TY - JOUR T1 - Functional genomics of trypanosomatids. JF - Parasite Immunol Y1 - 2012 A1 - Choi, J A1 - El-Sayed, N M KW - Animals KW - Genome, Protozoan KW - Genomics KW - HUMANS KW - Proteome KW - Protozoan Proteins KW - Transcriptome KW - Trypanosomatina AB -

The decoding of the Tritryp reference genomes nearly 7 years ago provided a first peek into the biology of pathogenic trypanosomatids and a blueprint that has paved the way for genome-wide studies. Although 60-70% of the predicted protein coding genes in Trypanosoma brucei, Trypanosoma cruzi and Leishmania major remain unannotated, the functional genomics landscape is rapidly changing. Facilitated by the advent of next-generation sequencing technologies, improved structural and functional annotation and genes and their products are emerging. Information is also growing for the interactions between cellular components as transcriptomes, regulatory networks and metabolomes are characterized, ushering in a new era of systems biology. Simultaneously, the launch of comparative sequencing of multiple strains of kinetoplastids will finally lead to the investigation of a vast, yet to be explored, evolutionary and pathogenomic space.

VL - 34 CP - 2-3 M3 - 10.1111/j.1365-3024.2011.01347.x ER - TY - Generic T1 - Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts. Y1 - 2012 A1 - Savage, Amy F A1 - Cerqueira, Gustavo C A1 - Regmi, Sandesh A1 - Wu, Yineng A1 - El Sayed, Najib M A1 - Aksoy, Serap KW - Animals KW - Computational Biology KW - Gastrointestinal Tract KW - Gene Expression Profiling KW - GPI-Linked Proteins KW - HUMANS KW - Male KW - Membrane Proteins KW - Protozoan Proteins KW - Real-Time Polymerase Chain Reaction KW - Salivary Glands KW - Trypanosoma brucei brucei KW - Trypanosomiasis, African KW - Tsetse Flies AB -

Human African Trypanosomiasis is a devastating disease caused by the parasite Trypanosoma brucei. Trypanosomes live extracellularly in both the tsetse fly and the mammal. Trypanosome surface proteins can directly interact with the host environment, allowing parasites to effectively establish and maintain infections. Glycosylphosphatidylinositol (GPI) anchoring is a common posttranslational modification associated with eukaryotic surface proteins. In T. brucei, three GPI-anchored major surface proteins have been identified: variant surface glycoproteins (VSGs), procyclic acidic repetitive protein (PARP or procyclins), and brucei alanine rich proteins (BARP). The objective of this study was to select genes encoding predicted GPI-anchored proteins with unknown function(s) from the T. brucei genome and characterize the expression profile of a subset during cyclical development in the tsetse and mammalian hosts. An initial in silico screen of putative T. brucei proteins by Big PI algorithm identified 163 predicted GPI-anchored proteins, 106 of which had no known functions. Application of a second GPI-anchor prediction algorithm (FragAnchor), signal peptide and trans-membrane domain prediction software resulted in the identification of 25 putative hypothetical proteins. Eighty-one gene products with hypothetical functions were analyzed for stage-regulated expression using semi-quantitative RT-PCR. The expression of most of these genes were found to be upregulated in trypanosomes infecting tsetse salivary gland and proventriculus tissues, and 38% were specifically expressed only by parasites infecting salivary gland tissues. Transcripts for all of the genes specifically expressed in salivary glands were also detected in mammalian infective metacyclic trypomastigotes, suggesting a possible role for these putative proteins in invasion and/or establishment processes in the mammalian host. These results represent the first large-scale report of the differential expression of unknown genes encoding predicted T. brucei surface proteins during the complete developmental cycle. This knowledge may form the foundation for the development of future novel transmission blocking strategies against metacyclic parasites.

JA - PLoS Negl Trop Dis VL - 6 CP - 6 M3 - 10.1371/journal.pntd.0001708 ER - TY - JOUR T1 - Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi. JF - Nucleic Acids Res Y1 - 2009 A1 - Bartholomeu, Daniella C A1 - Cerqueira, Gustavo C A1 - Leão, Ana Carolina A A1 - daRocha, Wanderson D A1 - Pais, Fabiano S A1 - Macedo, Camila A1 - Djikeng, Appolinaire A1 - Teixeira, Santuza M R A1 - El-Sayed, Najib M KW - 3' Flanking Region KW - 5' Flanking Region KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Conserved Sequence KW - Gene Expression Profiling KW - Genes, Protozoan KW - Genome, Protozoan KW - Membrane Proteins KW - Molecular Sequence Data KW - Mucins KW - Multigene Family KW - Protozoan Proteins KW - RNA, Messenger KW - Trypanosoma cruzi AB -

A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to approximately 6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5' and 3' untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system.

VL - 37 CP - 10 M3 - 10.1093/nar/gkp172 ER - TY - JOUR T1 - Genome sequence of the human malaria parasite Plasmodium falciparum JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Hall, Neil A1 - Fung, Eula A1 - White, Owen A1 - Berriman, Matthew A1 - Hyman, Richard W. A1 - Carlton, Jane M. A1 - Pain, Arnab A1 - Nelson, Karen E. A1 - Bowman, Sharen A1 - Paulsen, Ian T. A1 - James, Keith A1 - Eisen, Jonathan A. A1 - Rutherford, Kim A1 - Salzberg, Steven L. A1 - Craig, Alister A1 - Kyes, Sue A1 - Chan, Man-Suen A1 - Nene, Vishvanath A1 - Shallom, Shamira J. A1 - Suh, Bernard A1 - Peterson, Jeremy A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - Haft, Daniel A1 - Mather, Michael W. A1 - Vaidya, Akhil B. A1 - Martin, David M. A. A1 - Fairlamb, Alan H. A1 - Fraunholz, Martin J. A1 - Roos, David S. A1 - Ralph, Stuart A. A1 - McFadden, Geoffrey I. A1 - Cummings, Leda M. A1 - Subramanian, G. Mani A1 - Mungall, Chris A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Newbold, Chris A1 - Davis, Ronald W. A1 - Fraser, Claire M. A1 - Barrell, Bart KW - Animals KW - Chromosome Structures KW - DNA Repair KW - DNA Replication KW - DNA, Protozoan KW - Evolution, Molecular KW - Genome, Protozoan KW - HUMANS KW - Malaria Vaccines KW - Malaria, Falciparum KW - Membrane Transport Proteins KW - Molecular Sequence Data KW - Plasmodium falciparum KW - Plastids KW - Proteome KW - Protozoan Proteins KW - Recombination, Genetic KW - Sequence Analysis, DNA AB - The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368864?dopt=Abstract ER - TY - JOUR T1 - A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. JF - Eukaryot Cell Y1 - 2002 A1 - Bringaud, Frederic A1 - Biteau, Nicolas A1 - Melville, Sara E A1 - Hez, Stéphanie A1 - El-Sayed, Najib M A1 - Leech, Vanessa A1 - Berriman, Matthew A1 - Hall, Neil A1 - Donelson, John E A1 - Baltz, Théo KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Cloning, Molecular KW - DNA Primers KW - DNA, Protozoan KW - Escherichia coli KW - Genes, Protozoan KW - Molecular Sequence Data KW - Multigene Family KW - Mutagenesis, Insertional KW - Phylogeny KW - Polymorphism, Genetic KW - Protozoan Proteins KW - Pseudogenes KW - Retroelements KW - sequence alignment KW - Sequence Homology, Amino Acid KW - Telomere KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi AB -

We describe a novel gene family that forms clusters in subtelomeric regions of Trypanosoma brucei chromosomes and partially accounts for the observed clustering of retrotransposons. The ingi and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the T. brucei genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or ingi retrotransposon inserted at exactly the same relative position. Here these genes are called the RHS family, for retrotransposon hot spot. Comparison of the protein sequences encoded by RHS genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/ingi insertion site. The RHS proteins share between 13 and 96% identity, and six subfamilies, RHS1 to RHS6, can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the Trypanosoma brucei diploid genome contains about 280 RHS (pseudo)genes. Among the 52 identified RHS (pseudo)genes, 48 copies are in three RHS clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in T. brucei strain TREU927/4 GUTat10.1. RHS genes comprise the remaining sequence of the size-polymorphic "repetitive region" described for T. brucei chromosome I, and a homologous gene family is present in the Trypanosoma cruzi genome.

VL - 1 CP - 1 ER - TY - JOUR T1 - Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Shallom, Shamira J. A1 - Carlton, Jane M. A1 - Salzberg, Steven L. A1 - Nene, Vishvanath A1 - Shoaibi, Azadeh A1 - Ciecko, Anne A1 - Lynn, Jeffery A1 - Rizzo, Michael A1 - Weaver, Bruce A1 - Jarrahi, Behnam A1 - Brenner, Michael A1 - Parvizi, Babak A1 - Tallon, Luke A1 - Moazzez, Azita A1 - Granger, David A1 - Fujii, Claire A1 - Hansen, Cheryl A1 - Pederson, James A1 - Feldblyum, Tamara A1 - Peterson, Jeremy A1 - Suh, Bernard A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - White, Owen A1 - Cummings, Leda M. A1 - Smith, Hamilton O. A1 - Adams, Mark D. A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Fraser, Claire M. KW - Animals KW - Chromosomes KW - DNA, Protozoan KW - Genome, Protozoan KW - Plasmodium falciparum KW - Proteome KW - Protozoan Proteins KW - Sequence Analysis, DNA AB - The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368868?dopt=Abstract ER -