What are archaebacteria: Life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms

Molecular Microbiology

Volumn 29, Issue 3, 1998, Pages 695-707

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEBACTERIUM; EUKARYOTIC CELL; EVOLUTION; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; SEQUENCE HOMOLOGY; TAXONOMY;

AMINO ACID SEQUENCE; ARCHAEA; EUKARYOTIC CELLS; EVOLUTION; GRAM-POSITIVE BACTERIA; MOLECULAR SEQUENCE DATA; PROKARYOTIC CELLS;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; FIRMICUTES; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 0031880993     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1998.00978.x     Document Type: Review

References (39)

1. Baldauf, S.L., Palmer, J.D., and 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.
2. Benachenhou-Lahfa, N., Forterre, P., and Labedan, B. (1993) Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J Mol Evol 36: 335-346.
3. Brown, J.R., Masuchi, Y., Robb, F.T., and Doolittle, W.F. (1994) Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J Mol Evol 38: 566-576.
4. Brown, J.R., and Doolittle, W.F. (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92: 2441-2445.
5. Brown, J.R., and Doolittle, W.F. (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol Rev 61: 456-502.
6. Cavalier-Smith, T. (1992) Origins of secondary metabolism. Ciba Found Symp 171: 64-80.
7. Chatton, E. (1937) Titres et travaux scientifiques (1906-37) de Edouard Chatton. France: E. Sottano Sete.
8. Cohan, F.M. (1994) Genetic exchange and evolutionary divergence in prokaryotes. Science 264: 382-388.
9. De Rijk, P., Van de Peer, Y., Van den Broeck, I., and De Wachter, R. (1995) Evolution according to large ribosomal subunit RNA. J Mol Evol 41: 366-375.
10. Dennis, P.P. (1997) Ancient ciphers: translation in Archaea. Cell 89: 1007-1010.
11. Eisen, J.A. (1995) The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S RNAs from the same species. J Mol Evol 41: 1105-1123.
12. Glasby, J.S. (1979) Encylopedia of Antibiotics. New York: John Wiley and Sons.
13. Golding, G.B., and Gupta, R.S. (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol Biol Evol 12: 1-6.
14. 70-type sigma factors of group 1 and group 2. Bacteriology 179: 1734-1747.
15. Gupta, R.S. (1995a) Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol 15: 1-11.
16. Gupta, R.S. (1995b) Phylogenetic analysis of the 90 kDa heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species. Mol Biol Evol 12: 1063-1073.
17. Gupta, R.S. (1997) Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek 72: 49-61.
18. Gupta, R.S., and Golding, G.B. (1996) The origin of the eukaryotic cell. Trends Biochem Sci 21: 166-171.
19. Gupta, R.S., and Singh, B. (1994) Phylogenetic analysis of 70 kDa heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr Biol 4: 1104-1114.
20. Gupta, R.S., Aitken, K., Falah, M., and Singh, B. (1994) Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc Natl Acad Sci USA 91: 2895-2899.
21. Gupta, R.S., Bustard, K., Falah, M., and Singh, D. (1997) Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes. J Bacteriol 179: 345-357.
22. Hashimoto, T., and Hasegawa, M. (1996) Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G. Adv Biophys 32: 73-120.
23. 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.
24. Kandler, O., and Konig, H. (1993) Cell envelopes of archaea: structure and chemistry. In The Biochemistry of Archaea (Archaebacteria). Kates, M., Kushner, D.J., and Matheson, A.T. (eds). New York: Elsevier Science, pp. 223-259.
25. Karlin, S., Weinstock, G.M., and Brendel, V. (1995) Bacterial classifications derived from recA protein sequence comparisons. J Bacteriol 177: 6881-6893.
26. Koonin, E.V., Mushegian, A.R., Galperin, M.Y., and Walker, D.R. (1997) Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol 25: 619-637.
27. Lake, J.A., and Rivera, M.C. (1994) Was the nucleus the first endosymbiont? Proc Natl Acad Sci USA 91: 2880-2881.
28. Margulis, L. (1996) Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc Natl Acad Sci USA 93: 1071-1076.
29. Murray, R.G.E. (1968) Microbial structure as an aid to microbial classification and taxonomy. Spisy Prirodoved Fak University of JE Purkyne Brne 43: 249-252.
30. Olsen, G.J., and Woese, C.R. (1997) Archaeal genomics: an overview. Cell 89: 991-994.
31. Reeve, J.N., Sandman, K., and Daniels, C.J. (1997) Archaeal histones, nucleosomes, and transcription initiation. Cell 89: 999-1002.
32. Rivera, M.C., and Lake, J.A. (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257: 74-76.
33. Stanier, R.Y., Adelberg, E.A., and Ingraham, J.L. (1976) The Microbial World. New Jersey: Prentice-Hall, pp. 1-871.
34. Tiboni, O., Cammarano, P., and Sanangelantoni, A.M. (1993) Cloning and sequencing of the gene coding glutamine synthetase I from the archaeum Pyrococcus woesi: anomalous phylogenies inferred from analysis of archael and bacterial glutamine synthetase I sequence. J Bacteriol 175:2961-2969.
35. Viale, A.M., Arakaki, A.K., Soncini, F.C., and Ferreyra, R.G. (1994) Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int J Syst Bacteriol 44: 527-533.
36. Woese, C.R. (1987) Bacterial evolution. Microbiol Rev 51: 221-271.
37. Woese, C.R. (1991) The use of ribosomal RNA in reconstructing evolutionary relationships among bacteria. In Evolution at Molecular Level. Selander, R.K., Clark, A.G., and Whittmay, T.S. (eds). Sunderland, MA: Sinauer Associates, pp. 1-24.
38. Woese, C.R. (1992) Prokaryote systematics: the evolution of a science. In The Prokaryotes. Balows, A., Truper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds). New York: Springer-Verlag, pp. 3-18.
39. Woese, C.R., Kandler, O., and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-4579.