Plasmodium vivax apicoplast genome: A comparative analysis of major genes from Indian field isolates

Acta Tropica

Volumn 122, Issue 1, 2012, Pages 138-149

  Saxena, Vishal ^a   Garg, Shilpi ^a   Tripathi, Jyotsna ^a   Sharma, Sonal ^a   Pakalapati, Deepak ^a   Subudhi, Amit K ^a   Boopathi, P A ^a   Saggu, Gagandeep S ^a   Kochar, Sanjay K ^b   Kochar, Dhanpat K ^c   Das, Ashis ^a  

^a BIRLA INSTITUTE OF TECHNOLOGY AND SCIENCE   (India)

^b S P MEDICAL COLLEGE   (India)

^c Kothari Medical and Research Institute ^*  (India)

Author keywords

Apicoplast; Codon usage; Phylogeny; Plasmodium vivax; Plastid DNA

Indexed keywords

PROTOZOAL DNA;

COMPARATIVE STUDY; DISEASE INCIDENCE; DISEASE SEVERITY; DRUG RESISTANCE; EPIDEMIOLOGY; GENETIC ANALYSIS; GENOME; LABORATORY METHOD; MALARIA; PARASITE; PARASITE RESISTANCE; PHYLOGENY; PLASTID; PROTEIN; PROTIST;

APICOPLAST; ARTICLE; CLPC GENE; CODON USAGE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE; GENE AMPLIFICATION; GENE SEQUENCE; GENOME; INDIA; LSU RRNA GENE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; RPO B GENE; RPO C GENE; SEQUENCE ANALYSIS; SSU RRNA GENE; SUFB GENE; TUFA GENE;

CODON; CONSERVED SEQUENCE; DNA, CIRCULAR; DNA, PROTOZOAN; GENES, PROTOZOAN; GENOME; INDIA; MOLECULAR SEQUENCE DATA; ORGANELLES; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

INDIA;

PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PROKARYOTA;

EID: 84863402726     PISSN: 0001706X     EISSN: 18736254     Source Type: Journal    
DOI: 10.1016/j.actatropica.2012.01.007     Document Type: Article

References (45)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Alexandre M.A., Ferreira C.O., Siqueira A.M., Magalhães B.L., Mourão M.P.G., Lacerda M.V., Alecrim M.G.C. Severe Plasmodium vivax malaria, Brazilian Amazon. Emerg. Infect. Dis. 2010, 16:1611-1614.
3. Aurrecoechea C., Brestelli J., Brunk B.P., Dommer J., Fischer S., Gajria B., Gao X., Gingle A., Grant G., Harb O.S., Heiges M., Innamorato F., Iodice J., Kissinger J.C., Kraemer E., Li W., Miller J.A., Nayak V., Pennington C., Pinney D.F., Roos D.S., Ross C., Stoeckert C.J., Treatman C., Wang H. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009, 37:D539-D543.
4. Biswas S., Lim E.E., Gupta A., Saqib U., Mir S.S., Siddiqi M.I., Ralph S.A., Habib S. Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodium falciparum plastid. Int. J. Parasitol. 2011, 41:417-427.
5. Carlton J.M., Adams J.H., Silva J.C., Bidwell S.L., Lorenzi H., Caler E., Crabtree J., Angiuoli S.V., Merino E.F., Amedeo P., Cheng Q., Coulson R.M.R., Crabb B.S., Portillo H.A., Essien K., Feldblyum T.V., Fernandez-Becerra C., Gilson P.R., Gueye A.H., Guo X., Kang'a S., Kooij T.W.A., Korsinczky M., Meyer E.V.S., Nene V., Paulsen I., White O., Ralph S.A., Ren Q., Sargeant T.J., Salzberg S.L., Stoeckert C.J., Sullivan S.A., Yamamoto M.M., Hoffman S.L., Wortman J.R., Gardner M.J., Galinski M.R., Barnwell J.H., Fraser-Liggett C.M. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 2008, 455:757-763.
6. Chaubey S., Kumar A., Singh D., Habib S. The apicoplast of P. falciparum is translationally active. Mol. Microbiol. 2005, 56:81-89.
7. Chen N., Cheng Q. Codon usage in Plasmodium vivax nuclear genes. Int. J. Parasitol. 1999, 29:445-449.
8. Creasey A., Mendis K., Carlton J., Williamson D., Wilson I., Carter R. Material inheritance of extrachromosomal DNA in malaria parasites. Mol. Biochem. Parasitol. 1994, 65:95-98.
9. Das A., Holloway B., Collins W.E., Sharma V.P., Ghosh S.K., Sinha S., Hasnain S.E., Talwar G.P., Lal A.A. Species-specific 18S rRNA gene amplification for the detection of P. falciparum and P. vivax malaria parasites. Mol. Cell. Probes 1995, 9:161-165.
10. Ellis K.E.S., Clough B., Saldanha J.W., Wilson R.J.M. Nifs and Sufs in malaria. Mol. Microbiol. 2001, 41:973-981.
11. Escalante A.A., Cornejo O.E., Freeland D.E., Poe A.C., Durrego E., Collins W.E., Lal A.A. A monkey's tale: the origin of Plasmodium vivax as a human malaria parasite. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:1980-1985.
12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
13. Fichera M.E., Roos D.S. A plastid organelle as a drug target in apicomplexan parasites. Nature 1997, 390:407-409.
14. Foth B.J., McFadden G.I. The apicoplast: a plastid in Plasmodium falciparum and other apicomplexan parasites. Int. Rev. Cytol. 2003, 224:57-110.
15. Gardner M.J., Williamson D.H., Wilson R.J.M. A circular DNA in malaria parasites encodes an RNA polymerase like that of prokaryotes and chloroplasts. Mol. Biochem. Parasitol. 1991, 44:115-123.
16. Gardner M.J., Goldman N., Barnett P., Moore P.W., Rangachari K., Strath M., Whyte A., Williamson D.H., Wilson R.J. Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum. Mol. Biochem. Parasitol. 1994, 66:221-231.
17. Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., Gibson T.J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
18. Kochar D.K., Saxena V., Singh N., Kochar S.K., Kumar S.V., Das A. Plasmodium vivax malaria. Emerg. Infect. Dis. 2005, 11:132-134.
19. Kochar D.K., Pakalapati D., Kochar S.K., Sirohi P., Khatri M.P., Kochar A., Das A. An unexpected cause of fever and seizures. Lancet 2007, 370:908.
20. Kochar D.K., Das A., Kochar S.K., Saxena V., Sirohi P., Garg S., Kochar A., Khatri M.P., Gupta V. Severe Plasmodium vivax malaria: a report on serial cases from Bikaner in Northwestern India. Am. J. Trop. Med. Hyg. 2009, 80(2):194-198.
21. Kohler S., Delwiche C.F., Denny P.W., Tilney L.G., Webster P., Wilson R.J., Palmer J.D., Roos D.S. A plastid of probable green algal origin in apicomplexan parasites. Science 1997, 275:1485-1489.
22. Kumar S., Tamura K., Nei M. MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 2004, 5:150-163.
23. Lim L., McFadden G.I. The evolution, metabolism and functions of the apicoplast. Phil. Trans. R. Soc. B 2010, 365:749-763.
24. Marchler-Bauer A., Anderson J.B., Chitsaz F., Derbyshire M.K., DeWeese-Scott C., Fong J.H., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Lu S., Marchler G.H., Mullokandov M., Song J.S., Tasneem A., Thanki N., Yamashita R.A., Zhang D., Zhang N., Bryant S.H. CDD: specific functional annotation with the conserved domain database. Nucleic Acids Res. 2009, Database issue: D205-D210.
25. McFadden G.I., Roos D.S. Apicomplexan plastids as drug targets. Trends Microbiol. 1999, 7:328-333.
26. McFadden G.I., Waller R.F. Plastid in parasites of humans. Bioessays 1997, 9:1033-1040.
27. Mitsui H., Arisue N., Sakihama N., Inagaki Y., Horii T., Masami H., Tanabe K., Hashimoto T. Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile. Gene 2010, 450:32-38.
28. Nishimoto Y., Arisue N., Kawai S., Escalante A.A., Horii T., Tanabe K., Hashimoto T. Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium. Mol. Phylogenet. Evol. 2008, 47:45-53.
29. Okamoto N., JanouŠkovec J., Chrudimský T., LukeŠ J. Evolution of the apicoplast and its hosts: from heterotrophy to autotrophy and back again. Int. J. Parasitol. 2009, 39:1-2.
30. Patzer S.I., Hantke K. SufS is a NifS-like protein, and SufD is necessary for stability of the [2Fe-2S] FhuF protein in Escherichia coli. J. Bacteriol. 1999, 181:3307-3309.
31. Perkins S.L., Sarkar I.N., Carter R. The phylogeny of rodent malaria parasites: simultaneous analysis across three genomes. Infect. Genet. Evol. 2007, 7:74-83.
32. Ralph S.A., D'Ombrain M.C., McFadden G.I. The apicoplast as an antimalarial drug target. Drug Resist. Updat. 2001, 4:145-151.
33. Rathore D., Wahl A.M., Sullivan M., McCutchan T.F. A phylogenetic comparison of gene trees constructed from plastid, mitochondrial and genomic DNA of Plasmodium species. Mol. Biochem. Parasitol. 2001, 114:89-94.
34. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
35. Sambrook J., Russell D. Molecular Cloning: A Laboratory Manual 2000, Cold Spring Harb Protoc, Cold Spring Harbor Laboratory Press. 3rd ed.
36. Sato S., Tews I., Wilson R.J.M. Impact of a plastid-bearing endocytobiont on apicomplexan genomes. Int. J. Parasitol. 2000, 30:427-439.
37. Saxena V., Garg S., Ranjan S., Kochar D., Ranjan A., Das A. Analysis of elongation factor Tu (tuf A) of apicoplast from Indian Plasmodium vivax isolates. Infect. Genet. Evol. 2007, 7:618-626.
38. Sharma I., Pasha S.T., Sharma Y.D. Complete nucleotide sequence of the Plasmodium vivax 6kb element. Mol. Biochem. Parasitol. 1998, 97:259-263.
39. Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:11030-11035.
40. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
41. Williamson D.H., Preiser P.R., Moore P.W., McCready S., Strath M., Wilson R.J.M. The plastid DNA of the malaria parasite Plasmodium falciparum is replicated by two mechanisms. Mol. Microbiol. 2002, 45:533-542.
42. Wilson R.J.M., Denny P.W., Preiser P.R., Rangachari K., Roberts K., Roy A., Whyte A., Strath M., Moore D.J., Moore P.W., Williamson D.H. Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J. Mol. Biol. 1996, 261:155-172.
43. Wilson R.J.M., Williamson D.H. Extrachromosomal DNA in the Apicomplexa. Microbiol. Mol. Biol. Rev. 1997, 61:1-16.
44. Wilson R.J.M. Parasite plastids: approaching the endgame. Biol. Rev. 2005, 80:129-153.
45. Yap M.W.C., Kara U.A.K., Heggeler-Bordier B.T., Ting R.C.Y., Tan T.M.C. Partial nucleotide sequence and organization of extra-chromosomal plastid-like DNA in Plasmodium berghei. Gene 1997, 200:91-98.