The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage

Journal of Eukaryotic Microbiology

Volumn 46, Issue 4, 1999, Pages 367-375

  Blanchard, Jeffrey L ^a,b   Hicks, Justin S ^a  

^a UNIVERSITY OF OREGON   (United States)

^b PROMEGA CORPORATION   (United States)

Author keywords

Chloroplast; Genetic code; Genomic evolution; Plasmodium falciparum; Sporozoa

Indexed keywords

AMINO ACID SEQUENCE; DNA ANALYSIS; EVOLUTION; GENOME ANALYSIS; PHOTOSYNTHESIS; PLASTID;

PLASMODIUM FALCIPARUM;

EID: 0033167106     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.1999.tb04615.x     Document Type: Conference Paper

References (58)

1. Allison, L. A., Simon, D. L. & Maliga, P. 1996. Deletion of rpoB reveals a 2nd distinct transcription system in plastids of higher plants. EMBO J., 15:2802-2809.
2. Assali, N. E. & Loiseaux-de Göer, S. 1992. Sequence and phylogeny of the psaB gene of Phlaiella littoralis Phaeophyta. J. Phycol., 28: 209-213.
3. Baldauf, S. L., Manhart, J. R. & Palmer, J. D. 1990. Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae. Proc. Natl. Acad. Sci. USA., 87:5317-5321.
4. Baldauf, S. L., Palmer, J. D. & Doolittle, W. F. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA., 93:7749-7754.
5. Bhattacharya, D. & Medlin, L. 1995. The phylogeny of plastids: A review based on comparisons of small-subunit ribosomal RNA coding regions. J. Phycol., 31:489-498.
6. Boore, J. L., Lavrov, D. V. & Brown, W. M. 1998. Gene translocation links insects and crustaceans. Nature, 392:667-668.
7. Boore, J. L., Collins, T. M., Stanton, D., Daehler, L. L. & Brown, W. M. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature, 376:163-165.
8. Boudreau, E., Otis, C. & Turmel, M. 1994. Conserved gene clusters in the highly rearranged chloroplast genomes of Chlamydomonas moewusii and Chlamydmonas reinhardtii. Plant Mol. Biol., 24:585-602.
9. Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L. & Waddell, P. J. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol., 42:384-397.
10. Caron, L., Douady, D., Quinet-Szely, M., Loiseaux- de Goër, S. & Berkaloff, C. 1996. Gene Structure of a chlorophyll a/c-binding protein from a brown alga: presence of an intron and phylogenetic implications. J. Mol. Evol., 43:270-280.
11. Delwiche, C. F. & Palmer, J. D. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol. Biol. Evol., 13:873-882.
12. Delwiche, C. F., Kuhsel, M. & Palmer, J. D. 1995. Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol. Phylogenet. Evol., 4:110-128.
13. Denny, P., Preiser, P., Williamson, D. & Wilson, I. 1998. Evidence for a single origin of the 35kb plastid DNA in Apicomplexans. Protist, 149:51-59.
14. De Rijk, P. & De Wachten R. 1993. DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Appl. Biosci., 9:735-740.
15. De Rijk, P., Caers, A., Van de Peer, Y. & De Wachter, R. 1998. Database on the structure of large ribosomal subunit RNA. Nucl. Acids. Res., 26:183-186.
16. Deveraux, J., Haeberli, P. & Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucl. Acids. Res., 12:387-395.
17. Eaga, N. & Lang-Unnasch, N. 1995. Phylogeny of the large extrachromosomal DNA of organisms in the phylum Apicomplexa. J. Euk. Microbiol., 42:679-684.
18. Fichera, M. E. & Roos, D. S. 1997. A plastid organelle as a drug target in apicomplexan parasites. Nature, 390:407-409.
19. Gardner, M. J., Williamson, D. H. & Wilson, R. J. M. 1991. A circular DNA in malaria parasites encodes an RNA polymerase like that of prokaryotes and chloroplasts. Mol. Biochem. Parasitiol., 44:115-123.
20. Gardner, M. J., Goldman, N., Barnett, P., Moore, P. W., Rangachari, K., Strath, M., Whyte, A., Williamson, D. H. & Wilson, R. J. M. 1994. Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum. Molecular and Biochemical Parasitology, 66:221-231.
21. Gibbs, S. P. 1978. The chloroplasts of Euglena may have evolved from symbiotic green algae. Can. J. Bot., 56:2882-2889.
22. Gray, M. W., Lang, B. F., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Tunnel, M., Brossard, N., Delage, E., Littlejohn, T. G. et al. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucl. Acids Res., 26:865-878.
23. Hallick, R. B., Hong, L., Drager, R. G., Favreau, M. R., Monfort, A., Orat, B., Spielman, A. & Stutz, E. 1993. Complete sequence of the Euglena gracilis chloroplast DNA. Nucl. Acids Res., 21:3537-3544.
24. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol., 47:3-8.
25. Howe, C. J. 1992. Plastid origin of an extrachromosomal DNA molecular from Plasmodium, the causative agent of malaria. J. Theor. Biol., 158:199-205.
26. Köhler, S., Delwiche, C. F., Denny, P. W., Tilney, L. G., Webster, P., Wilson, R. J. M., Palmer, J. D. & Roos, D. S. 1997. A plastid of probable green algal origin in apicomplexan parasites. Science, 275: 1485-1489
27. Levine, N. D. 1987. Phylum II. Apicomplexa Levine. 1970. In: Lee, J. J., Hutner, S. H. and Bovee, H. C. (ed.), An Illustrated Guide to the Protozoa. Society of Protozoologists, Lawrence, Kansas. p. 322-374.
28. Lockhart, P. J., Steel, M. A., Hendy, M. D. & Penny, D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol., 11:605-612.
29. Madison, W. P. & Madison, D. R. 1992. MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland, MA.
30. Manhart, J. R. & Palmer, J. D. 1990. The gain of two chloroplast transfer RNA introns marks the green algal ancestors of land plants. Nature, 345:268-270.
31. Martin, W., Stoebe, B., Goremykin, V., Hansmann, S., Hasegawa, M. & Kowallik, K. V. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393:162-165.
32. McFadden, G. I. & Waller, R. F. 1997. Plastids in parasites of humans. BioEssays, 19:1033-1040.
33. McFadden, G. I., Reith, M. E., Munholland, J. & Lang-Unnasch, N. 1996. Plastid in human parasites. Nature, 381:482.
34. Morden, C. W., Delwiche, C. F., Kuhsel, M. & Palmer, J. D. 1992. Gene phytogenies and the endosymbiotic origin of plastids. BioSystems, 28: 75-90.
35. Naylor, G. J. P. & Brown, W. M. 1998. Amphioxus mitochondrial DNA, chordate phytogeny, and the limits of inference based on comparisons of sequences. Syst. Biol., 47:61-76.
36. Ohta, N., Sato, N., Nozaki, H. & Kuroiwa, T. 1997. Analysis of the cluster of ribosomal protein gene in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: Translocation of the str cluster as an early event in the Rhodophyte-Chromophyte lineage of plastid evolution. J. Mol. Evol., 45:688-695.
37. Osawa, S., Jukes, T. H., Watanabe, K. & Muto, A. 1992. Recent evidence for the evolution of the genetic code. Microbiol. Rev., 56:229-264.
38. Palmer, J. 1991. Plastid chromosomes: structure and evolution. In: Bogorad, L. & Vasil, I. K. (ed.), Cell Culture and Somatic Cell Genetics of Plants, Vol 7A: The molecular biology of plastids. Academic Press, San Diego. p. 5-53.
39. Palmer, J. D. & Delwiche, C. F. 1996. Second-hand chloroplasts and the case of the disappearing nucleus. Proc. Natl. Acad. Sci. USA, 93: 7432-7435.
40. Popadic, A., Rusch, D., Peterson, M., Rogers, B. T. & Kaufman, T. C. 1996. Origin of the arthropod mandible. Nature, 380:395.
41. Preiser, P., Williamson, D. H. & Wilson, R. J. M. 1995. Transfer-RNA genes transcribed from the plastid-like DNA of Plasmodium falciparum. Nucl. Acids Res., 23:4329-4336.
42. Reith, M. & Munholland, J. 1993. A high-resolution gene map of the chloroplast genome of the red alga Porphyra purpurea. Plant Cell, 5:465-475.
43. Saunders, G.W., Potter, D., Paskind, M. P. & Andersen, R. A. 1995. Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage. Proc. Natl. Acad. Sci. USA, 92:244-248.
44. Shimada, H. & Suguira, M. 1991. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucl. Acids Res., 19:148-153.
45. Siddall, M. E., Reece, K. R., Graves, J. & Burreson, E. M. 1997. "Total evidence" refutes inclusion of Perkinsus species in the phylum Apicomplexa. Int. J. Parasitol., 115:165-176.
46. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. & Steinberg, S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res., 26:148-153.
47. Stiller, J. W., Duffield, E. C. S. & Hall, B. D. 1998. Amitochondriate amoebe and the evolution of DNA-dependent RNA polymerase II. Proc. Natl. Acad. Sci. USA, 95:11769-11774.
48. Swofford, D. L. 1998. Phylogenetic analysis using parsimony. PAUP*. Smithsonian Institution, Washington, D. C.
49. Van de Peer, Y., Rensing, S. A., Maier, U.-G. & De Wachter, R. 1996. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachiophyte endosymbionts as remnants of green algae. Proc. Natl. Acad. Sci. USA, 93:7732-7736.
50. Varshney, U., Lee, C. P., Seong, B. L. & Rajbhandry, U. L. 1991. Mutants of initiator transfer RNA that function both as initiators and elongators. J. Biol. Chem., 266:18018-18024.
51. Wakasugi, T., Nagai, T., Kapoor, M., Sugita, M., Ito, M., Ito, S., Tsudzuki, J., Nakashima, K., Tsudzuki, T., Suzuki, Y., Hamada, A., Ohta, T., Inamura, A., Yoshinaga, K. & Suguira, M. 1997. Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc. Natl. Acad. Sci. USA, 94:5967-5972.
52. Waller, R. F., Keeling, P. J., Donald, R. G. K., Striepen, B., Handman, E., Lang-Unnasch, N., Cowman, A. F., Besra, G. S., Roos, D. S. & McFadden, G. I. 1998. Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum. Proc. Natl. Acad. Sci. USA, 95:12352-12357.
53. Wang, S.-L., Liu, X.-Q. & Douglas, S. E. 1997. The large ribosomal protein gene cluster of a cryptomonad plastid: gene organization, sequence and evolutionary implications. Biochem. Mol. Biol. Int., 41: 1035-1044.
54. Wilson, R. J. M. & Williamson, D. H. 1997. Extrachromosomal DNA in the Apicomplexa. Microbiol. Mol. Biol. Rev., 61:1-16.
55. 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., et al. 1996. Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J. Mol. Biol., 261:155-172.
56. Yap, M. W. C., Kara, U. A. K., Heggeler-Bordier, B. T., Ting, R. C. Y. & Tan, T. M. C. 1997. Partial nucleotide sequence and organisation of extrachromosomal plastid-like DNA in Plasmodium berghei. Gene, 200:91-98.
57. Yoder, A. D., Vilgalys, R. & Ruvolo, M. 1996. Molecular evolutionary dynamics of cytochrome b in Strepsirrhine primates: The phylogenetic significance of third-position transversions. Mol. Biol. Evol., 13: 1339-1350.
58. Zardoya, R., Cao, Y., Hasegawa, M. & Meyer, A. 1998. Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data. Mol. Biol. Evol., 15:506-517.