Comparative genomics, minimal gene-sets and the last universal common ancestor

Nature Reviews Microbiology

Volumn 1, Issue 2, 2003, Pages 127-136

  Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN;

BACTERIUM; BIOLOGY; COMPARATIVE STUDY; ESSENTIAL GENE; EUKARYOTIC CELL; GENETICS; GENOMICS; METABOLISM; MOLECULAR EVOLUTION; REVIEW;

BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENES, ESSENTIAL; GENOMICS; PROTEINS;

EID: 1542272747     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro751     Document Type: Article

References (71)

1. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512 (1995).
2. Fraser, C. M. et al. The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403 (1995).
3. Fraser, C. M., Eisen, J. A. & Salzberg, S. L. Microbial genome sequencing. Nature 406, 799-803 (2000).
4. Koonin, E. V, Aravind, L. & Kondrashov, A. S. The impact of comparative genomics on our understanding of evolution. Cell 101, 573-576 (2000).
5. Alberts, B. et al. Molecular Biology of the Cell (Garland Science, New York, 2002).
6. Gerstein, M. & Hegyi, H. Comparing genomes in terms of protein structure: surveys of a finite parts list. FEMS Microbiol. Rev. 22, 277-304 (1998).
7. Mushegian, A. R. & Koonin, E. V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. NatiAcad. Sci. USA 93, 10268-10273 (1996).
8. Maniloff, J. The minimal cell genome: 'on being the right size'. Proc. Natl Acad. Sci. USA 93, 10004-10006 (1996).
9. Mushegian, A. The minimal genome concept. Curr. Opin. Genet. Dev. 9, 709-714 (1999).
10. Koonin, E. V How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1, 99-116 (2000).
11. Zimmer, C. Tinker, tailor: can Venter stitch together a genome from scratch? Science 299, 1006-1007 (2003).
12. Katinka, M. D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephaiitozoon cunicuii. Nature 414, 450-453 (2001).
13. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 (2002).
14. Deckert, G. et al. The complete genome of the hyperthermophilic bacterium Aquifex aeoiicus. Nature 392, 353-358 (1998).
15. Gerdes, S. Y. et al. Experimental determination and system-level analysis of essential genes in Escherichia coli MG 1655. J. Bacteriol. 185, 5673-5684.
16. Rottem, S. Interaction of mycoplasmas with host cells. Physiol. Rev. 83, 417-432 (2003).
17. Pauling, L. & Zuckerkandl, E. Chemical paleogenetics. Molecular 'restoration studies' of extinct forms of life. Acta Chemica Scandinavica 17, S9-S16 (1963).
18. Fitch, W. M. Distinguishing homologous from analogous proteins. Systematic Zoology 19, 99-106 (1970).
19. Fitch, W. M. Homology: a personal view on some of the problems. Trends Genet. 16, 227-231 (2000).
20. Sonnhammer, E. L. & Koonin, E. V. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18, 619-620 (2002).
21. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631-637 (1997).
22. Huynen, M. A. & Bork, P. Measuring genome evolution. Proc. Nati Acad. Sci. USA 95, 5849-5856 (1998).
23. Koonin, E. V., Mushegian, A. R. & Bork, P. Non-orthologous gene displacement. Trends Genet. 12, 334-336 (1996).
24. Koonin, E. V & Galperin, M. Y. Sequence — Evolution — Function. Computational Approaches in Comparative Genomics (Kluwer Academic, New York, 2002).
25. Gil, R. et al. The genome sequence of Biochmannia fioridanus. comparative analysis of reduced genomes. Proc. Natl Acad. Sci. USA 100, 9388-9393 (2003).
26. Itaya, M. An estimation of minimal genome size required for life. FEBS Lett. 362, 257-260 (1995).
27. Venter, J. C., Levy, S., Stockwell, T., Remington, K. & Halpern, A. Massive parallelism, randomness and genomic advances. Nature Genet. 33 (Suppl.), 219-227 (2003).
28. Judson, N. & Mekalanos, J. J. Transposon-based approaches to identify essential bacterial genes. Trends Microbiol. 8, 521-526 (2000).
29. Vagner, V., Dervyn, E. & Ehrlich, S. D. A vector for systematic gene inactivation in Bacillus subtilis. Microbiology 144, 3097-3104 (1998).
30. Ji, Y., Woodnutt, G., Rosenberg, M. & Burnham, M. K. Identification of essential genes in Staphyiococcus aureus using inducible antisense RNA. Methods Enzymoi. 358, 123-128 (2002).
31. Hutchison, C. A. et ai. Global transposon mutagenesis and a minimal Mycopiasma genome. Science 286, 2165-2169 (1999).
32. Akerley, B. J. et al. A genome-scale analysis for identification of genes required for growth or survival of Haemophiius influenzae. Proc. Nati Acad. Sci. USA 99, 966-971 (2002).
33. Kobayashi, K. et al. Essential Baciiius subtiiis genes. Proc. Nati Acad. Sci. USA 100, 4678-4683 (2003).
34. Tatusov, R. L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucieic Acids Res. 29, 22-28 (2001).
35. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003 Sep 11; [epub ahead of print].
36. Yu, B. J. et al. Minimization of the Escherichia coli genome using a Tn5-targeted Cre/IoxPexcision system. Nature Biotechnoi. 20, 1018-1023 (2002).
37. Mills, D. R., Peterson, R. L. & Spiegelman, S. An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Nati Acad. Sci. USA 58, 217-224 (1967).
38. Jordan, I. K., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12, 962-968 (2002).
39. Lazcano, A. & Forterre, P. The molecular search for the last common ancestor. J. Moi. Evoi. 49, 411-412 (1999).
40. Woese, C. The universal ancestor. Proc. Nati Acad. Sci. USA 95, 6854-6859 (1998).
41. Snel, B., Bork, P. & Huynen, M. A. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12, 17-25 (2002).
42. Mirkin, B. G., Fenner, T. I., Galperin, M. Y. & Koonin, E. V. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evoi. Bioi. 3 [online], (cited 22 Sept. 2003), (2003).
43. Kunin, V. & Ouzounis, C. A. The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13, 1589-1594 (2003).
44. Doolittle, W. F. Phylogenetic classification and the universal tree. Science 284, 2124-2129 (1999).
45. Doolittle, W. F. Lateral genomics. Trends Ceii Bioi. 9, M5-M8 (1999).
46. Gogarten, J. P, Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Moi. Bioi. Evoi. 19, 2226-2238 (2002).
47. Doolittle, W. F. Uprooting the tree of life. Sci. Am. 282, 90-95 (2000).
48. Pennisi, E. Genome data shake tree of life. Science 280, 672-674 (1998).
49. Pennisi, E. Is it time to uproot the tree of life? Science 284, 1305-1307 (1999).
50. Kurland, C. G., Canback, B. & Berg, O. G. Horizontal gene transfer: a critical view. Proc. Nati Acad. Sci. USA 100, 9658-9662 (2003).
51. Clarke, G. D., Beiko, R. G., Ragan, M. A. & Charlebois, R. L. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacterioi. 184, 2072-2080 (2002).
52. Wolf, Y. I., Rogozin, I. B., Grishin, N. V, Tatusov, R. L. & Koonin, E. V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evoi. Bioi. 1 [online], (cited 22 Sept. 2003), < http://www.biomedcentral.com/1471-2148/1/8> (2003).
53. Wolf, Y. I., Rogozin, I. B., Grishin, N. V. & Koonin, E. V Genome trees and the tree of life. Trends Genet. 18, 472-479 (2002).
54. Korbel, J. O., Snel, B., Huynen, M. A. & Bork, P SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18, 158-162 (2002).
55. Daubin, V, Gouy, M. & Perriere, G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12, 1080-1090 (2002).
56. Nei, M. & Kumar, S. Moiecuiar Evoiution and Phyiogenetics (Oxford Univ. Press, Oxford, 2001).
57. Moran, N. A. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108, 583-586 (2002).
58. Glansdorff, N. About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Moi. Microbioi. 38, 177-185 (2000).
59. Brochier, C., Philippe, H. & Moreira, D. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16, 529-533 (2000).
60. Matte-Tailliez, O., Brochier, C., Forterre, P. & Philippe, H. Archaeal phylogeny based on ribosomal proteins. Moi. Bioi. Evoi. 19, 631-639 (2002).
61. Makarova, K. S., Ponomarev, V. A. & Koonin, E. V. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Bioiogy 2 [online], (cited 11 Sept. 2003), (2001).
62. Woese, C. R. On the evolution of cells. Proc. Nati Acad. Sci. USA 99, 8742-8747 (2002).
63. Harris, J. K., Kelley, S. T., Spiegelman, G. B. & Pace, N. R. The genetic core of the universal ancestor. Genome Res. 13, 407-412 (2003).
64. Leipe, D. D., Aravind, L. & Koonin, E. V. Did DNA replication evolve twice independently? Nucieic Acids Res. 27, 3389-3401 (1999).
65. Forterre, P The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbioi. 5, 525-532 (2002).
66. Forterre, P. Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol. 33, 457-465 (1999).
67. Delaye, L., Vazquez, H. & Lazcano, A. in First Step in the Origin of Life in the Universe (ed. Chela-Flores, J.) 223-230 (Kluwer Academic, Amsterdam, 2001).
68. Dworkin, J. P., Lazcano, A. & Miller, S. L. The roads to and from the RNA world. J. Theor. Biol. 222, 127-134 (2003).
69. Olsen, G. J., Woese, C. R. & Overbeek, R. The winds of (evolutionary) change: breathing new life into microbiology J. Bacteriol. 176, 1-6 (1994).
70. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002).
71. Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237 (2003).