De Novo Assembly of a Field Isolate Genome Reveals Novel Plasmodium vivax Erythrocyte Invasion Genes

PLoS Neglected Tropical Diseases

Volumn 7, Issue 12, 2013, Pages

  Hester, James ^a   Chan, Ernest R ^a   Menard, Didier ^b   Mercereau Puijalon, Odile ^c   Barnwell, John ^d   Zimmerman, Peter A ^e   Serre, David ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

^b INSTITUT PASTEUR DU CAMBODGE   (Cambodia)

^c INSTITUT PASTEUR   (France)

^d CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^e CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; ERYTHROCYTE BINDING PROTEIN; ERYTHROCYTE MEMBRANE PROTEIN 1; UNCLASSIFIED DRUG;

ADAPTIVE IMMUNITY; ARTICLE; CELL INVASION; CONTROLLED STUDY; DNA POLYMORPHISM; DNA SEQUENCE; ERYTHROCYTE; GENE CLUSTER; GENE IDENTIFICATION; GENE ISOLATION; GENE MAPPING; GENETIC VARIABILITY; MICROBIAL GENOME; NONHUMAN; PHYLOGENY; PLASMODIUM VIVAX; PROTEIN DOMAIN; VALIDATION PROCESS;

ANIMALS; DNA, PROTOZOAN; ENDOCYTOSIS; ERYTHROCYTES; GENES, PROTOZOAN; GENOME, PROTOZOAN; HAPLORHINI; HUMANS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PLASMODIUM VIVAX; SEQUENCE ANALYSIS, DNA; VIRULENCE FACTORS;

EID: 84892695546     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0002569     Document Type: Article

References (45)

1. Wertheimer SP, Barnwell JW, (1989) Plasmodium vivax interaction with the human Duffy blood group glycoprotein: identification of a parasite receptor-like protein. Exp Parasitol 69: 340-350.
2. Fang XD, Kaslow DC, Adams JH, Miller LH, (1991) Cloning of the Plasmodium vivax Duffy receptor. Mol Biochem Parasitol 44: 125-132.
3. Galinski MR, Medina CC, Ingravallo P, Barnwell JW, (1992) A reticulocyte-binding protein complex of Plasmodium vivax merozoites. Cell 69: 1213-1226.
4. Collins WE (2002) Nonhuman Primate Models. In: Doolan DL, editor. Malaria Methods and Protocols: Methods and Protocols. Totowa, New Jersey: Humana Press. pp. 77-84.
5. Neafsey DE, Galinsky K, Jiang RH, Young L, Sykes SM, et al. (2012) The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet 44: 1046-1050.
6. Chan ER, Menard D, David PH, Ratsimbasoa A, Kim S, et al. (2012) Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax. PLoS Negl Trop Dis 6: e1811.
7. Dharia NV, Bright AT, Westenberger SJ, Barnes SW, Batalov S, et al. (2010) Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A 107: 20045-20050.
8. Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, et al. (2008) Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455: 757-763.
9. Menard D, Chan ER, Benedet C, Ratsimbasoa A, Kim S, et al. (2013) Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains. PLoS Negl Trop Dis 7: e2489.
10. Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, et al. (2012) Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade. Nat Genet 44: 1051-1055.
11. Flicek P, Birney E, (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods 6: S6-S12.
12. Pain A, Bohme U, Berry AE, Mungall K, Finn RD, et al. (2008) The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature 455: 799-803.
13. Korf I, (2004) Gene finding in novel genomes. BMC Bioinformatics 5: 59.
14. del Portillo HA, Fernandez-Becerra C, Bowman S, Oliver K, Preuss M, et al. (2001) A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax. Nature 410: 839-842.
15. Fernandez-Becerra C, Yamamoto MM, Vencio RZ, Lacerda M, Rosanas-Urgell A, et al. (2009) Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily. Trends Parasitol 25: 44-51.
16. Merino EF, Fernandez-Becerra C, Durham AM, Ferreira JE, Tumilasci VF, et al. (2006) Multi-character population study of the vir subtelomeric multigene superfamily of Plasmodium vivax, a major human malaria parasite. Mol Biochem Parasitol 149: 10-16.
17. Carvalho BO, Lopes SC, Nogueira PA, Orlandi PP, Bargieri DY, et al. (2010) On the cytoadhesion of Plasmodium vivax-infected erythrocytes. J Infect Dis 202: 638-647.
18. Lopez FJ, Bernabeu M, Fernandez-Becerra C, del Portillo HA, (2013) A new computational approach redefines the subtelomeric vir superfamily of Plasmodium vivax. BMC Genomics 14: 8.
19. Bernabeu M, Lopez FJ, Ferrer M, Martin-Jaular L, Razaname A, et al. (2012) Functional analysis of Plasmodium vivax VIR proteins reveals different subcellular localizations and cytoadherence to the ICAM-1 endothelial receptor. Cell Microbiol 14: 386-400.
20. Rodriguez M, Lustigman S, Montero E, Oksov Y, Lobo CA, (2008) PfRH5: a novel reticulocyte-binding family homolog of plasmodium falciparum that binds to the erythrocyte, and an investigation of its receptor. PLoS One 3: e3300.
21. Adams JH, Sim BK, Dolan SA, Fang X, Kaslow DC, et al. (1992) A family of erythrocyte binding proteins of malaria parasites. Proc Natl Acad Sci U S A 89: 7085-7089.
22. Withers-Martinez C, Haire LF, Hackett F, Walker PA, Howell SA, et al. (2008) Malarial EBA-175 region VI crystallographic structure reveals a KIX-like binding interface. J Mol Biol 375: 773-781.
23. Hans D, Pattnaik P, Bhattacharyya A, Shakri AR, Yazdani SS, et al. (2005) Mapping binding residues in the Plasmodium vivax domain that binds Duffy antigen during red cell invasion. Mol Microbiol 55: 1423-1434.
24. VanBuskirk KM, Sevova E, Adams JH, (2004) Conserved residues in the Plasmodium vivax Duffy-binding protein ligand domain are critical for erythrocyte receptor recognition. Proc Natl Acad Sci U S A 101: 15754-15759.
25. Treeck M, Struck NS, Haase S, Langer C, Herrmann S, et al. (2006) A conserved region in the EBL proteins is implicated in microneme targeting of the malaria parasite Plasmodium falciparum. J Biol Chem 281: 31995-32003.
26. Gilberger TW, Thompson JK, Reed MB, Good RT, Cowman AF, (2003) The cytoplasmic domain of the Plasmodium falciparum ligand EBA-175 is essential for invasion but not protein trafficking. J Cell Biol 162: 317-327.
27. Ahouidi AD, Bei AK, Neafsey DE, Sarr O, Volkman S, et al. (2010) Population genetic analysis of large sequence polymorphisms in Plasmodium falciparum blood-stage antigens. Infect Genet Evol 10: 200-206.
28. Duraisingh MT, Triglia T, Ralph SA, Rayner JC, Barnwell JW, et al. (2003) Phenotypic variation of Plasmodium falciparum merozoite proteins directs receptor targeting for invasion of human erythrocytes. EMBO J 22: 1047-1057.
29. Jennings CV, Ahouidi AD, Zilversmit M, Bei AK, Rayner J, et al. (2007) Molecular analysis of erythrocyte invasion in Plasmodium falciparum isolates from Senegal. Infect Immun 75: 3531-3538.
30. Menard D, Barnadas C, Bouchier C, Henry-Halldin C, Gray LR, et al. (2010) Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proc Natl Acad Sci U S A 107: 5967-5971.
31. Cavasini CE, de Mattos LC, Couto AA, Couto VS, Gollino Y, et al. (2007) Duffy blood group gene polymorphisms among malaria vivax patients in four areas of the Brazilian Amazon region. Malar J 6: 167.
32. Ryan JR, Stoute JA, Amon J, Dunton RF, Mtalib R, et al. (2006) Evidence for transmission of Plasmodium vivax among a duffy antigen negative population in Western Kenya. Am J Trop Med Hyg 75: 575-581.
33. Mendes C, Dias F, Figueiredo J, Mora VG, Cano J, et al. (2011) Duffy negative antigen is no longer a barrier to Plasmodium vivax-molecular evidences from the African West Coast (Angola and Equatorial Guinea). PLoS Negl Trop Dis 5: e1192.
34. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
35. Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
36. Kelley DR, Schatz MC, Salzberg SL, (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol 11: R116.
37. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123.
38. Harris RS (2007) Improved pairwise alignment of genomic DNA: The Pennsylvania State University.
39. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, et al. (2009) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 37: D539-543.
40. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-229.
41. Krogh A, Larsson B, von Heijne G, Sonnhammer EL, (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580.
42. Petersen TN, Brunak S, von Heijne G, Nielsen H, (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
43. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
44. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
45. Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.