A first glimpse into the pattern and scale of gene transfer in the Apicomplexa

International Journal for Parasitology

Volumn 34, Issue 3, 2004, Pages 265-274

  Huang, Jinling ^a   Mullapudi, Nandita ^b   Sicheritz Ponten, Thomas ^c   Kissinger, Jessica C ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b Technical University of Denmark ^*  (United States)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Apicomplexa; Comparative genomics; Evolution; Gene transfer; PyPhy

Indexed keywords

GENE TRANSFER;

APICOMPLEXA; ARTICLE; BACTERIAL GENE; CHLOROPLAST; CONTROLLED STUDY; CRYPTOSPORIDIUM PARVUM; CYANOBACTERIUM; GENE IDENTIFICATION; GENE SEQUENCE; GENE TRANSFER; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; PROTOZOAL GENETICS;

ANIMALS; APICOMPLEXA; CRYPTOSPORIDIUM PARVUM; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, PROTOZOAN; GENOMICS; PHYLOGENY; PLASMODIUM FALCIPARUM; THEILERIA ANNULATA; TOXOPLASMA;

ALGAE; APICOMPLEXA; CRYPTOSPORIDIUM PARVUM; CYANOBACTERIA; KINETOPLASTIDA; PROTEOBACTERIA;

EID: 1542345724     PISSN: 00207519     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijpara.2003.11.025     Document Type: Article

References (47)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
2. Bahl A., Brunk B., Crabtree J., Fraunholz M.J., Gajria B., Grant G.R., Ginsburg H., Gupta D., Kissinger J.C., Labo P., Li L., Mailman M.D., Milgram A.J., Pearson D.S., Roos D.S., Schug J., Stoeckert C.J. Jr, Whetzel P. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 31:2003;212-215.
3. Baldauf S.L. The deep roots of eukaryotes. Science. 300:2003;1703-1706.
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res. 31:2003;23-27.
5. Cavalier-Smith T. Membrane heredity and early chloroplast evolution. Trends Plant Sci. 5:2000;174-182.
6. Denny P.W., Preiser P.R., Williams D.C., Wilson I. Evidence for a single origin of the 35 kb plastid DNA in apicomplexans. Protist. 149:1998;51-59.
7. Dzierszinski F., Popescu O., Toursel C., Slomianny C., Yahiaoui B., Tomavo S. The protozoan parasite Toxoplasma gondii expresses two functional plant-like glycolytic enzymes. Implications for evolutionary origin of apicomplexans. J. Biol. Chem. 274:1999;24888-24895.
8. Fast N.M., Kissinger J.C., Roos D.S., Keeling P.J. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 18:2001;418-426.
9. Felsenstein, J., 2002. PHYLIP (Phylogeny Inference Package) version 3.6a3. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
10. Fichera M.E., Roos D.S. A plastid organelle as a drug target in apicomplexan parasites. Nature. 390:1997;407-409.
11. Foth B.J., Ralph S.A., Tonkin C.J., Sturck N.S., Fraunholz M., Roos D.S., Cowman A.F., McFadden G.I. Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum. Science. 299:2003;705-708.
12. Funes S., Davidson E., Reyes-Prieto A., Magallon S., Herion P., King M.P., Gonzalez-Halphen D. A green algal apicoplast ancestor. Science. 298:2002;2155.
13. Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W., Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T., James K., Eisen J.A., Rutherford K., Salzberg S.L., Craig A., Kyes S., Chan M.S., Nene V., Shallom S.J., Suh B., Peterson J., Angiuoli S., Pertea M., Allen J., Selengut J., Haft D., Mather M.W., Vaidya A.B., Martin D.M., Fairlamb A.H., Fraunholz M.J., Roos D.S., Ralph S.A., McFadden G.I., Cummings L.M., Subramanian G.M., Mungall C., Venter J.C., Carucci D.J., Hoffman S.L., Newbold C., Davis R.W., Fraser C.M., Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419:2002;498-511.
14. 2+ signal? Trends Plant Sci. 5:2000;154-159.
15. Harmon A.C., Gribskov M., Gubrium E., Harper J.F. The CDPK superfamily of protein kinases. New Phytol. 151:2001;175-183.
16. Harper J.T., Keeling P.J. Nucleus-encoded plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol. 10:2003;1730-1735.
17. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., Gibson T.J. Multiple sequence alignment with ClustalX. Trends Biochem. Sci. 23:1998;403-405.
18. Ji Y.E., Mericle B.L., Rehkopf D.H., Anderson J.D., Feagin J.E. The Plasmodium falciparum 6 kb element is polycistronically transcribed. Mol. Biochem. Parasitol. 81:1996;211-223.
19. Jomaa H., Wiesner J., Sanderbrand S., Altincicek B., Weidemeyer C., Hintz M., Turbachova I., Eberl M., Zeidler J., Lichtenthaler H.K., Soldati D., Beck E. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science. 285:1999;1573-1576.
20. Kieschnick H., Wakefield T., Narducci C.A., Beckers C. Toxoplasma gondii attachment to host cells is regulated by a calmodulin-like domain protein kinase. J. Biol. Chem. 276:2001;12369-12377.
21. Kissinger J.C., Brunk B.P., Crabtree J., Fraunholz M.J., Gajria B., Milgram A.J., Pearson D.S., Schug J., Bahl A., Diskin S.J., Ginsburg H., Grant G.R., Gupta D., Labo P., Li L., Mailman M.D., McWeeney S.K., Whetzel P., Stoeckert C.J., Roos D.S. The Plasmodium genome database. Nature. 419:2002;490-492.
22. Kissinger J.C., Gajria B., Li L., Paulsen I.T., Roos D.S. ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Res. 31:2003;234-236.
23. 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. 275:1997;1485-1489.
24. Kurland C.G., Canback B., Berg O.G. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. USA. 100:2003;9658-9662.
25. Lang B.F., Gray M.W., Burger G. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33:1999;351-397.
26. Martin W., Rujan T., Richly E., Hansen A., Cornelsen S., Lins T., Leister D., Stoebe B., Hasegawa M., Penny D. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA. 99:2002;12246-12251.
27. McFadden G. Chloroplasts. Ever decreasing circles. Nature. 400:1999;119-120.
28. McFadden G.I. Plastids and protein targeting. J. Euk. Microbiol. 46:1999;339-346.
29. Palmer J.D. The symbiotic birth and spread of plastids: how many times and whodunit? J. Phycol. 39:2003;4-12.
30. Palmer J.D., Delwiche C.F. Second-hand chloroplasts and the case of the disappearing nucleus. Proc. Natl. Acad. Sci. USA. 93:1996;7432-7435.
31. Puiu D., Enomoto S., Buck G.A., Abrahamsen M., Kissinger J.C. CryptoDB: the Cryptosporidium genome resource. Nucleic Acids Res. 32:2004;D329-D331.
32. Roos D.S., Crawford M.J., Donald R.G., Kissinger J.C., Klimczak L.J., Striepen B. Origin, targeting, and function of the apicomplexan plastid. Curr. Opin. Microbiol. 2:1999;426-432.
33. Rujan T., Martin W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet. 17:2001;113-120.
34. Salzberg S.L., Pertea M., Delcher A.L., Gardner M.J., Tettelin H. Interpolated Markov models for eukaryotic gene finding. Genomics. 59:1999;24-31.
35. Schmatz D.M. The mannitol cycle in Eimeria. Parasitology. 114:1997;S81-S89.
36. Schmidt H.A., Strimmer K., Vingron M., von Haesler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:2002;502-504.
37. Sicheritz-Ponten T., Andersson S.G. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 29:2001;545-552.
38. Stanhope M.J., Lupas A., Italia M.J., Koretke K.K., Volker C., Brown J.R. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature. 411:2001;940-944.
39. Stechmann A., Cavalier-Smith T. Rooting the Eukaryote tree by using a derived gene fusion. Science. 297:2002;89-91.
40. Striepen B., White M.W., Li C., Guerini M.N., Malik S.B., Logsdon J.M. Jr., Liu C., Abrahamsen M.S. Genetic complementation in apicomplexan parasites. Proc. Natl. Acad. Sci. USA. 99:2002;6304-6309.
41. Striepen B., Pruijssers A.J.P., Huang J., Li C., Gubbels M.J., Umejiego N.N., Hedstrom L., Kissinger J.C. Gene transfer in the evolution of parasite nucleotide biosynthesis. Proc. Natl. Acad. Sci. USA. 2004;. in press.
42. Swofford D.L. PAUP* Phylogenetic Analysis Using Parsimony (*and other methods). 1998;Sinauer Press, Sunderland, MA.
43. Waller R.F., Keeling P.J., Donald R.G., Striepen B., Handman E., Lang-Unnasch N., Cowman A.F., Besra G.S., Roos D.S., McFadden G.I. Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum. Proc. Natl. Acad. Sci. USA. 95:1998;12352-12357.
44. Waller R.F., Keeling P.J., van Dooren G.G., McFadden G. Comment on A green Algal Apicoplast Ancestor. Science. 301:(49a):2003.
45. Waller R.F., Reed M.B., Cowman A.F., McFadden G.I. Protein trafficking to the plastid of Plasmodium falciparum is via the secretory pathway. Eur. Mol. Biol. Org. J. 19:2000;1794-1802.
46. Wilson R.J., 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. 261:1996;155-172.
47. Zhu G., Marchewka M.J., Keithly J.S. Cryptosporidium parvum appears to lack a plastid genome. Microbiol. Mol. Biol. Rev. 146:2000;315-321.