Phylogenetic position of kinetoplastid protozoa inferred from the protein phylogenies of elongation factors 1α and 2

Journal of Biochemistry

Volumn 119, Issue 1, 1996, Pages 70-79

  Nakamura, Yoshihiro ^a   Hashimoto, Tetsuo ^b   Kamaishi, Takashi ^a,c   Adachi, Jun ^b   Nakamura, Fuminori ^a   Okamoto, Ken Ichi ^a   Hasegawa, Masami ^b  

^a SHOWA UNIVERSITY   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Early evolution of eukaryotes; Elongation factor; Kinetoplastid protozoa; Protein phylogeny; Trypanosoma cruzi

Indexed keywords

ELONGATION FACTOR; ELONGATION FACTOR 1ALPHA; ELONGATION FACTOR 2; MESSENGER RNA; RIBOSOME RNA;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARCHAEBACTERIUM; ARTICLE; EUKARYOTIC CELL; MITOCHONDRION; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTOZOON; STOCHASTIC MODEL; TRYPANOSOMA CRUZI;

EID: 0030039648     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021218     Document Type: Article

References (44)

1. Sogin, M.L., Edman, U., and Elwood, H. (1989) A single kingdom of eukaryotes in The Hierarchy of Life (Fernholm, B., Bremer, K., and Jörnvall, H., eds.) pp. 133-143, Elsevier Science, Amsterdam
2. Sogin, M.L., Gunderson, J.H., Elwood, H.J., Alonso, R.A., and Peattie, D.A. (1989) Phylogenetic meaning of the kingdom concept: An unusual ribosomal RNA from Giardia lamblia. Science 243, 75-77
3. Sogin, M.L. (1991) Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1, 457-463
4. + of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol. Biochem. Parasitol. 59, 41-48
5. Hasegawa, M. and Hashimoto, T. (1993) Ribosomal RNA trees misleading? Nature 361, 23
6. Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N., and Miyata, T. (1993) Early branchings in the evolution of eukaryotes: Ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. J. Mol. Evol. 36, 380-388
7. Hashimoto, T., Nakamura, Y., Nakamura, F., Shirakura, T., Adachi, J., Goto, N., Okamoto, K., and Hasegawa, M. (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryotes: Phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol. Biol. Evol. 11, 65-71
8. Hashimoto, T., Nakamura, Y., Kamaishi, T., Adachi, J., Nakamura, F., Okamoto, K., and Hasegawa, M. (1995) Phylogenetic place of kinetoplastid protozoa inferred from a protein phylogeny of elongation factor 1α. Mol. Biochem. Parasitol. 70, 181-185
9. Hasegawa, M., Hashimoto, T., and Adachi, J. (1992) Origin and evolution of eukaryotes as inferred from protein sequence data in The Origin and Evolution of the Cell (Hartman, H. and Matsuno, K., eds.) pp. 107-130, World Scientific, Singapore
10. Hashimoto, T., Adachi, J., and Hasegawa, M. (1992) Phylogenetic place of Giardia lamblia, a protozoan that lacks mitochondria. Endocytobiosis Cell Res. 9, 59-69
11. Shirakura, T., Hashimoto, T., Nakamura, Y., Kamaishi, T., Cao, Y., Adachi, J., Hasegawa, M., Yamamoto, A., and Goto, N. (1994) Phylogenetic place of a mitochondria-lacking protozoan, Entamoeba histolytica, inferred from amino acid sequences of elongation factor 2. Jpn. J. Genet. 69, 119-135
12. Hashimoto, T., Nakamura, Y., Kamaishi, T., Nakamura, F., Adachi, J., Okamoto, K., and Hasegawa, M. (1995) Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2. Mol. Biol. Evol. 12, 782-793
13. Simpson, L. (1987) The mitochondrial genome of kinetoplastid protozoa: Genomic organization, transcription, replication, and evolution. Annu. Rev. Microbiol. 41, 363-382
14. Benne, R. (1994) RNA editing in trypanosomes. Eur. J. Biochem. 221, 9-23
15. Hannaert, V. and Michels, P.A.M. (1994) Structure, function, and biogenesis of glycosomes in Kinetoplastida. J. Bioenerg. Biomembr. 26, 205-212
16. Vanhamme, L. and Pays, E. (1995) Control of gene expression in Trypanosomes. Microbiol. Rev. 59, 223-240
17. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., and Miyata, T. (1989) Evolutionary relationship of archaebacteria, eubacteria and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86, 9355-9359
18. Miyata, T., Iwabe, N., Kuma, K., Kawanishi, Y., Hasegawa, M., Kishino, H., Mukohata, Y., Ihara, K., and Osawa, S. (1991) Evolution of archaebacteria: Phylogenetic relationships among archaebacteria, eubacteria, and eukaryotes in Evolution of Life: Fossils, Molecules, and Culture (Osawa, S. and Honjo, T., eds.) pp. 337-351, Springer-Verlag, Tokyo
19. Creti, R., Ceccarelli, E., Bocchetta, M., Sanangelantoni, A.M., Tiboni, O., Palm, P., and Cammarano, P. (1994) Evolution of translational elongation factor (EF) sequences: Reliability of global phylogenies inferred from EF-1α(Tu) and EF-2(G) proteins. Proc. Natl. Acad. Sci. USA 91, 3255-3259
20. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
21. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557-580
22. Jones, D.T., Taylor, W.R., and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282
23. Cao, Y., Adachi, J., Janke, A., Pääbo, S., and Hasegawa, M. (1994) Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene. J. Mol. Evol. 39, 519-527
24. Kishino, H., Miyata, T., and Hasegawa, M. (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 30, 151-160
25. Hasegawa, M., Cao, Y., Adachi, J., and Yano, T. (1992) Rodent polyphyly? Nature 355, 595
26. Kishino, H. and Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179
27. Hasegawa, M. and Kishino, H. (1994) Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol. Biol. Evol. 11, 142-145
28. Sakamoto, Y., Ishiguro, M., and Kitagawa, G. (1986) Akaike Information Criterion Statistics, D. Reidel, Dordrecht
29. Adachi, J. and Hasegawa, M. (1992) MOLPHY: Programs for Molecular Phylogenetics, I.- PROTML: Maximum Likelihood Inference of Protein Phylogeny, Institute of Statistical Mathematics, Tokyo
30. Adachi, J. (1995) Modeling of Molecular Evolution and Maximum Likelihood Inference of Molecular Phylogeny, Ph.D. thesis of The Graduate Univ. for Advanced Studies
31. Thorne, J.L. and Churchill, G.A. (1994) Estimation and reliability of molecular sequence alignments. Biometrics 51, 100-113
32. Kohno, K., Uchida, T., Ohkubo, H., Nakanishi, S., Nakanishi, T., Fukui, T., Ohtsuka, E., Ikehara, M., and Okada, Y. (1986) Amino acid sequence of mammalian elongation factor 2 deduced from the cDNA sequence: Homology with GTP-binding proteins. Proc. Natl. Acad. Sci. USA 83, 4978-4982
33. Bourne, H.R., Sanders, D.A., and McCormick, F. (1991) The GTPase superfamily: Conserved structure and molecular mechanism. Nature 349, 117-127
34. Van Ness, B.G., Howard, J.B., and Bodley, J.W. (1980) ADP-ribosylation of elongation factor 2 by diphtheria toxin. J. Biol. Chem. 255, 10710-10716
35. Nilsson, L. and Nygård, O. (1985) Localization of the sites of ADP-ribosylation and GTP binding in the eukaryotic elongation factor EF-2. Eur. J. Biochem. 148, 299-304
36. Guillot, D., Penin, F., Di Pietro, A., Sontag, B., Lavergne, J.-P., and Reboud, J.-P. (1993) GTP binding to elongation factor eEF-2 unmasks a tryptophan residue required for biological activity. J. Biol. Chem. 268, 20911-20916
37. 221 is involved in the protective effect of elongation factor eEF-2 on the ricin/α-sarcin site of the ribosome. J. Biol. Chem. 268, 26082-26084
38. Price, N.T., Redpath, N.T., Severinov, K.V., Campbell, D.G., Russell, J.M., and Proud, C.G. (1991) Identification of the phosphorylation sites in elongation factor-2 from rabbit reticulocytes. FEBS Lett. 282, 253-258
39. Kuma, K., Nikoh, N., Iwabe, N., and Miyata, T. (1995) Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J. Mol. Evol. 41, 238-246
40. Toda, K., Tasaka, M., Mashima, K., Kohno, K., Uchida, T., and Takeuchi, I. (1989) Structure and expression of elongation factor 2 gene during development of Dictyostelium discoideum. J. Biol. Chem. 264, 15489-15493
41. Perentesis, J.P., Phan, L.D., Gleason, W.B., LaPorte, D.C., Livingston, D.M., and Bodley, J.W. (1992) Saccharomyces cerevisiae elongation factor 2: Genetic cloning, characterization of expression, and G-domain modeling. J. Biol. Chem. 267, 1190-1197
42. Que, X. and Reed, S.L. (1991) Nucleotide sequence of a small subunit ribosomal RNA (16S-like rRNA) gene from Entamoeba histolytica: Differentiation of pathogenic from nonpathogenic isolates. Nucleic Acids Res. 19, 5438
43. Clark, C.G. and Roger, A.J. (1995) Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc. Natl. Acad. Sci. USA 92, 6518-6521
44. Rivera, M.C. and Lake, J.A. (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257, 74-76