DNA repeats lead to the accelerated loss of gene order in bacteria

Trends in Genetics

Volumn 19, Issue 11, 2003, Pages 600-603

  Rocha, Eduardo P C ^a,b  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; REPETITIVE DNA;

BACTERIAL GENETICS; CHROMOSOME REARRANGEMENT; CORRELATION ANALYSIS; ESCHERICHIA COLI; GENE ORDER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC MODEL; GENETIC RECOMBINATION; GRAM NEGATIVE BACTERIUM; LINEAR REGRESSION ANALYSIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SALMONELLA ENTERICA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GAMMAPROTEOBACTERIA; NEGIBACTERIA; PROTEOBACTERIA; SALMONELLA; SALMONELLA ENTERICA;

EID: 0242380287     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2003.09.011     Document Type: Short Survey

References (26)

1. Mushegian A.R., Koonin E.V. Gene order is not conserved in bacterial evolution. Trends Genet. 12:1996;289-290.
2. Itoh T., et al. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16:1999;332-346.
3. Tamames J. Evolution of gene order conservation in prokaryotes. Genome Biol. 2:2001;0020.1-0020.11.
4. Wolf Y.I., et al. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:2001;356-372.
5. Ochman H., et al. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:2000;299-304.
6. Tillier E.R., Collins R.A. Genome rearrangement by replication-directed translocation. Nat. Genet. 26:2000;195-197.
7. Eisen J.A., et al. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1:2000;11.
8. Suyama M., Bork P. Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17:2001;10-13.
9. Roth J.R., et al. Neinhardt H., et al. Escherichia coli and Salmonella: Cellular and Molecular Biology. 1996;2256-2276 ASM Press.
10. Louarn J.M., et al. Characterization and properties of very large inversions of the E. coli chromosome along the origin-to-terminus axis. Mol. Gen. Genet. 201:1985;467-476.
11. Segall A., et al. Rearrangement of the bacterial chromosome: forbidden inversions. Science. 241:1988;1314-1318.
12. Hill C.W., Gray J.A. Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics. 119:1988;771-778.
13. Hughes D. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol. 1:2000;6.
14. Rocha E.P., Danchin A. Essentiality, not expressiveness, drives gene strand bias in bacteria. Nat. Genet. 34:2003;377-378.
15. Zivanovic Y., et al. Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30:2002;1902-1910.
16. Achaz G., et al. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics. 164:2002;1279-1289.
17. Sankoff D., et al. Early eukaryote evolution based on mitochondrial gene order breakpoints. J. Comput. Biol. 7:2000;521-535.
18. Blanchette M., et al. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49:1999;193-203.
19. Draper N.R., Smith H. Applied Regression Analysis. 1998;John Wiley & Sons.
20. Huynen M.A., Bork P. Measuring genome evolution. Proc. Natl. Acad. Sci. U. S. A. 95:1998;5849-5856.
21. Shen P., Huang H.V. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics. 112:1986;441-457.
22. Silva F.J., et al. Why are the genomes of endosymbiotic bacteria so stable? Trends Genet. 19:2003;176-180.
23. Rocha E.P.C., Blanchard A. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 30:2002;2031-2042.
24. Schmidt H.A., et al. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:2002;502-504.
25. Pevzner P., Tesler G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 13:2003;37-45.
26. Rocha E.P.C., et al. Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol. Biol. Evol. 16:1999;1219-1230.