Associations between inverted repeats and the structural evolution of bacterial genomes

Genetics

Volumn 164, Issue 4, 2003, Pages 1279-1289

  Achaz, Guillaume ^a,d   Coissac, Eric ^a,e   Netter, Pierre ^a   Rocha, Eduardo P C ^b,c  

^a INSTITUT JACQUES MONOD   (France)

^b INSTITUT PASTEUR   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d HARVARD UNIVERSITY   (United States)

^e INRIA RHÔNE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; TRANSPOSASE;

ARTICLE; BACTERIAL GENOME; CHROMOSOME INVERSION; CHROMOSOME STRUCTURE; DNA REPLICATION; GENETIC STABILITY; HOMOLOGOUS RECOMBINATION; INVERTED REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; INVERSION, CHROMOSOME; MODELS, GENETIC; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0042318548     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. ACHAZ, G., E. COISSAC, A. VIARI and P. NETTER, 2000 Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin. Mol. Biol. Evol. 17:1268-1275.
2. ACHAZ, G., E. P. C. ROCHA, P. NETTER and E. COISSAC, 2002 Origin and fate of repeats in bacteria. Nucleic Acids Res. 30: 2987-2994.
3. AMUNDSEN, S. K., and G. R. SMITH, 2003 Interchangeable parts of the Escherichia coli recombination machinery. Cell 112: 741-744.
4. BERGTHORSSON, U., and H. OCHMAN, 1998 Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15: 6-16.
5. CASJENS, S., 1998 The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32: 339-377.
6. COURCELLE, J., A. K. GANESAN and P. C. HANAWALT, 2001 Therefore, what are recombination proteins there for? Bioessays 23: 463-470.
7. DENG, W., V. BURLAND, G. PLUNKETT, III, A. BOUTIN, G. F. MAYHEW et al., 2002 Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184: 4601-4611.
8. EISEN, J. A., and P. C. HANAWALT, 1999 A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435: 171-213.
9. EISEN, J. A., J. F. HEIDELBERG, O. WHITE and S. L. SALZBERG, 2000 Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1: 11.1-11.9.
10. FRANK, A. C., and J. R. LOBRY, 1999 Asymmetric patterns: a review of possible underlying mutational or selective mechanisms. Gene 238: 65-77.
11. GUIJO, M. I., J. PATTE, M. DEL MAR CAMPOS, J. M. LOUARN and J. E. REBOLLO, 2001 Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus. Genetics 157: 1413-1423.
12. HILL, C. W., and J. A. GRAY, 1988 Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics 119: 771-778.
13. HIMMELREICH, R., H. PLAGENS, H. HILBERT, B. REINER and R. HERRMANN, 1997 Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25: 701-712.
14. HUGHES, D., 1999 Impact of homologous recombination on genome organization and stability, pp. 109-128 in Organization of the Prokaryotic Genome, edited by R. L. CHARLEBOIS. ASM Press, Washington, DC.
15. HUGHES, D., 2000 Co-evolution of the tuf genes links gene conversion with the generation of chromosomal inversions. J. Mol. Biol. 297: 355-364.
16. ITOH, T., K. TAKEMOTO, H. MORI and T. GOJOBORI, 1999 Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16: 332-346.
17. KARLIN, S., and F. OST, 1985 Maximal segmental match length among random sequences from a finite alphabet, pp. 225-243 in Proceedings of the Berkeley Conference in Honor of Jerzy Neyman and Jack Kiefer, edited by L. M. L. CAM and R. A. OLSHEN. Wadsworth, New York.
18. KURTZ, S., and C. SCHLEIERMACHER, 1999 REPuter: fast computation of maximal repeats in complete genomes. BioInformatics 15: 426-427.
19. LIU, S. L., and K. E. SANDERSON, 1996 Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93: 10303-10308.
20. LOBRY, J. R., 1996 Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
21. LOUARN, J. M., J. P. BOUCHE, F. LEGENDRE, J. LOUARN and J. PATTE, 1985 Characterization and properties of very large inversions of the E. coli chromosome along the origin-to-terminus axis. Mol. Gen. Genet. 201: 467-476.
22. LOUARN, J.-M., J. LOUARN, V. FRANÇOIS and J. PATTE, 1991 Analysis and possible role of hyperrecombination in the termination region of the E. coli chromosome. J. Bacteriol. 173: 5097-5104.
23. MACKIEWICZ, P., D. MACKIEWICZ, A. GIERLIK, M. KOWALCZUK, A. NOWICKA et al., 2001 The differential killing of genes by inversions in prokaryotic genomes. J. Mol. Evol. 53: 615-621.
24. MARIANS, K. J., 1992 Prokaryotic DNA replication. Annu. Rev. Biochem. 61: 673-719.
25. McLEAN, M. J., K. H. WOLFE and K. M. DEVINE, 1998 Base composition skews, replication orientation and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47: 691-696.
26. OCHMAN, H., J. G. LAWRENCE and E. A. GROISMAN, 2000 Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
27. OGATA, H., S. AUDIC, V. BARBE, F. ARTIGUENAVE, P. E. FOURNIER et al., 2000 Selfish DNA in protein-coding genes of Rickettsia. Science 290: 347-350.
28. ROBERTS, M. S., and F. M. COHAN, 1993 The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics 134: 401-408.
29. ROCHA, E. P. C., 2002 Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol. 10: 393-396.
30. ROCHA, E. P. C., and A. BLANCHARD, 2002 Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 30: 2031-2042.
31. ROCHA, E. P. C., and A. DANCHIN, 2001 Ongoing evolution of strand composition in bacterial genomes. Mol. Biol. Evol. 18:1789-1799.
32. ROCHA, E. P. C., A. DANCHIN and A. VIARI, 1999a Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol. Biol. Evol. 16: 1219-1230.
33. ROCHA, E. P. C., A. DANCHIN and A. VIARI, 1999b Functional and evolutionary roles of long repeats in prokaryotes. Res. Microbiol. 150: 725-733.
34. ROMERO, D., and R. PALACIOS, 1997 Gene amplification and genomic plasticity in prokaryotes. Annu. Rev. Genet. 31: 91-111.
35. ROTH, J. R., N. BENSON, T. GALITSKI, K. HAACK, J. G. LAWRENCE et al., 1996 Rearrangements of the bacterial chromosome: formation and applications, pp. 2256-2276 in Escherichia coli and Salmonella: Cellular and Molecular Biology, edited by R. C. H. NEINHARDT, J. L. INGRAHAM, E. C. C. LIN, K. BROOKS LOW, B. MAGASANIK et al. ASM Press, Washington, DC.
36. SAUNDERS, N. J., A. C. JEFFRIES, J. F. PEDEN, D. W. HOOD, H. TETTELIN et al., 2000 Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol. Microbiol. 37: 207-215.
37. SEGALL, A., M. J. MAHAN and J. R. ROTH, 1988 Rearrangement of the bacterial chromosome: forbidden inversions. Science 241: 1314-1318.
38. SHEN, P., and H. V. HUANG, 1986 Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112: 441-457.
39. SHIGENOBU, S., H. WATANABE, M. HATTORI, Y. SAKAKI and H. ISHIKAWA, 2000 Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
40. SMITH, G. R., 1988 Homologous recombination in procaryotes. Microbiol. Rev. 52: 1-28.
41. SMITH, T. F., and M. S. WATERMAN, 1981 Comparison of bio-sequences. Adv. Appl. Math. 2: 482-489.
42. SUYAMA, M., and P. BORK, 2001 Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17: 10-13.
43. TAMAS, I., L. KLASSON, B. CANBACK, A. K. NASLUND, A. S. ERIKSSON et al., 2002 50 million years of genomic stasis in endosymbiotic bacteria. Science 296: 2376-2379.
44. TILLIER, E. R., and R. A. COLLINS, 2000a Genome rearrangement by replication-directed translocation. Nat. Genet. 26: 195-197.
45. TILLIER, E. R., and R. A. COLLINS, 2000b Replication orientation affects the rate and direction of bacterial gene evolution. J. Mol. Evol. 51: 459-463.
46. VULIC, M., F. DIONISIO, F. TADDEI and M. RADMAN, 1997 Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. USA 94: 9763-9767.
47. WOLF, Y. I., I. B. ROGOZIN, A. S. KONDRASHOV and E. V. KOONIN, 2001 Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11: 356-372.
48. ZIVANOVIC, Y., P. LOPEZ, H. PHILIPPE and P. FORTERRE, 2002 Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30: 1902-1910.