytes, yet disruption of the nek-4 gene in the rodent malaria parasite P. berghei has no effect on gamete formation and subsequent fertilization. However, further differentiation of zygotes into ookinetes is abolished. Measurements of nuclear DNA content indicate that zygotes lacking Nek-4 fail to undergo the genome replication to the tetraploid level that precedes meiosis. Cell cycle progression in the zygote is identified as a likely precondition for its morphological transition to the ookinete and for the successful establishment of a malaria infection in the mosquito. Glasgow, Glasgow G11 6NU, Scotland, United Kingdom.","Amino Acid Sequence!Animals!Catalytic Domain!Cell Cycle/*physiology!DNA Replication/physiology!Evolution, Molecular!Humans!Life Cycle Stages/*physiology!Meiosis/physiology!Molecular Sequence Data!Phylogeny!Plasmodium falciparum/*enzymology/genetics/*growth & development!Protein Kinases/genetics/*physiology!Protozoan Proteins/genetics/*physiology!RNA, Messenger/metabolism!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Research Support, U.S. Gov't, P.H.S.!Sequence Alignment!",scholar,2005,Journal of Biological Chemistry,280,36,31957
15975905,A Plasmodium actin-depolymerizing factor that binds exclusively to actin monomers.,http://www.molbiolcell.org/cgi/content/abstract/16/9/4013,"ADF/cofilins (AC) are essential F- and G-actin binding proteins that modulate microfilament turnover. The genome of Plasmodium falciparum, the parasite causing malaria, contains two members of the AC family. Interestingly, P. falciparum ADF1 lacks the F-actin binding residues of the AC consensus. Reverse genetics in the rodent malaria model system suggest that ADF1 performs vital functions during the pathogenic red blood cell stages, whereas ADF2 is not present in these stages. We show that recombinant PfADF1 interacts with monomeric actin but does not bind to actin polymers. Although other AC proteins inhibit nucleotide exchange on monomeric actin, the Plasmodium ortholog stimulates nucleotide exchange. Thus, PfADF1 differs in its biochemical properties from previously known AC proteins and seems to promote turnover exclusively by interaction with actin monomers. These findings provide important insights into the low cytosolic abundance and unique turnover characteristics of actin polymers in parasites of the phylum Apicomplexa. Stockholm, Sweden. herwig.schuler@mbb.ki.se","Actins/*metabolism!Amino Acid Sequence!Animals!Binding Sites!Kinetics!Malaria, Falciparum/*metabolism!Molecular Sequence Data!Plasmodium falciparum/*metabolism!Protein Binding/physiology!Protein Structure, Tertiary!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Temperature!",scholar,,Molecular Biology of the Cell,,,
15978954,Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum.,http://www.pubmedcentral.nih.gov/articlerender.fcgi%3Fartid%3D1242185,"The relationship between gene expression across the life cycle and protein conservation in Plasmodium falciparum was examined by comparing gene expression data for six life-history stages with the number of nonsynonymous substitutions per site dN between 901 orthologous gene pairs of P. falciparum and Plasmodium yoelii. A high level of expression across the life history was associated with decreased dN and thus with protein conservation. By contrast, differential expression in the sporozoite and merozoite stages was associated with increased dN. At least some sporozoite- and merozoite-expressed genes with high dN have probably been subject to positive selection arising from parasite-host coevolution. A high level of expression across the life history was associated with higher than average G+C content at the first and second codon positions, whereas a high level of expression in the sporozoite and merozoite was associated with reduced G+C content at the first and second codon positions, the latter pattern evidently reflecting the relaxation of constraint on the amino acid sequence. Life Sciences Bldg, 700 Sumter St., Columbia, SC 29205, USA. austin@biol.sc.edu","*Amino Acid Sequence!Animals!Base Composition!Codon!*Evolution, Molecular!*Gene Expression Regulation, Developmental!Humans!Life Cycle Stages!Plasmodium falciparum/*genetics/*growth & development/metabolism!Plasmodium yoelii/genetics/growth & development/metabolism!Principal Component Analysis!Protozoan Proteins/genetics!Research Support, N.I.H., Extramural!Research Support, U.S. Gov't, P.H.S.!",scholar,2005,Mol Biochem Parasitol,142,2,170
15984931,"Identification, molecular cloning and functional characterization of an octaprenyl pyrophosphate synthase in intra-erythrocytic stages of Plasmodium falciparum.",http://www.biochemj.org/bj/imps_x/pdf/BJ20050441.pdf,"Isoprenoids play important roles in all living organisms as components of structural cholesterol, steroid hormones in mammals, carotenoids in plants, and ubiquinones. Significant differences occur in the length of the isoprenic side chains of ubiquinone between different organisms, suggesting that different enzymes are involved in the synthesis of these side chains. Whereas in Plasmodium falciparum the isoprenic side chains of ubiquinone contain 7-9 isoprenic units, 10-unit side chains are found in humans. In a search for the P. falciparum enzyme responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, we cloned and expressed a putative polyprenyl synthase. Polyclonal antibodies raised against the corresponding recombinant protein confirmed the presence of the native protein in trophozoite and schizont stages of P. falciparum. The recombinant protein, as well as P. falciparum extracts, showed an octaprenyl pyrophosphate synthase activity, with the formation of a polyisoprenoid with eight isoprenic units, as detected by reverse-phase HPLC and reverse-phase TLC, and confirmed by electrospray ionization and tandem MS analysis. The recombinant and native versions of the enzyme had similar Michaelis constants with the substrates isopentenyl pyrophosphate and farnesyl pyrophosphate. The recombinant enzyme could be competitively inhibited in the presence of the terpene nerolidol. This is the first report that directly demonstrates an octaprenyl pyrophosphate synthase activity in parasitic protozoa. Given the rather low similarity of the P. falciparum enzyme to its human counterpart, decaprenyl pyrophosphate synthase, we suggest that the identified enzyme and its recombinant version could be exploited in the screening of novel drugs. of Sao Paulo, 05508-900 Sao Paulo, Brazil.","Alkyl and Aryl Transferases/antagonists & inhibitors/*genetics/*metabolism!Amino Acid Sequence!Animals!Cloning, Molecular!*Gene Expression Regulation, Developmental!*Gene Expression Regulation, Enzymologic!Molecular Sequence Data!Plasmodium falciparum/drug effects/*enzymology/*growth & development!Research Support, Non-U.S. Gov't!Sequence Alignment!Sequence Homology, Amino Acid!Sesquiterpenes/pharmacology!Substrate Specificity!",scholar,2005,Biochemical journal(London. 1984),392,,117
15996767,Identification of a subtelomeric gene family expressed during the asexual-sexual stage transition in Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001672&_version=1&_returnURL=&md5=f8e5ef0295f8e8ae1dcab94ea17730f6,"For malaria transmission, the parasite must undergo sexual differentiation into mature gametocytes. However, the molecular basis for this critical transition in the parasites life cycle is unknown. Six previously uncharacterized genes, Pfg14.744, Pfg14.745, Pfg14.748, Pfg14.763, Pfg14.752 and Pfg6.6 that are members of a 36 gene Plasmodium falciparum-specific subtelomeric superfamily were found to be expressed in parasites that are committed to sexual development as suggested by co-expression of Pfs16 and Pfg27. Northern blots demonstrated that Pfg14.744 and Pfg14.748 were first expressed before the parasites differentiated into morphologically distinct gametocytes, transcription continued to increase until stage II gametocytes were formed and then rapidly decreased. Immunofluorescence assays indicated that both proteins were only produced in the subpopulation of ring stage parasites that are committed to gametocytogenesis and both localized to the parasitophorous vacuole (PV)b of the early ring stage parasites. As the parasites continued to develop Pfg14.748 remained within the parasitophorous vacuole, while Pfg14.744 was detected in the erythrocyte. The 5' flanking region of either gene alone was sufficient to drive early gametocyte specific expression of green fluorescent protein (GFP). In parasites transfected with a plasmid containing the Pfg14.748 5' flanking region immediately upstream of GFP, fluorescence was observed in a small number of schizonts the cycle before stage I gametocytes were observed. This expression pattern is consistent with commitment to sexual differentiation prior to merozoite release and erythrocyte invasion. Further investigation into the role of these genes in the transition from asexual to sexual differentiation could provide new strategies to block malaria transmission. Road, Chicago, IL 60626, USA.","Amino Acid Sequence!Animals!Blotting, Northern!Consensus Sequence!DNA Primers!Female!Genes, Protozoan!Genes, Reporter!Green Fluorescent Proteins/genetics!Male!Molecular Sequence Data!*Multigene Family!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/growth & development!Polymerase Chain Reaction!Research Support, N.I.H., Extramural!Research Support, U.S. Gov't, P.H.S.!Sexual Maturation/*genetics!Telomere!",scirus,2005,Molecular & Biochemical Parasitology,143,1,90
16005087,The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001623&_version=1&_returnURL=&md5=228461539194bfefbe273958f0e443fe,"The sexual stages of malarial parasites are essential for the mosquito transmission of the disease and therefore are the focus of transmission-blocking drug and vaccine development. In order to better understand genes important to the sexual development process, the transcriptomes of high-purity stage I-V Plasmodium falciparum gametocytes were comprehensively profiled using a full-genome high-density oligonucleotide microarray. The interpretation of this transcriptional data was aided by applying a novel knowledge-based data-mining algorithm termed ontology-based pattern identification (OPI) using current information regarding known sexual stage genes as a guide. This analysis resulted in the identification of a sexual development cluster containing 246 genes, of which approximately 75% were hypothetical, exhibiting highly-correlated, gametocyte-specific expression patterns. Inspection of the upstream promoter regions of these 246 genes revealed putative cis-regulatory elements for sexual development transcriptional control mechanisms. Furthermore, OPI analysis was extended using current annotations provided by the Gene Ontology Consortium to identify 380 statistically significant clusters containing genes with expression patterns characteristic of various biological processes, cellular components, and molecular functions. Collectively, these results, available as part of a web-accessible OPI database (http://carrier.gnf.org/publications/Gametocyte), shed light on the components of molecular mechanisms underlying parasite sexual development and other areas of malarial parasite biology. North Torrey Pines Road, La Jolla, CA 92037, USA.","Animals!Base Sequence!DNA, Protozoan/genetics!Female!*Gene Expression Profiling!Genome, Protozoan!Male!Multigene Family!*Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/*genetics/growth & development!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, Non-P.H.S.!Sequence Alignment!Sexual Maturation!*Transcription, Genetic!",scirus,2005,Molecular & Biochemical Parasitology,143,1,67
16007716,Structurally simple farnesyltransferase inhibitors arrest the growth of malaria parasites.,http://doi.wiley.com/10.1002/anie.200500674,,,scholar,2005,Angewandte Chemie(International ed. Print),44,31,4903
16014411,The protozoan parasite Cryptosporidium parvum possesses two functionally and evolutionarily divergent replication protein A large subunits.,http://www.jbc.org/cgi/content/abstract/280/36/31460,"Very little is known about protozoan replication protein A (RPA), a heterotrimeric complex critical for DNA replication and repair. We have discovered that in medically and economically important apicomplexan parasites, two unique RPA complexes may exist based on two different types of large subunit RPA1. In this study, we characterized the single-stranded DNA binding features of two distinct types (i.e. short and long) of RPA1 subunits from Cryptosporidium parvum (CpRPA1A and CpRPA1B). These two proteins differ from human RPA1 in their intrinsic single-stranded DNA binding affinity (K) and have significantly lower cooperativity (omega). We also identified the RPA2 and RPA3 subunits from C. parvum, the latter of which had yet to be reported to exist in any protozoan. Using fluorescence resonance energy transfer technology and pull-down assays, we confirmed that these two subunits interact with each other and with CpRPA1A and CpRPA1B. This suggests that the heterotrimeric structure of RPA complexes may be universally conserved from lower to higher eukaryotes. Bioinformatic analyses indicate that multiple types of RPA1 are present in the other apicomplexans Plasmodium and Toxoplasma. Apicomplexan RPA1 proteins are phylogenetically more related to plant homologues and probably arose from a single gene duplication event prior to the expansion of the apicomplexan lineage. Differential expression during the life cycle stages in three apicomplexan parasites suggests that the two RPA1 types exercise specialized biological functions. Biomedical Sciences, Texas A&M University, College Station 77843, USA.","Amino Acid Sequence!Animals!Comparative Study!Conserved Sequence!Cryptosporidium parvum/chemistry/genetics/*metabolism!DNA, Single-Stranded/metabolism!DNA-Binding Proteins/*chemistry/genetics/metabolism!*Evolution, Molecular!Humans!Molecular Sequence Data!Protein Binding!Protein Structure, Quaternary!Protozoan Proteins/*chemistry/genetics/metabolism!Replication Factor A!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!",scholar,2005,Journal of Biological Chemistry,280,36,31460
16026866,Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001751&_version=1&_returnURL=&md5=86ab2ea5d37aeca1c535699e1a9cf93e,"A genome-wide expression analysis was undertaken to identify novel genes specifically activated from early stages of gametocytogenesis in Plasmodium falciparum. A comparative analysis was conducted on sexually induced cultures of reference parasite clone 3D7 and its gametocyteless derivative clone F12. Competitive hybridisations on long-oligomer microarrays representing 4488 P. falciparum genes identified a remarkably small number of transcripts differentially produced in the two clones. Upregulation of the mRNAs for the early gametocyte markers Pfs16 and Pfg27 was however readily detected in 3D7, and such genes were used as reference transcripts in a comparative time course analysis of 3D7 and F12 parasites between 30 and 40 h post-invasion in cultures induced to enter gametocytogenesis. One hundred and seventeen genes had expression profiles which correlated to those of pfs16 and pfg27, and Northern blot analysis and published proteomic data identified those whose expression was gametocyte-specific. Immunofluorescence analysis with antibodies against two of these gene products identified two novel parasite membrane associated, sexual stage-specific proteins. One was produced from stage I gametocytes and the second showed peak production in stage II gametocytes. The two proteins were named Pfpeg-3 and Pfpeg-4, for P. falciparum proteins of early gametocytes. Superiore di Sanita, Viale Regina Elena 299, 00161 Rome, Italy.","Animals!Gene Expression Profiling!*Genome, Protozoan!Germ Cells/*physiology!Plasmodium falciparum/*genetics/growth & development!RNA, Messenger/genetics!RNA, Protozoan/genetics!Research Support, Non-U.S. Gov't!*Transcription, Genetic!",scirus,2005,Molecular & Biochemical Parasitology,143,1,100
16038615,"PfPDE1, a novel cGMP-specific phosphodiesterase from the human malaria parasite Plasmodium falciparum.",http://www.biochemj.org/bj/imps/pdf/BJ20050425.pdf,"This is the first report of molecular characterization of a novel cyclic nucleotide PDE (phosphodiesterase), isolated from the human malaria parasite Plasmodium falciparum and designated PfPDE1. PfPDE1 cDNA encodes an 884-amino-acid protein, including six putative transmembrane domains in the N-terminus followed by a catalytic domain. The PfPDE1 gene is a single-copy gene consisting of two exons and a 170 bp intron. PfPDE1 transcripts were abundant in the ring form of the asexual blood stages of the parasite. The C-terminal catalytic domain of PfPDE1, produced in Escherichia coli, specifically hydrolysed cGMP with a K(m) value of 0.65 microM. Among the PDE inhibitors tested, a PDE5 inhibitor, zaprinast, was the most effective, having an IC50 value of 3.8 microM. The non-specific PDE inhibitors IBMX (3-isobutyl-1-methylxanthine), theophylline and the antimalarial chloroquine had IC50 values of over 100 microM. Membrane fractions prepared from P. falciparum at mixed asexual blood stages showed potent cGMP hydrolytic activity compared with cytosolic fractions. This hydrolytic activity was sensitive to zaprinast with an IC50 value of 4.1 microM, but insensitive to IBMX and theophylline. Furthermore, an in vitro antimalarial activity assay demonstrated that zaprinast inhibited the growth of the asexual blood parasites, with an ED50 value of 35 microM. The impact of cyclic nucleotide signalling on the cellular development of this parasite has previously been discussed. Thus this enzyme is suggested to be a novel potential target for the treatment of the disease malaria. 2-chome, Toda, Saitama 335-8505, Japan.","Animals!Cloning, Molecular!Cyclic GMP/*metabolism!Erythrocytes!Gene Expression Regulation, Developmental!Gene Expression Regulation, Enzymologic!Humans!Molecular Sequence Data!Phosphoric Diester Hydrolases/genetics/*metabolism!Phylogeny!Plasmodium falciparum/*enzymology!RNA, Messenger!",scholar,2005,Biochemical journal(London. 1984),392,,221
16039160,A glycine-cleavage complex as part of the folate one-carbon metabolism of Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492205001868&_version=1&_returnURL=&md5=58e8125a1524d796ccc68f09dbdedf78,"The glycine-cleavage complex (GCV) and serine hydroxymethyltransferase represent the two systems of one-carbon transfer that are employed in the biosynthesis of active folate cofactors in eukaryotes. Although the understanding of this area of metabolism in Plasmodium falciparum is still at an early stage, we discuss evidence that genes and transcription products of the GCV are present and expressed in this parasite. The potential role of the GCV and its relevance to the life cycle and pathogenesis of the malaria erythrocytic stages are also considered. According to its expression profile, the GCV seems to be particularly active in gametocytes. The GCV enzyme dihydrolipoamide dehydrogenase has two isoforms encoded by two different genes. It has been demonstrated recently that both genes are functional, with one of them identified as being part of a pyruvate dehydrogenase complex that is present exclusively in the apicoplast of Plasmodium species. The other isoform probably forms part of the Plasmodium GCV. The GCV is the first enzyme complex involved in folate metabolism in this parasite that can be assumed, with a good degree of certainty, to be located in the mitochondria. Granada, Bogota, Colombia.","Amino Acid Oxidoreductases/chemistry/genetics/*metabolism!Animals!Carrier Proteins/chemistry/genetics/*metabolism!Dihydrolipoamide Dehydrogenase/genetics/metabolism!Erythrocytes/*parasitology!Folic Acid/chemistry/*metabolism!Gene Expression Regulation, Enzymologic!Glycine/metabolism!Glycine Hydroxymethyltransferase/genetics/*metabolism!Malaria, Falciparum/parasitology!Multienzyme Complexes/chemistry/genetics/*metabolism!Plasmodium falciparum/*enzymology/genetics/metabolism!Research Support, Non-U.S. Gov't!Transferases/chemistry/genetics/*metabolism!",scirus,2005,Trends in Parasitology,21,9,406
16040597,Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.,http://nar.oxfordjournals.org/cgi/content/abstract/33/13/3994,"The comparative genomics of apicomplexans, such as the malarial parasite Plasmodium, the cattle parasite Theileria and the emerging human parasite Cryptosporidium, have suggested an unexpected paucity of specific transcription factors (TFs) with DNA binding domains that are closely related to those found in the major families of TFs from other eukaryotes. This apparent lack of specific TFs is paradoxical, given that the apicomplexans show a complex developmental cycle in one or more hosts and a reproducible pattern of differential gene expression in course of this cycle. Using sensitive sequence profile searches, we show that the apicomplexans possess a lineage-specific expansion of a novel family of proteins with a version of the AP2 (Apetala2)-integrase DNA binding domain, which is present in numerous plant TFs. About 20-27 members of this apicomplexan AP2 (ApiAP2) family are encoded in different apicomplexan genomes, with each protein containing one to four copies of the AP2 DNA binding domain. Using gene expression data from Plasmodium falciparum, we show that guilds of ApiAP2 genes are expressed in different stages of intraerythrocytic development. By analogy to the plant AP2 proteins and based on the expression patterns, we predict that the ApiAP2 proteins are likely to function as previously unknown specific TFs in the apicomplexans and regulate the progression of their developmental cycle. In addition to the ApiAP2 family, we also identified two other novel families of AP2 DNA binding domains in bacteria and transposons. Using structure similarity searches, we also identified divergent versions of the AP2-integrase DNA binding domain fold in the DNA binding region of the PI-SceI homing endonuclease and the C-terminal domain of the pleckstrin homology (PH) domain-like modules of eukaryotes. Integrating these findings, we present a reconstruction of the evolutionary scenario of the AP2-integrase DNA binding domain fold, which suggests that it underwent multiple independent combinations with different types of mobile endonucleases or recombinases. It appears that the eukaryotic versions have emerged from versions of the domain associated with mobile elements, followed by independent lineage-specific expansions, which accompanied their recruitment to transcription regulation functions. Medicine, National Institutes of Health, Bethesda, MD 20894, USA.","Amino Acid Sequence!Animals!Apicomplexa/*genetics/growth & development!Cryptosporidium/genetics!DNA-Binding Proteins/*chemistry/genetics!*Evolution, Molecular!Gene Expression!Genomics!Homeodomain Proteins/chemistry!Integrases/chemistry!Molecular Sequence Data!Nuclear Proteins/chemistry!Plant Proteins/chemistry!Plasmodium falciparum/genetics!Protein Structure, Tertiary!Research Support, N.I.H., Intramural!Sequence Alignment!Theileria/genetics!Transcription Factors/*chemistry/genetics/physiology!",scholar,2005,Nucleic Acids Research,33,13,3994
16042788,Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes.,http://www.biomedcentral.com/1471-2164/6/100,"BACKGROUND: To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcription machinery, which is otherwise well-conserved in the crown group of eukaryotes, has yet been reported. In this study, we have used a combination of sensitive sequence analysis methods to predict the existence of several parasite encoded general transcription factors associated with RNA polymerase II. RESULTS: Several orthologs of general transcription factors associated with RNA polymerase II can be predicted among the hypothetical proteins of the P. falciparum genome using the two-dimensional Hydrophobic Cluster Analysis (HCA) together with profile-based search methods (PSI-BLAST). These predicted orthologous genes encoding putative transcription factors include the large subunit of TFIIA and two candidates for its small subunit, the TFIIE beta-subunit, which would associate with the previously known TFIIE alpha-subunit, the TFIIF beta-subunit, as well as the p62/TFB1 subunit of the TFIIH core. Within TFIID, the putative orthologs of TAF1, TAF2, TAF7 and TAF10 were also predicted. However, no candidates for TAFs with classical histone fold domain (HFD) were found, suggesting an unusual architecture of TFIID complex of RNA polymerase II in the parasite. CONCLUSION: Taken together, these results suggest that more general transcription factors may be present in the P. falciparum proteome than initially thought. The prediction of these orthologous general transcription factors opens the way for further studies dealing with transcriptional regulation in P. falciparum. These alternative and sensitive sequence analysis methods can help to identify candidates for other transcriptional regulatory factors in P. falciparum. They will also facilitate the prediction of biological functions for several orphan proteins from other apicomplexan parasites such as Toxoplasma gondii, Cryptosporidium parvum and Eimeria. Paris 6 et Paris 7, Departement de Biologie Structurale, IMPMC, 75252 Paris Cedex 05, France. Isabelle.Callebaut@impmc.jussieu.fr","Amino Acid Sequence!Animals!Cluster Analysis!Conserved Sequence!Databases, Protein!*Genome!Humans!Models, Biological!Models, Genetic!Molecular Sequence Data!Plasmodium falciparum/*enzymology!Protein Structure, Tertiary!RNA/metabolism!RNA Polymerase II/*genetics/metabolism!Research Support, Non-U.S. Gov't!Sequence Homology, Amino Acid!Transcription Factor TFIIA/genetics!Transcription Factor TFIID/genetics!Transcription Factor TFIIH/genetics!Transcription Factors, General/*genetics/physiology!Transcription Factors, TFII/genetics!Transcription, Genetic!",scholar,2005,BMC Genomics,2005,6,100
16046185,Targeting malaria parasite proteins to the erythrocyte.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492205001935&_version=1&_returnURL=&md5=e86e65cb0e8d3560f737ad9e8af9f67e,"The intraerythrocytic stages of the protozoan parasite Plasmodium falciparum reside within a parasitophorous vacuole (PV) and set up unique "extraparasite, intraerythrocyte" protein-trafficking pathways that target parasite-encoded proteins to the erythrocyte cytoplasm and cell surface. Two recent articles report the identification of trafficking motifs that regulate the transport of parasite-encoded proteins across the PV. These articles greatly aid the annotation of the parasite "secretome" catalog of proteins that are targeted to the erythrocyte cytoplasm or cell membrane. Cornell University, 1300 York Avenue, Box 62, New York, NY 10021, USA. tjt2001@med.cornell.edu","Amino Acid Sequence!Animals!Erythrocytes/*parasitology/ultrastructure!Genes, Protozoan!Host-Parasite Relations!Humans!Malaria, Falciparum/blood/*parasitology!Plasmodium falciparum/growth & development/metabolism/*physiology!Protozoan Proteins/*metabolism!Sequence Alignment!Vacuoles/*parasitology!",scirus,2005,Trends in Parasitology,21,9,399
16046186,Pexel/VTS: a protein-export motif in erythrocytes infected with malaria parasites.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S1471492205001911&_version=1&_returnURL=&md5=015618287ebece9604aa88e98eaff1c9,"The trafficking of proteins from the malaria parasite into the erythrocyte host has an important role in both the adaptation by the parasite of its immediate environment and the pathophysiology of disease. The molecular basis of these trafficking processes, particularly export from the parasitophorous vacuole (PV), is poorly understood and a matter of some controversy. In this article, we highlight two recent, independent reports that have provided new insights into protein translocation across the PV membrane, characterizing a novel signalling motif as a key signature in cataloguing the parasite secretome. Radcliffe Hospital, Oxford OX3 9DS, UK. horrocks@hammer.imm.ox.ac.uk","Amino Acid Motifs!Animals!Cytosol/metabolism/parasitology!Erythrocyte Membrane/metabolism/parasitology!Erythrocytes/*parasitology!*Host-Parasite Relations!Humans!Membrane Proteins/*metabolism!Plasmodium falciparum/growth & development/metabolism/*physiology!Protozoan Proteins/*metabolism!Research Support, Non-U.S. Gov't!Secretory Vesicles/metabolism/parasitology!",scirus,2005,Trends in Parasitology,21,9,396
16048916,Countrywide survey shows very high prevalence of Plasmodium falciparum multilocus resistance genotypes in Cambodia.,http://aac.asm.org/cgi/content/abstract/49/8/3147,"Cambodia is located in an area of resistance to multiple antimalarials and has been the first country to implement the systematic use of an artesunate-mefloquine combination as first-line treatment for Plasmodium falciparum malaria. Little is known, however, about the prevalence of resistance mutations within the natural parasite populations, impeding rational drug policy in this context. Using direct sequencing of PCR products, we have analyzed sequence polymorphism of the dihydrofolate reductase-thymidylate synthase, dihydropteroate synthetase, and multidrug resistance 1 genes in a large number of clinical P. falciparum isolates collected in various areas of Cambodia. This highlighted a 100% prevalence of haplotypes with multiple mutations in the target genes of antifolates after more than a decade without use of antifolates for malaria therapy. A high prevalence of mutations in Pfmdr1, including mutations associated with decreased in vitro susceptibility to mefloquine and quinine, was also observed. In addition, novel, low-frequency mutations were detected in Pfmdr1. Our findings show an alarming rate of multilocus resistance genotypes in Cambodia, requiring diligent surveillance and imposing limitations on possible future drug combinations. d'Immunologie Parasitaire et de Vaccinologie, 31, avenue Monge Parc Grandmont, 37200 Tours, France. thierry.fandeur@univ-tours.fr","ATP-Binding Cassette Transporters/genetics!Animals!Antimalarials/*pharmacology!Cambodia/epidemiology!Dihydropteroate Synthase/genetics!Drug Resistance, Multiple/*genetics!Genes, Protozoan!Genotype!Humans!Malaria, Falciparum/*epidemiology/parasitology!Mutation!Parasitic Sensitivity Tests!Plasmodium falciparum/classification/*drug effects/genetics!Prevalence!Protozoan Proteins/*genetics!Research Support, Non-U.S. Gov't!Tetrahydrofolate Dehydrogenase/genetics!Thymidylate Synthase/genetics!",scholar,2005,Antimicrobial Agents and Chemotherapy,49,8,3147
16085323,Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105001982&_version=1&_returnURL=&md5=02e33fa262e94491a73eee43ae78618f,"Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence. University Park, PA 16802, USA. luc2@psu.edu","Animals!DNA, Complementary/genetics!DNA, Protozoan/genetics!Expressed Sequence Tags!Gene Library!*Genes, Protozoan!Humans!Malaria, Vivax/parasitology!Molecular Sequence Data!Plasmodium vivax/*genetics!Research Support, N.I.H., Extramural!Research Support, U.S. Gov't, P.H.S.!",scirus,2005,Molecular & Biochemical Parasitology,144,1,1
11163454,Myosin A expressions in sporogonic stages of Plasmodium.,,,"Plasmodium falciparum,Amino Acid Sequence,Myosins,Plasmodium berghei,Sequence Analysis, DNA,Molecular Sequence Data,Life Cycle Stages,Animals",NCBI,2000,Molecular and biochemical parasitology,111,2,465-9
2183186,Nucleotide sequence of the Plasmodium berghei circumsporozoite protein gene from the ANKA clone 2.34L.,http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=330291,,"Genes,Amino Acid Sequence,Plasmodium berghei,Cloning, Molecular,Antigens, Protozoan,Molecular Sequence Data,Base Sequence,Animals,Protozoan Proteins",NCBI,1990,Nucleic acids research,18,2,376
1625704,Stage-specific expression of aldolase isoenzymes in the rodent malaria parasite Plasmodium berghei.,,"We have cloned two gene (aldo-1 and aldo-2) encoding the glycolytic enzyme aldolase of the rodent malaria parasite Plasmodium berghei. The amino acid sequence of one gene product, ALDO-1, is virtually identical to P. falciparum aldolase whereas ALDO-2, the second gene product, is different and has 13% sequence diversity to ALDO-1. We expressed ALDO-2 as an active enzyme in Escherichia coli and compared the biochemical and kinetic properties to that of P. falciparum recombinant aldolase (ALDO-1 type). Based on the Km and Vmax constants for FMP and FBP, neither ALDO-1 nor ALDO-2 can be clearly assigned to any of the known mammalian isoenzyme classes. We demonstrate that expression of the two isoenzymes is developmentally regulated: specific antibody probes detect ALDO-1 in sporozoite stages of P. berghei and ALDO-2 is found in blood stage parasites.","Amino Acid Sequence,Restriction Mapping,Humans,Fructose-Bisphosphate Aldolase,Kinetics,Sequence Alignment,Plasmodium berghei,Blotting, Western,Cloning, Molecular,Substrate Specificity,Isoenzymes,Molecular Sequence Data,Animals,Evolution",NCBI,1992,Molecular and biochemical parasitology,52,1,15-27
10613710,The rodent malaria parasite Plasmodium berghei does not contain a typical O-type small subunit ribosomal RNA gene.,,,"Gene Expression,Genes, Protozoan,Sequence Alignment,Plasmodium berghei,DNA, Protozoan,Sequence Analysis, DNA,Molecular Sequence Data,RNA, Ribosomal,Genes, rRNA,Base Sequence,Transcription, Genetic,Blotting, Northern,Animals",NCBI,2000,Molecular and biochemical parasitology,105,1,169-74
16095562,Characterization of amino acid variation at strategic positions in parasite and human proteases for selective inhibition of falcipains in Plasmodium falciparum.,http://www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26list_uids%3D16095562%26dopt%3DCitation,"Falcipains (FP) of Plasmodium falciparum are important virulence factors marked as potential targets for antimalarial drug discovery. In this study, the previously uncharacterized fp2B (PF11_0161) was shown to be highly expressed as an active enzyme during the erythrocytic stage. With three related proteases in the FP family and the existence of human homologues, it is prudent to identify clusters of residues unique to the parasite proteases that can be targeted selectively for drug design. Using bioinformatic tools, we have carefully mapped out a highly conserved and unique region constituted by I85, S149, and A151 in the plasmodial proteases that can influence the development of compounds capable of inhibiting the entire FP family. Taking drug interactions with the human homologues into consideration, these residues in FP2B were replaced with the cognate residues found in human cathepsin L (catL) for evaluation. Despite the high sequence similarity between the FP2 isozymes (97.5%), FP2B is found to be more tolerant to amino acid substitution at position 149 than FP2A. This structural disparity implied that residues mediating peptide substrate interactions are not fully conserved across the FP family and warrant attention in the design and evaluation of protease inhibitors focused on the FPs. The simultaneous substitution of the neighboring residues (I85 or A151) rendered the double mutants (S149A/I85M and S149A/A151D) completely inactive. Significantly, the mutations did not result in 'catL-like' specificity, suggesting that substrate-based inhibitors could be rationally designed against these important parasite-specific structural determinants. Singapore, MD4A, 5 Science Drive 2, Singapore 117597, Singapore.","Amino Acid Sequence!Animals!Base Sequence!Chromatography, Gel!Cloning, Molecular!Cysteine Endopeptidases/chemistry/genetics/*metabolism!DNA Primers!Electrophoresis, Polyacrylamide Gel!Humans!Models, Molecular!Molecular Sequence Data!Mutagenesis, Site-Directed!Peptide Hydrolases/*chemistry/metabolism!Plasmodium falciparum/*enzymology/genetics!Polymerase Chain Reaction!Recombinant Proteins/chemistry/metabolism!Research Support, Non-U.S. Gov't!Reverse Transcriptase Polymerase Chain Reaction!Sequence Homology, Amino Acid!Species Specificity!Transcription, Genetic!",scholar,2005,Biochem Biophys Res Commun,335,3,762
16099989,Complete genome sequence and lytic phase transcription profile of a Coccolithovirus.,http://www.sciencemag.org/cgi/data/309/5737/1090/DC1/1,"The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Among the 472 predicted genes of the 407,339-base pair genome are a variety of unexpected genes, most notably those involved in biosynthesis of ceramide, a sphingolipid known to induce apoptosis. Uniquely for algal viruses, it also contains six RNA polymerase subunits and a novel promoter, suggesting this virus encodes its own transcription machinery. Microarray transcriptomic analysis reveals that 65% of the predicted virus-encoded genes are expressed during lytic infection of E. huxleyi. UK. whw@pml.ac.uk","Algae/virology!Apoptosis!Base Composition!Ceramides/biosynthesis!Computational Biology!DNA, Viral/chemistry/genetics!DNA-Directed RNA Polymerases/genetics!Gene Expression!Gene Expression Profiling!Genes, Viral!*Genome, Viral!Oligonucleotide Array Sequence Analysis!Peptide Hydrolases/genetics!Phycodnaviridae/classification/*genetics/*physiology!Promoter Regions (Genetics)!Protein Subunits!Research Support, Non-U.S. Gov't!*Sequence Analysis, DNA!Sphingolipids/biosynthesis!*Transcription, Genetic!Virus Replication!",scholar,2005,Science,309,5737,1090
16102004,Distinct mechanisms govern proteolytic shedding of a key invasion protein in apicomplexan pathogens.,http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2958.2005.04772.x,"Apical membrane antigen-1 (AMA1) is a conserved apicomplexan protein that plays an important but undefined role in host cell invasion. We have studied the fate of Plasmodium falciparum AMA1 (PfAMA1) during erythrocyte invasion by the malaria merozoite, and compared it with that of the Toxoplasma gondii orthologue, TgAMA1. Shedding of the PfAMA1 ectodomain goes essentially to completion during invasion, and occurs predominantly or exclusively via juxtamembrane cleavage at the previously identified sheddase cleavage site, Thr517. Only the resulting juxtamembrane stub of the ectodomain is efficiently carried into the host cell, and this remains distributed around the plasma membrane of the intracellular ring-stage parasite. Inhibition of normal shedding, however, results in proteolysis at an intramembrane, rhomboid-like cleavage site, and PfAMA1 is susceptible to cleavage by Drosophila rhomboid-1, showing that it can be a substrate for intramembrane cleavage but is not normally processed in this manner. In contrast, shedding of TgAMA1 from the surface of extracellular tachyzoites occurs exclusively via cleavage within the luminal half of its transmembrane domain by a rhomboid-like protease. Also unlike PfAMA1, complete TgAMA1 shedding does not accompany Toxoplasma invasion as the intact protein was readily detected on the surface of newly invaded tachyzoites. This work reveals unexpected differences in the manner in which Plasmodium and Toxoplasma shed AMA1 from the surface of invasive zoites, and demonstrates the presence at the malaria merozoite surface of a rhomboid-like protease. Mill Hill, London NW7 1AA, UK.","Amino Acid Sequence!Animals!Antigens, Protozoan/*metabolism!Comparative Study!Erythrocyte Membrane/metabolism/parasitology!Erythrocytes/*parasitology!Membrane Proteins/*metabolism!Molecular Sequence Data!Peptide Hydrolases/drug effects/*metabolism!Plasmodium falciparum/*pathogenicity!Protease Inhibitors/pharmacology!Protein Structure, Tertiary!Protozoan Proteins/*metabolism!Toxoplasma/*pathogenicity!",scholar,2005,Mol Microbiol,57,5,1342
16115694,Plasmodium berghei alpha-tubulin II: a role in both male gamete formation and asexual blood stages.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105002161&_version=1&_returnURL=&md5=8ca6515cc6ddf3e01cffd64d196a1dd9,"Plasmodium falciparum contains two genes encoding different isotypes of alpha-tubulin, alpha-tubulin I and alpha-tubulin II. alpha-Tubulin II is highly expressed in male gametocytes and forms part of the microtubules of the axoneme of male gametes. Here we present the characterization of Plasmodium berghei alpha-tubulin I and alpha-tubulin II that encode proteins of 453 and 450 amino acids, respectively. alpha-Tubulin II lacks the well-conserved three amino acid C-terminal extension including a terminal tyrosine residue present in alpha-tubulin I. Investigation of transcription by Northern analysis and RT-PCR and analysis of promoter activity by GFP tagging showed that alpha-tubulin I is expressed in all blood and mosquito stages. As expected, alpha-tubulin II was highly expressed in the male gametocytes, but transcription was also observed in the asexual blood stages, female gametocytes, ookinetes and oocysts. Gene disruption experiments using standard transfection technologies did not produce viable parasites indicating that both alpha-tubulin isotypes are essential for the asexual blood stages. Targeted modification of alpha-tubulin II by the addition of the three C-terminal amino acids of alpha-tubulin I did not affect either blood stage development nor male gamete formation. Attempts to modify the C-terminal region by adding a TAP tag to the endogenous alpha-tubulin II gene were not successful. Introduction of a transgene, expressing TAP-tagged alpha-tubulin II, next to the endogenous alpha-tubulin II gene, had no effect on the asexual blood stages but strongly impaired formation of male gametes. These results show that alpha-tubulin II not only plays an important role in the male gamete but is also expressed in and essential for asexual blood stage development. Centre, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.","Animals!Gene Expression!Germ Cells/growth & development/metabolism!*Life Cycle Stages!Male!Plasmodium berghei/*chemistry/cytology/genetics/growth & development!Promoter Regions (Genetics)/genetics!Protozoan Proteins/genetics/*physiology!Research Support, Non-U.S. Gov't!Tubulin/genetics/*physiology!",scirus,2005,Molecular & Biochemical Parasitology,144,1,16
16123303,Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes.,http://171.66.122.53/cgi/content/abstract/309/5739/1384,"The malaria parasite, Plasmodium falciparum, exploits multiple ligand-receptor interactions, called invasion pathways, to invade the host erythrocyte. Strains of P. falciparum vary in their dependency on sialated red cell receptors for invasion. We show that switching from sialic acid-dependent to -independent invasion is reversible and depends on parasite ligand use. Expression of P. falciparum reticulocyte-binding like homolog 4 (PfRh4) correlates with sialic acid-independent invasion, and PfRh4 is essential for switching invasion pathways. Differential activation of PfRh4 represents a previously unknown mechanism to switch invasion pathways and provides P. falciparum with exquisite adaptability in the face of erythrocyte receptor polymorphisms and host immune responses. 3050, Australia. development/metabolism/*pathogenicity","Animals!Animals, Genetically Modified!Erythrocytes/*parasitology!Gene Expression Profiling!Gene Silencing!Genes, Protozoan!Humans!Ligands!Membrane Proteins/analysis/genetics/*physiology!Neuraminidase/pharmacology!Oligonucleotide Array Sequence Analysis!Plasmodium falciparum/genetics/growth &!Polymerase Chain Reaction!Protozoan Proteins/analysis/genetics/*physiology!Recombinant Fusion Proteins/metabolism!Research Support, Non-U.S. Gov't!Sialic Acids/metabolism!Transcription, Genetic!",scholar,2005,Science,309,5739,1384
16125802,MSP8 is a non-essential merozoite surface protein in Plasmodium falciparum.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105002197&_version=1&_returnURL=&md5=5aef375b48da231d631ee482f5dae041,"MSP8 is a recently identified merozoite surface protein that shares similar structural features with the leading vaccine candidate MSP1. Both proteins contain two C-terminal epidermal growth factor (EGF)-like domains, a glycosylphosphatidylinositol (GPI) anchor attachment sequence and undergo proteolytic processing. By double recombination, we have disrupted the MSP8 gene in P. falciparum 3D7 parasites, and confirmed integration by southern hybridisation and PCR. Western blot analysis of lysates from asynchronous cultures and isolated merozoites demonstrated the absence of MSP8 in two cloned knockout lines. There was no significant difference in growth rate observed between 3D7 and the cloned DeltaMSP8 lines. Thus, unlike MSP1, MSP8 is not required for asexual stage parasite growth and replication in vitro. Further analysis of the cloned lines showed that loss of MSP8 had no effect on the levels of expression of other merozoite surface proteins including MSP1-5, 7 and 10. Stage-specific immunoblots showed that MSP8 expression commences in late rings and extends throughout the rest of the erythrocytic life cycle in the 3D7 parent line, but is absent from all stages in the DeltaMSP8 transfectants. Monash University, Clayton, Vic. 3800, Australia. casilda.black@med.monash.edu.au","Animals!Antigens, Protozoan/genetics/metabolism/*physiology!Blotting, Western!Erythrocytes/parasitology!Fluorescent Antibody Technique!Life Cycle Stages!Plasmodium falciparum/cytology/*growth & development/metabolism!Protozoan Proteins/genetics/metabolism/*physiology!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Transfection!",scirus,2005,Molecular & Biochemical Parasitology,144,1,27
16131758,Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.,http://dx.doi.org/10.1107/S0907444905020251,"Purine metabolism in the parasite Plasmodium has been identified as a promising target for antimalarial therapies. Purine nucleoside phosphorylase (PNP) is part of a salvage pathway for the biosynthesis of purines, which are essential for parasite survival. Two crystal structures of PNP from Plasmodium falciparum (PfPNP) in two space groups, each with a single subunit in the asymmetric unit, are described here. One structure, refined to 2.4 A, has an empty nucleoside-binding site and a sulfate ion bound in the phosphate-binding pocket. The second structure, refined to 2.0 A, has the substrate inosine bound to the active centre. Structure comparison reveals alterations in the active site upon ligand binding. The new structures presented here specifically highlight the likely roles of Asp206 and two loops flanking the active site: the beta7-alpha6 loop (residues approximately 161-169) and the beta9-alpha8 loop (residues approximately 208-223). Comparison with PNP in complex with transition-state inhibitors suggests that the purine substrate moves towards the phosphate substrate, rather than vice versa, upon forming the transition state. The single-substrate-containing PfPNP structures also appear to be more flexible than PfPNP bound to inhibitors. Together, these structures serve as a basis for better understanding of ligand binding and mechanism that can be further exploited to optimize the specificity of anti-PfPNP drugs. York, York YO10 5YW, England. Aug 16.","Animals!Binding Sites!Crystallization!Crystallography, X-Ray!Inosine/*chemistry!Models, Molecular!Plasmodium falciparum/*enzymology!Protein Binding!Protein Structure, Quaternary!Purine-Nucleoside Phosphorylase/*chemistry!Research Support, N.I.H., Extramural!Research Support, Non-U.S. Gov't!Research Support, U.S. Gov't, P.H.S.!Sulfates/*chemistry!",scholar,2005,"Acta crystallographica. Section D, Biological crystallography""""",61,,1245
16138199,Rapid turnover of Plasmodium falciparum var gene transcripts and genotypes during natural non-symptomatic infections.,http://www.scielo.br/scielo.php%3Fscript%3Dsci_arttext%26pid%3DS0036-46652005000400004,"The var genes of Plasmodium falciparum code for the antigenically variant erythrocyte membrane proteins 1 (PfEMP1), a major factor for cytoadherence and immune escape of the parasite. Herein, we analyzed the var gene transcript turnover in two ongoing, non-symptomatic infections at sequential time points during two weeks. The number of different circulating genomes was estimated by microsatellite analyses. In both infections, we observed a rapid turnover of plasmodial genotypes and var transcripts. The rapidly changing repertoire of var transcripts could have been caused either by swift elimination of circulating var-transcribing parasites stemming from different or identical genetic backgrounds, or by accelerated switching of var gene transcription itself. Universidade de Sao Paulo, 05508-900 Sao Paulo, SP, Brazil. gwunder@usp.br","Adult!Animals!Antigenic Variation/*genetics!Antigens, Protozoan/*genetics!DNA, Protozoan/genetics!Female!Genome, Protozoan!Genotype!Humans!Malaria, Falciparum/*parasitology!Male!Plasmodium falciparum/*genetics!Polymerase Chain Reaction!Protozoan Proteins/*genetics!RNA, Protozoan/genetics!Research Support, Non-U.S. Gov't!Time Factors!Transcription, Genetic/genetics!",scholar,2005,Rev. Inst. Med. trop. S. Paulo,47,4,
16159678,Toxoplasma gondii is capable of exogenous folate transport. A likely expansion of the BT1 family of transmembrane proteins.,http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=ScienceSearch&_method=citationSearch&_piikey=S0166685105002227&_version=1&_returnURL=&md5=50bc55f76c4a6db622a608bf31b42b09,"Folates are key elements in eukaryotic biosynthetic processes. The protozoan parasite Toxoplasma gondii possesses the enzymes necessary for de novo folate synthesis and has been