How many genes can make a cell: The minimal-gene-set concept

Annual Review of Genomics and Human Genetics

Volumn 1, Issue 2000, 2000, Pages 99-116

  Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Comparative genomics; Genome evolution; Nonorthologous gene displacement; Orthologs; Transposon mutagenesis

Indexed keywords

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); HAEMOPHILUS INFLUENZAE; MYCOPLASMA GENITALIUM; MYCOPLASMA PNEUMONIAE;

BACTERIAL GENOME; BIOLOGICAL MODEL; CELL; COMPARATIVE STUDY; GENETICS; GENOME; HAEMOPHILUS INFLUENZAE; MYCOPLASMA; PHYLOGENY; REVIEW;

CELLS; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, FUNGAL; HAEMOPHILUS INFLUENZAE; MODELS, GENETIC; MYCOPLASMA; PHYLOGENY;

EID: 0034571148     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.1.1.99     Document Type: Article

References (37)

1. Aravind L, Koonin EV. 1999. Gleaning nontrivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 287:1023-40
2. Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:442-44
3. Arigoni F, Talabot F, Peitsch M, Edgerton MD, Meldrum E. 1998. A genome-based approach for the identification of essential bacterial genes. Nat. Biotechnol. 16:851-56
4. Bellgard MI, Gojobori T. 1999. Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences. FEBS Lett. 445:6-8
5. Cho MK, Magnus D, Caplan AL, McGee D. 1999, Policy forum: genetics - ethical considerations in synthesizing a minimal genome. Science 286:2087-90
6. Doolittle WF. 1999. Lateral genomics. Trends Cell Biol. 9:M5-M8
7. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-29
8. Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-106
9. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
10. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403
11. Gaasterland T, Ragan MA. 1998. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics 3:199-217
12. Deleted in proof
13. Deleted in proof
14. Hutchison CA, Peterson SN, Gil SR, Cline RT, White O, et al. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165-69
15. Ibba M, Curnow AW, Soll D. 1997. Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem. Sci. 22:39-42
16. Itaya M. 1995. An estimation of minimal genome size required for life. FEBS Lett. 362:257-60
17. Koonin EV, Aravind L. 1998. Genomics: re-evaluation of translation machinery evolution. Curr. Biol. 8:R266-69
18. Deleted in proof
19. Koonin EV, Mushegian AR. 1996. Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr. Opin. Genet. Dev. 6:757-62
20. Koonin EV, Mushegian AR, Bork P. 1996. Non-orthologous gene displacement. Trends Genet. 12:334-36
21. Koonin EV, Mushegian AR, Galperin MY, Walker DR. 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. 25:619-37
22. Koonin EV, Tatusov RL, Galperin MY. 1998. Beyond complete genomes: from sequence to structure and function. Curr. Opin. Struct. Biol. 8:355-63
23. Kyrpides N, Overbeek R, Ouzounis C. 1999. Universal protein families and the functional content of the last universal common anceslor. J. Mol. Evol. 49:413-23
24. Leipe DD, Aravind L, Koonin EV. 1999. Did DNA replication evolve twice independently? Nucleic Acids Res. 27:3389-401
25. Logsdon JM, Faguy DM. 1999. Thermotoga heats up lateral gene transfer. Curr. Biol. 9:R747-51
26. Mellors A, Lo RY. 1995. O-sialoglycoprotease from Pasteurella haemolytica. Methods Enzymol. 248:728-40
27. Mills DR, Peterson RL, Spiegelman S. 1967. An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Natl. Acad. Sci. USA 58:217-24
28. Mossi R, Hubscher U. 1998. Clamping down on clamps and clamp loaders - the eukaryotic replication factor C. Eur. J. Biochem. 254:209-16
29. Mushegian A. 1999. The minimal genome concept. Curr. Opin. Genet. Dev. 9:709-14
30. Mushegian AR, Koonin EV. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93:10268-73
31. Mushegian AR, Koonin EV. 1998. A minimal gene complement for cellular life and reconstruction of primitive life forms by analysis of complete bacterial genomes. In Bacterial Genomes. Physical Structure and Analysis, ed. FJ De Bruijn, JR Lupski, GM Weinstock, pp. 478-88. New York: Chapman & Hall
32. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, et al. 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-29
33. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96:4285-88
34. Razin S, Yogev D, Naot Y. 1998. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 62:1094-156
35. Stathopoulos C, Li T, Longman R, Vothknecht UC, Becker HD, et al. 2000. One polypeptide with two aminoacyl-tRNA synthetase activities. Scienci 287: 479-82
36. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33-36
37. Tatusov RL, Koonin EV. Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-37