How essential are nonessential genes?

Molecular Biology and Evolution

Volumn 22, Issue 11, 2005, Pages 2147-2156

  Fang, Gang ^a   Rocha, Eduardo ^a,b   Danchin, Antoine ^a  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

Bacterial evolution; Essentiality; Gene content; Gene expression; Gene strand bias; Protein evolution

Indexed keywords

ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; COMPARATIVE STUDY; CULTURE MEDIUM; DNA REPLICATION; EVOLUTION; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENETIC ANALYSIS; GENETIC CONSERVATION; GENOMICS; NONHUMAN; PHENOTYPE; RNA DEGRADATION; STRESS;

CODON; EVOLUTION, MOLECULAR; GAMMAPROTEOBACTERIA; GENE EXPRESSION; GENES, BACTERIAL; GENES, ESSENTIAL; GENOME, BACTERIAL; GENOMICS; GRAM-POSITIVE BACTERIA;

BACTERIA (MICROORGANISMS); FIRMICUTES; GAMMAPROTEOBACTERIA;

EID: 26444558214     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msi211     Document Type: Article

References (56)

1. Akerley, B. J., E. J. Rubin, V. L. Novick, K. Amaya, N. Judson, and J. J. Mekalanos. 2002. A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc. Natl. Acad. Sci. USA 99:966-971.
2. Bentley, S. D., and J. Parkhill. 2004. Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 38:771-792.
3. Brochier, C., H. Philippe, and D. Moreira. 2000. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:529-533.
4. Chalker, A. F., and R. D. Lunsford. 2002. Rational identification of new antibacterial drug targets that are essential for viability using a genomics-based approach. Pharmacol. Ther. 95:1-20.
5. Cohen, S. 1998. A guide to the polyamines. Oxford University Press, Oxford.
6. Dabbs, E. R. 1978. Mutational alterations in 50 proteins of the Escherichia coli ribosome. Mol. Gen. Genet. 165:73-78.
7. De Angelis, M., R. Di Cagno, C. Huet, C. Crecchio, P. F. Fox, and M. Gobbetti. 2004. Heat shock response in Lactobacillus plantarum. Appl. Environ. Microbiol. 70:1336-1346.
8. Dervyn, E., C. Suski, R. Daniel, C. Bruand, J. Chapuis, J. Errington, J. Janniere, and S. D. Ehrlich. 2001. Two essential DNA polymerases at the bacterial replication fork. Science 294:1716-1719.
9. Ellis, J. C., and J. W. Brown. 2003. Genes within genes within bacteria. Trends Biochem. Sci. 28:521-523.
10. Ermolaeva, M. D., H. G. Khalak, O. White, H. O. Smith, and S. L. Salzberg. 2000. Prediction of transcription terminators in bacterial genomes. J. Mol. Biol. 301:27-33.
11. Forsyth, R. A., R. J. Haselbeck, K. L. Ohlsen et al. (23 co-authors). 2002. A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol. Microbiol. 43:1387-1400.
12. Galperin, M. Y., and E. V. Koonin. 2004. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res. 32:5452-5463.
13. Gerdes, S. Y., M. D. Scholle, J. W. Campbell et al. (21 co-authors). 2003. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185:5673-5684.
14. Gongadze, G. M., A. P. Korepanov, E. A. Stolboushkina et al. (11 co-authors). 2005. The crucial role of conserved intermolecular H-bonds inaccessible to the solvent in formation and stabilization of the TL5-5S rRNA complex. J. Biol. Chem. 280:16151-16156.
15. Hegeman, G. D., and S. L. Rosenberg. 1970. The evolution of bacterial enzyme systems. Annu. Rev. Microbiol. 24:429-462.
16. Hutchison, C. A. III, S. N. Peterson, S. R. Gill, R. T. Cline, O. White, C. M. Fraser, H. O. Smith, and J. C. Venter. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165-2169.
17. Inoue, K., J. Chen, I. Kato, and M. Inouye. 2002. Specific growth inhibition by acetate of an Escherichia coli strain expressing Era-dE, a dominant negative Era mutant. J. Mol. Microbiol. Biotechnol. 4:379-388.
18. Ito, M., A. A. Guffanti, W. Wang, and T. A. Krulwich. 2000. Effects of nonpolar mutations in each of the seven Bacillus subtilis mrp genes suggest complex interactions among the gene products in support of Na+ and alkali but not cholate resistance. J. Bacteriol. 182:5663-5670.
19. Jacobs, M. A., A. Alwood, I. Thaipisuttikul et al. (15 co-authors). 2003. Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 100:14339-14344.
20. Jensen, R. A. 1976. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30:409-425.
21. Jordan, I. K., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 2002. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12:962-968.
22. Klasson, L., and S. G. E. Andersson. 2004. Evolution of minimal-gene-sets in host-dependent bacteria. Trends Microbiol. 12:37-43.
23. Kobayashi, K., S. D. Ehrlich, A. Albertini et al. (99 co-authors). 2003. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100:4678-4683.
24. Koonin, E. V. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1:127-136.
25. Korbel, J. O., L. J. Jensen, C. von Mering, and P. Bork. 2004. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat. Biotechnol. 22:911-917.
26. Krylov, D. M., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13:2229-2235.
27. Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
28. Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the Gamma-proteobacteria. PLoS Biol. 1:1-9.
29. Lerat, E., V. Daubin, H. Ochman, and N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:e130.
30. Lobry, J. R. 1996. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78:323-326.
31. Maguire, B. A., and D. G. Wild. 1997. The effects of mutations in the rpmB,G operon of Escherichia coli on ribosome assembly and ribosomal protein synthesis. Biochim. Biophys. Acta 1353:137-147.
32. Maniloff, J. 1996. The minimal cell genome: "on being the right size." Proc. Natl. Acad. Sci. USA 93:10004-10006.
33. Mira, A., H. Ochman, and N. A. Moran. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-596.
34. Moore, P. B., and T. A. Steitz. 2003. The structural basis of large ribosomal subunit function. Annu. Rev. Biochem. 72:813-850.
35. 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. USA 93:10268-10273.
36. Nitschke, P., P. Guerdoux-Jamet, H. Chiapello, G. Faroux, H. Henaut, A. Henaut, and A. Danchin. 1998. Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol. Rev. 22:207-227.
37. Noria, S., and A. Danchin. 2002. Just so genome stories: what does my neighbor tell me? Pp. 3-13 in H. Yoshikawa, N. Ogasawara, and N. Satoh, eds. Proceedings of the Uehara Memorial Foundation Symposium; Genome Science: towards a new paradigm? Elsevier Science BV, Tokyo.
38. Oussenko, I. A., R. Sanchez, and D. H. Bechhofer. 2002. Bacillus subtilis YhaM, a member of a new family of 3′-to-5′ exonucleases in gram-positive bacteria. J. Bacteriol. 184:6250-6259.
39. Papp, B., C. Pal, and L. D. Hurst. 2004. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429:661-664.
40. Podkovyrov, S., and T. J. Larson. 1995. Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed. FEBS Lett. 368:429-431.
41. Reams, A. B., and E. L. Neidle. 2004. Selection for gene clustering by tandem duplication. Annu. Rev. Microbiol. 58:119-142.
42. Rocha, E. P. C. 2002. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol. 10:393-395.
43. _. 2003. DNA repeats lead to the accelerated loss of gene order in bacteria. Trends Genet. 19:600-603.
44. Rocha, E. P. C., and A. Danchin. 2003. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat. Genet. 34:377-378.
45. _. 2004. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21:108-116.
46. Romby, P., and M. Springer. 2003. Bacterial translational control at atomic resolution. Trends Genet. 19:155-161.
47. Salama, N. R., B. Shepherd, and S. Falkow. 2004. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J. Bacteriol. 186:7926-7935.
48. Salgado, H., S. Gama-Castro, A. Martinez-Antonio et al. (11 co-authors). 2004. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 32:D303-D306.
49. Sankoff, D. 2003. Rearrangements and chromosomal evolution. Curr. Opin. Genet. Dev. 13:583-587.
50. Schmalisch, M., I. Langbein, and J. Stulke. 2002. The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4:495-501.
51. Sharp, P. M. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J. Mol. Evol. 33:23-33.
52. Sharp, P. M., and W.-H. Li. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
53. Stepkowski, T., and A. B. Legocki. 2001. Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat. Acta Biochim. Pol. 48:367-381.
54. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
55. Uzan, M., and A. Danchin. 1976. A rapid test for the rel A mutation in E. coli. Biochem. Biophys. Res. Commun. 69:751-758.
56. Zar, J. H. 1996. Biostatistical analysis. Prentice-Hall International Limited, London.