Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

Trends in Microbiology

Volumn 10, Issue 9, 2002, Pages 393-395

  Rocha, Eduardo P C ^a,b  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; CORRELATION ANALYSIS; CYANOBACTERIUM; ESCHERICHIA COLI; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA PULMONIS; NONHUMAN; PRIORITY JOURNAL; STREPTOMYCES COELICOLOR; THERMOTOGA MARITIMA;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MYCOBACTERIUM; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA; MYCOPLASMA PULMONIS; NEGIBACTERIA; PROKARYOTA; STREPTOMYCES; STREPTOMYCES COELICOLOR; THERMOTOGA; THERMOTOGA MARITIMA;

EID: 0036709941     PISSN: 0966842X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0966-842X(02)02420-4     Document Type: Review

References (19)

1. Frank A.C., Lobry J.R. Asymmetric patterns: a review of possible underlying mutational or selective mechanisms. Gene. 238:1999;65-77.
2. Lopez P., Philippe H. Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation. C.R. Acad. Sci. III. 324:2001;201-208.
3. McLean M.J., et al. Base composition skews, replication orientation and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:1998;691-696.
4. Brewer B. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell. 53:1988;679-686.
5. Liu B., Alberts B.M. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science. 267:1995;1131-1137.
6. Liu B., et al. The DNA replication fork can pass RNA polymerase without displacing the nascent transcript. Nature. 366:1993;33-39.
7. French S. Consequences of replication fork movement through transciption units in vivo. Science. 258:1992;1362-1365.
8. Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13:1996;660-665.
9. Rocha E.P.C., et al. Universal replication bias in bacteria. Mol Microbiol. 32:1999;11-16.
10. Tillier E.R., Collins R.A. Replication orientation affects the rate and direction of bacterial gene evolution. J. Mol. Evol. 51:2000;459-463.
11. Rocha E.P.C., Danchin A. Ongoing evolution of strand composition in bacterial genomes. Mol. Biol. Evol. 18:2001;1789-1799.
12. Yuzhakov A., et al. Replisome assembly reveals the basis for asymetric function in leading and lagging strand replication. Cell. 86:1996;877-886.
13. Glover B.P., McHenry C.S. The DNA polymerase III holoenzyme: an asymmetric dimeric replicative complex with leading and lagging strand polymerases. Cell. 105:2001;925-934.
14. Fijalkowska I.J., et al. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli genome. Proc. Natl. Acad. Sci. U. S. A. 95:1998;10020-10025.
15. Dervyn E., et al. Two essential DNA polymerases at the bacterial replication fork. Science. 294:2001;1716-1719.
16. Nelson K.E., et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Themotoga maritima. Nature. 399:1999;323-329.
17. Huang Y-P., Ito J. The hyperthermophilic bacterium Thermotoga maritima has two different classes of family C DNA polymerases: evolutionary implications. Nucleic Acids Res. 26:1998;5300-5309.
18. Lemon K.P., Grossman A.D. Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science. 282:1998;1516.
19. Norris V., et al. A SeqA hyperstructure and its interactions direct the replication and sequestration of DNA. Mol. Microbiol. 37:2000;696-702.