Comparative genomics of the archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell

Genome Research

Volumn 9, Issue 7, 1999, Pages 608-628

  Makarova, Kira S ^a,b,d   Aravind, L ^a,c   Galperin, Michael Y ^a   Grishin, Nick V ^a   Tatusov, Roman L ^a   Wolf, Yuri I ^a,d   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

^d INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARCHAEOGLOBUS FULGIDUS; ARTICLE; BACTERIAL GENETICS; EURYARCHAEOTA; EVOLUTION; GENE LOSS; GENE REPLICATION; GENE TRANSFER; GENETIC CONSERVATION; METHANOBACTERIUM THERMOAUTOTROPHICUM; METHANOCOCCUS JANNASCHII; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; PYROCOCCUS; SEQUENCE HOMOLOGY;

ARCHAEA; ARCHAEOGLOBUS FULGIDUS; BACTERIA (MICROORGANISMS); EUKARYOTA; EURYARCHAEOTA; METHANOBACTERIUM; METHANOBACTERIUM THERMOAUTOTROPHICUM; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; METHANOCOCCUS JANNASCHII; METHANOTHERMOBACTER THERMAUTOTROPHICUS; PROKARYOTA; PYROCOCCUS; PYROCOCCUS HORIKOSHII;

EID: 0032766490     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (93)

1. Adams, E. and L. Frank. 1980. Metabolism of proline and the hydroxyprolines. Annu. Rev. Biochem. 49: 1005-1061.
2. Altschul, S.F. and W. Gish. 1996. Local alignment statistics. Methods Enzymol. 266: 460-480.
3. Altschul, S.F. and E.V. Koonin. 1998. PSI-BLAST - A tool for making discoveries in sequence databases. Trends Biochem. Sci. 23: 444-447.
4. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
5. Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and DJ. Eipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
6. Aravind, L. 1998. An evolutionary classification of the metallo-beta lactamase fold proteins. In Silica Biol. 1: 8.
7. Aravind, L. and E.V. Koonin. 1998a. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 26: 3746-3752.
8. _. 1998b. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23: 469-472.
9. _. 1999a. Gleaning non-trivial structural, functional, and evolutionary information about proteins by iterative database searches. J. Mol. Evol. 287: 1023-1040.
10. _. 1999b. DNA polymerase beta-like nucleotidyltransferase superfamily: Identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27: 1609-1618.
11. Aravind, L., D.D. Eeipe, and E.V. Koonin. 1998. Toprim - A conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26: 4205-4213.
12. Aravind, L., D.R. Walker, and E.V. Koonin. 1999. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27: 1223-1242.
13. Bateman, A. 1997. The structure of a domain common to archaebacteria and the homocystinuria disease protein. Trends Biochem. Sci. 22: 12-13.
14. Bell, S.D. and S.P. Jackson. 1998. Transcription and translation in Archaea: A mosaic of eukaryal and bacterial features. Trends Microbiol. 6: 222-228.
15. Bell, S.D., C. Jaxel, M. Nadal, P.F. Kosa, and S.P. Jackson. 1998. Temperature, template topology, and factor requirements of archaeal transcription. Proc. Natl. Acad. Sci. 95: 15218-15222.
16. Branden, C. and J. Tooze. 1991. Introduction to protein structure. Garland Publishing, Inc., New York-London.
17. Brown, J.R. and W.F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61: 456-502.
18. Bult, C.J., O. White, G.J. Olsen, L. Zhou, R.D. Fleischmann, G.G. Sutton, J.A. Blake, L.M. FitzGerald, R.A. Clayton, J.D. Gocayne et al. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii Science 273: 1058-1073.
19. Cann, I.K.O., K. Komori, H. Toh, S. Kanai, and Y. Ishino. 1998. A heterodimeric DNA polymerase: Evidence that members of euryarchaeota possess a distinct DNA polymerase. Proc. Natl. Acad. Sci. 95: 14250-14255.
20. Chervitz, S.A., L. Aravind, G. Sherlock, C.A. Ball, E.V. Koonin, S.S. Dwight, M.A. Harris, K. Dolinski, S. Mohr, T. Smith et al. 1998. Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 282: 2022-2028.
21. Doolittle R.F. 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64: 287-314.
22. Doolittle, R.F. and P. Bork. 1993. Evolutionary mobile modules in proteins. Sci. Am. 269: 50-56.
23. Doolittle, W.F. and J.M. Logsdon Jr. 1998. Archaeal genomics: Do archaea have a mixed heritage? Curr. Biol. 8: R209-211.
24. Eberhardt, S., S. Korn, P. Lottspelch, and A. Bacher. 1997. Biosynthesis of riboflavin synthase of methenobacterium thermoantotrophium. J. Bacteriol. 179: 2938-2940.
25. Edgell, D.R. and W.F. Doolittle. 1997. Archaea and the origin(s) of DNA replication proteins. Cell 89: 995-998.
26. Feng, D.F., G. Cho, and R.F. Doolittle. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proc. Natl. Acad. Sci. 94: 13028-13033.
27. Freestone, P., T. Nystrom, M. Trinei, and V. Norris. 1997. The universal stress protein, UspA, of Escherichia coli is phosphorylated in response to stasis. J. Mol. Biol. 274: 318-324.
28. Gogarten, J.P., H. Kibak, P. Dittrich, L. Taiz, E.J. Bowman, B.J. Bowman, M.F. Manolson, R.J. Poole, T. Date, T. Oshima et al. 1989a. Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. 86: 6661-6665.
29. Gogarten, J.P., T. Rausch, P. Bernasconi, H. Kibak, and L. Taiz. 1989b. Molecular evolution of H+-ATPases. I. Methanococcus and Sulfolobus are monophyletic with respect to eukaryotes and Eubacteria. Z. Naturforsch. Teil C 44: 641-650.
30. Gonzalez, J.M., Y. Masuchi, F.T. Robb, J.W. Ammerman, D.L. Maeder, M. Yanagibayashi, J. Tamaoka, and C. Kato. 1998. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2: 123-130.
31. Gribaldo, S. and P. Cammarano. 1998. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery [In Process Citation]. J. Mol. Evol. 47: 508-516.
32. Ishino, Y., K. Komori, I.K. Cann, and Y. Koga. 1998. A novel DNA polymerase family found in Archaea. J. Bacteriol. 180: 2232-2236.
33. Ishiura, M., S. Kutsuna, S. Aoki, H. Iwasaki, C.R. Andersson, A. Tanabe, S.S. Golden, C.H. Johnson, and T. Kondo. 1998. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281: 1519-1523.
34. Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. 86: 9355-9359.
35. Karlin, S. and S.F. Altschul. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. 87: 2264-2268.
36. Karlin, S., P. Bucher, V. Brendel, and S.F. Altschul. 1991. Statistical methods and insights for protein and DNA sequences. Annu. Rev. Biophys. Biophys. Chem. 20: 175-203.
37. Kawarabayasi, Y., M. Sawada, H. Horikawa, Y. Haikawa, Y. Hino, S. Yamamoto, M. Sekine, S. Baba, H. Kosugi, A. Hosoyama et al. 1998a. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5: 55-76.
38. _. 1998b. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 (suppl.). DNA Res. 5: 147-155.
39. Kawashima, T., C. Berthet-Colominas, M. Wulff, S. Cusack, and R. Leberman. 1996. The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5 A resolution. Nature 379: 511-518.
40. Keeling, P.J., R.L. Charlebois, and W.F. Doolittle. 1994. Archaebacterial genomes: Eubacterial form and eukaryotic content. Curr. Opin. Genet. Dev. 4: 816-822.
41. Kinoshita, N., M. Goebl, and M. Yanagida. 1991. The fission yeast dis3+ gene encodes a 110-kDa essential protein implicated in mitotic control. Mol. Cell. Biol. 11: 5839-5847.
42. Klenk, H.P., R.A. Clayton, J.F. Tomb, O. White, K.E. Nelson, K.A. Ketchum, R.J. Dodson, M. Gwinn, E.K. Hickey, J.D. Peterson et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
43. Koonin, E.V. 1997. Evidence for a family of archaeal ATPases. Science 275: 1489-1490.
44. Koonin, E.V. and M.Y. Galperin. 1997. Prokaryotic genomes: The emerging paradigm of genome-based microbiology. Curr. Opin. Genet. Dev. 7: 757-763.
45. Koonin, E.V., A.R. Mushegian, R.L. Tatusov, S.F. Altschul, S.H. Bryant, P. Bork, and A. Valencia. 1994. Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain - Study of a diverse, ancient protein superfamily using motif search and structural modeling. Protein Sci. 3: 2045-2054.
46. Koonin, E.V., A.R. Mushegian, and P. Bork. 1996a. Non-orthologous gene displacement Trends Genet. 12: 334-336.
47. Koonin, E.V., R.L. Tatusov, and K.E. Rudd. 1996b. Protein sequence comparison at genome scale. Methods Enzymol. 266: 295-322.
48. Koonin, E.V., A.R. Mushegian, M.Y. Galperin, and D.R. Walker. 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.
49. Koonin, E.V., R.L. Tatusov, and M.Y. Galperin. 1998. Beyond complete genomes: From sequence to structure and function. Curr. Opin. Struct. Biol. 8: 355-363.
50. Krishna, T.S., X.P. Kong, S. Gary, P.M. Burgers, and J. Kuriyan. 1994. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233-1243.
51. Kyrpides, N.C. and C.R. Woese. 1998. Universally conserved translation initiation factors. Proc. Natl. Acad. Sci. 95: 224-228.
52. Langer, D., J. Hain, P. Thuriaux, and W. Zillig. 1995. Transcription in archaea: Similarity to that in eucarya. Proc. Natl. Acad. Sci. 92: 5768-5772.
53. Leffers, H., F. Gropp, F. Lottspeich, W. Zillig, and R.A. Garrett. 1989. Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae. J. Mol. Biol. 206: 1-17.
54. Mitchell, P., E. Petfalski, A. Shevchenko, M. Mann, and D. Tollervey. 1997. The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′ → 5′ exoribonucleases. Cell 91: 457-466.
55. Mushegian, A.R. and E.V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. 93: 10268-10273.
56. Neidhardt, F.C., R. Curtiss III, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasanik, W.S. Reznekoff, M. Riley, M. Schaechter, and H.E. Umbarger, eds. 1996. Escherichia coli and Salmonella. Cell. molecular biology. 2nd ed. ASM Press, Washington, D.C.
57. Noguchi, E., N. Hayashi, Y. Azuma, T. Seki, M. Nakamura, N. Nakashima, M. Yanagida, X. He, U. Mueller, S. Sazer et al.. 1996. Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J. 15: 5595-5605.
58. Olsen, G.J., C.R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: Breathing new life into microbiology. J. Bacterial. 176: 1-6.
59. Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
60. Pace, N.R., G.J. Olsen, and C.R. Woese. 1986. Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45: 325-326.
61. Peitsch, M.C. 1996. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24: 274-279.
62. Pooting, C.P. 1997. CBS domains in CIC chloride channels implicated in myotonia and nephrolithiasis (kidney stones). J. Mol. Med. 75: 160-163.
63. Powers, T. and P. Walter. 1996. The nascent polypeptide-associated complex modulates interactions between the signal recognition particle and the ribosome. Curr. Biol. 6: 331-338.
64. Puhler, G., H. Leffers, F. Gropp, P. Palm, H.P. Klenk, F. Lottspeich, R.A. Garrett, and W. Zillig. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl. Acad. Sci. 86: 4569-4573.
65. Riley, M. and B. Labedan. 1997. Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268: 857-868.
66. Rost, B. and C. Sander. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19: 55-72.
67. Sans, N., U. Schindler, and J. Schroder. 1988. Ornithine cyclodeaminase from Ti plasmid C58: DNA sequence, enzyme properties and regulation of activity by arginine. Eur. J. Biochem. 173: 123-130.
68. Schafer, G., W. Purschke, and C.L. Schmidt. 1996a. On the origin of respiration: Electron transport proteins from archaea to man. FEMS Microbiol. Rev. 18: 173-188.
69. Schafer, G., W.G. Purschke, M. Gleissner, and C.L. Schmidt. 1996b. Respiratory chains of archaea and extremophiles. Biochim. Biophys. Acta 1275: 16-20.
70. Shiomi, T., K. Fukushima, N. Suzuki, N. Nakashima, E. Noguchi, and T. Nishimoto. 1998. Human dis3p, which binds to either GTP-or GDP-Ran, complements Saccharomyces cerevisiae dis3. J. Biochem. (Tokyo) 123: 883-890.
71. Smith, D.R., L.A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J. Bacteriol. 179: 7135-7155.
72. Tabuchi, A., Y.N. Min, D.D. Womble, and R.H. Rownd. 1992. Autoregulation of the stability operon of IncFII plasmid NR1. J. Bacteriol. 174: 7629-7634.
73. Tatusov, R.L., A.R. Mushegian, P. Bork, N.P. Brown, W.S. Hayes, M. Borodovsky, K.E. Rudd, and E.V. Koonin. 1996. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol. 6: 279-291.
74. Tatusov, R.L., E.V. Koonin, and D.J. Lipman. 1997. A genomic perspective on protein families. Science 278: 631-637.
75. Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
76. Thomson, G.J., G.J. Howlett, A.E. Ashcroft, and A. Berry. 1998. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem. J. 331: 437-445.
77. Uemori, T., Y. Sato, I. Kato, H. Doi, and Y. Ishino. 1997. A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: Gene cloning, expression, and characterization. Genes Cells 2: 499-512.
78. Walker, D.R. and E.V. Koonin. 1997. SEALS: A system for easy analysis of lots of sequences. ISMB 5: 333-339.
79. Wang, S., H. Sakai, and M. Wiedmann. 1995. NAC covers ribosome-associated nascent chains thereby forming a protective environment for regions of nascent chains just emerging from the peptidyl transferase center. J. Cell. Biol. 130: 519-528.
80. Watanabe, H. and J. Otsuka. 1995. A comprehensive representation of extensive similarity linkage between large numbers of proteins. Comput. Appl. Biosci. 11: 159-166.
81. Wickner, W. 1995. The nascent-polypeptide-associated complex: Having a "NAC" for fidelity in translocation. Proc. Natl. Acad. Sci. 92: 9433-9434.
82. Woese, C.R. 1994. There must be a prokaryote somewhere: Microbiology's search for itself. Microbiol. Rev. 58: 1-9.
83. Woese, C.R. and R. Gupta. 1981. Are archaebacteria merely derived prokaryotes? Nature 289: 95-96.
84. Woese, C.R., L.J. Magrum, and G.E. Fox. 1978. Archaebacteria. J. Mol. Evol. 11: 245-251.
85. Woese, C.R., O. Kandler, and M.L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. 87: 4576-4579.
86. Wolf, Y.I., S.E. Brenner, P.A. Bash, and E.V. Koonin. 1999. Distribution of protein folds in the three superkingdoms of life. Genome Res. 9: 17-26.
87. Wootton, J.C. 1994. Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput. Chem. 18: 269-285.
88. Wootton, J.C. and S. Federhen. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266: 554-571.
89. Yotov, W.V., A. Moreau, and R. St-Arnaud. 1998. The alpha chain of the nascent polypeptide-associated complex functions as a transcriptional coactivator. Mol. Cell. Biol. 18: 1303-1311.
90. Zarembinski, T.I., L.W. Hung, H.J. Mueller-Dieckmann, K.K. Kim, H. Yokota, R. Kim, and S.H. Kim. 1998. Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics. Proc. Natl. Acad. Sci. 95: 15189-15193.
91. Zhang, Y., V. Sun, and L.L. Spremulli. 1997. Role of domains in Escherichia coli and mammalian mitochondrial elongation factor Ts in the interaction with elongation factor Tu. J. Biol. Chem. 272: 21956-21963.
92. Zillig, W. 1991. Comparative biochemistry of Archaea and Bacteria. Curr. Opin. Genet. Dev. 1: 544-551.
93. Zillig, W., H.P. Klenk, P. Palm, G. Puhler, F. Gropp, R.A. Garrett, and H. Leffers. 1989. The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria. Can. J. Microbiol. 35: 73-80.