Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum

Molecular and Biochemical Parasitology - Tập 150 - Trang 10-24 - 2006
Lara L. Bethke1, Martine Zilversmit2, Kaare Nielsen2, Johanna Daily1, Sarah K. Volkman1, Daouda Ndiaye3, Elena R. Lozovsky2, Daniel L. Hartl2, Dyann F. Wirth1
1Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
2Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
3Cheikh Anta Diop University, Dakar, Senegal

Tài liệu tham khảo

Price, 2004, Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number, Lancet, 364, 438, 10.1016/S0140-6736(04)16767-6 Kappe, 1998, A family of chimeric erythrocyte binding proteins of malaria parasites, Proc Natl Acad Sci USA, 95, 1230, 10.1073/pnas.95.3.1230 Freitas-Junior, 2000, Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum, Nature, 407, 1018, 10.1038/35039531 Nielsen, 2003, Gene conversion as a source of nucleotide diversity in Plasmodium falciparum, Mol Biol Evol, 20, 726, 10.1093/molbev/msg076 Carlton, 2002, Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii, Nature, 419, 512, 10.1038/nature01099 Gardner, 2002, Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, 419, 498, 10.1038/nature01097 Scherf, 2001, Plasmodium telomeres: a pathogen's perspective, Curr Opin Microbiol, 4, 409, 10.1016/S1369-5274(00)00227-7 Hall, 2005, A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses, Science, 307, 82, 10.1126/science.1103717 Militello, 2004, Identification of regulatory elements in the Plasmodium falciparum genome, Mol Biochem Parasitol, 134, 75, 10.1016/j.molbiopara.2003.11.004 Trager, 1976, Human malaria parasites in continuous culture, Science, 193, 673, 10.1126/science.781840 Kissinger, 2002, The Plasmodium genome database, Nature, 419, 490, 10.1038/419490a Wootton, 1993, Statistics of local complexity in amino acid sequences and sequence databases, Comput Chem, 17, 149, 10.1016/0097-8485(93)85006-X Daily, 2005, In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins, J Infect Dis, 191, 1196, 10.1086/428289 Daily, 2004, In vivo transcriptional profiling of Plasmodium falciparum, Malaria J, 3, 30, 10.1186/1475-2875-3-30 Le Roch, 2003, Discovery of gene function by expression profiling of the malaria parasite life cycle, Science, 301, 1503, 10.1126/science.1087025 Zhou, 2002, Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis, BMC Bioinform, 3, 3, 10.1186/1471-2105-3-3 Rozas, 1995, DnaSP DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data, Comput Appl Biosci, 11, 621 Cargill, 1999, Characterization of single-nucleotide polymorphisms in coding regions of human genes, Nat Genet, 22, 231, 10.1038/10290 Mu, 2002, Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum, Nature, 418, 323, 10.1038/nature00836 Nei, 1986, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions, Mol Biol Evol, 3, 418 Jukes, 1969, Evolution of protein molecules, 21 Tajima, 1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, 123, 585, 10.1093/genetics/123.3.585 Fu, 1993, Statistical tests of neutrality of mutations, Genetics, 133, 693, 10.1093/genetics/133.3.693 McDonald, 1991, Adaptive protein evolution at the Adh locus in Drosophila, Nature, 351, 652, 10.1038/351652a0 Hudson, 1987, A test of neutral molecular evolution based on nucleotide data, Genetics, 116, 153, 10.1093/genetics/116.1.153 Notredame, 1987, T-coffee: a novel method for fast and accurate multiple sequence alignment, J Mol Biol, 302, 205, 10.1006/jmbi.2000.4042 Matesanz, 2003, The Plasmodium falciparum fatty acyl-CoA synthetase family (PfACS) and differential stage-specific expression in infected erythrocytes, Mol Biochem Parasitol, 126, 109, 10.1016/S0166-6851(02)00242-6 Hisanaga, 2004, Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimmer, J Biol Chem, 279, 31717, 10.1074/jbc.M400100200 Flick, 2004, var genes, PfEMP1 and the human host, Mol Biochem Parasitol, 134, 3, 10.1016/j.molbiopara.2003.09.010 Bozdech, 2003, The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum, PLoS Biol, 1, E5, 10.1371/journal.pbio.0000005 Black, 1997, Mutational analysis of a fatty acyl-coenzyme A synthetase signature motif identifies seven amino acid residues that modulate fatty acid substrate specificity, J Biol Chem, 272, 4896, 10.1074/jbc.272.8.4896 Lynch, 1997, The analysis of population survey data on DNA sequence variation, Mol Biol Evol, 7, 377 Gerber, 2001, Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?, Annu Rev Genet, 35, 539, 10.1146/annurev.genet.35.102401.091106 Tellez, 2003, The C-terminal domain of the Plasmodium falciparum acyl-CoA synthetases PfACS1 and PfACS3 functions as ligand for ankyrin, Mol Biochem Parasitol, 129, 191, 10.1016/S0166-6851(03)00123-3 DiRusso, 1999, Long-chain fatty acid transport in bacteria and yeast. Paradigms for defining the mechanism underlying this protein-mediated process, Mol Cell Biochem, 192, 41, 10.1023/A:1006823831984 Zhu, 2004, Current progress in the fatty acid metabolism in Cryptosporidium parvum, J Eukaryot Microbiol, 51, 381, 10.1111/j.1550-7408.2004.tb00384.x Knoll, 1995, Comparison of the reactivity of tetradecenoic acids, a triacsin, and unsaturated oximes with four purified Saccharomyces cerevisiae fatty acid activation proteins, J Biol Chem, 270, 20090, 10.1074/jbc.270.34.20090 Jiang, 2001, Four Trypanosoma brucei fatty acyl-CoA synthetases: fatty acid specificity of the recombinant proteins, Biochem J, 358, 757, 10.1042/0264-6021:3580757 Mashek, 2004, Revised nomenclature for the mammalian long-chain acyl-CoA synthetase gene family, J Lipid Res, 45, 1958, 10.1194/jlr.E400002-JLR200 Coleman, 2002, Do long-chain acyl-CoA synthetases regulate fatty acid entry into synthetic versus degradative pathways?, J Nutr, 132, 2123, 10.1093/jn/132.8.2123 Florens, 2002, A proteomic view of the Plasmodium falciparum life cycle, Nature, 419, 520, 10.1038/nature01107 Beaumelle, 1988, Acyl-CoA synthetase activity in Plasmodium knowlesi-infected erythrocytes displays peculiar substrate specificities, Biochim Biophys Acta, 958, 1, 10.1016/0005-2760(88)90239-1 Vial, 2003, Phospholipids in parasitic protozoa, Mol Biochem Parasitol, 126, 143, 10.1016/S0166-6851(02)00281-5 Vial, 1998, Malarial Lipids, 159 Beaumelle, 1988, Correlation of the efficiency of fatty acid derivatives in suppressing Plasmodium falciparum growth in culture with their inhibitory effect on acyl-CoA synthetase activity, Mol Biochem Parasitol, 28, 39, 10.1016/0166-6851(88)90177-6 Baum, 2003, Evidence for diversifying selection on erythrocyte-binding antigens of Plasmodium falciparum and P. vivax, Genetics, 163, 1327, 10.1093/genetics/163.4.1327 McCarrey, 1986, Determinator–inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes, Proc Natl Acad Sci USA, 83, 679, 10.1073/pnas.83.3.679 Zhang, 2004, Large-scale analysis of pseudogenes in the human genome, Curr Opin Genet Dev, 14, 328, 10.1016/j.gde.2004.06.003 Vargas-Madrazo, 1995, Structural repertoire in VH pseudogenes of immunoglobulins: comparison with human germline genes and human amino acid sequences, J Mol Biol, 246, 74, 10.1006/jmbi.1994.0067 Figueiredo, 2005, The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus, Nucl Acids Res, 33, 1111, 10.1093/nar/gki260