The distribution of recombination repair genes is linked to information content in bacteria

Gene

Volumn 528, Issue 2, 2013, Pages 295-303

  Garcia Gonzalez, A ^a   Vicens, L ^a   Alicea, M ^a   Massey, S E ^a  

^a UNIVERSITY OF PUERTO RICO RIO PIEDRAS   (Puerto Rico)

Author keywords

DNA repair; GC content; Information content; Proteome size; Proteomic constraint; Recombination repair

Indexed keywords

ADDA PROTEIN; ADDB PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; CYTIDINE; EXODEOXYRIBONUCLEASE VIII; GUANOSINE; LIGD PROTEIN; PRIA PROTEIN; PROTEOME; RECA PROTEIN; RECB PROTEIN; RECC PROTEIN; RECD PROTEIN; RECF PROTEIN; RECG HELICASE; RECJ PROTEIN; RECN PROTEIN; RECO PROTEIN; RECQ HELICASE; RECR PROTEIN; RECU PROTEIN; RECX PROTEIN; RUVA PROTEIN; RUVB PROTEIN; RUVC PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; DNA REPAIR; EFFECTIVE POPULATION SIZE; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONTENT; RECOMBINATION REPAIR;

ADENINE/THYMINE; AT; DNA REPAIR; GC; GC CONTENT; GUANINE/CYTOSINE; IMG; INFORMATION CONTENT; INTEGRATED MICROBIAL GENOMES; LATERAL GENE TRANSFER; LGT; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION; NCBI; NHEJ; NON-HOMOLOGOUS END JOINING; PROTEOME SIZE; PROTEOMIC CONSTRAINT; RECOMBINATION REPAIR; ULTRAVIOLET; UV;

BACTERIA; BACTERIAL PROTEINS; BASE COMPOSITION; CLUSTER ANALYSIS; DNA REPAIR ENZYMES; GENOME, BACTERIAL; MODELS, GENETIC; PROTEOME; RECOMBINATIONAL DNA REPAIR;

BACTERIA (MICROORGANISMS);

EID: 84883054793     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.05.082     Document Type: Article

References (47)

1. Agnez-Lima L.F., et al. DNA damage by singlet oxygen and cellular protective mechanisms. Mutat. Res./Rev. Mutat. Res. 2012, 751:15-28.
2. Amundsen S.K., Taylor A.F., Chaudhury A.M., Smith G.R. recD: the gene for an essential third subunit of exonuclease V. Proc. Natl. Acad. Sci. U. S. A. 1986, 83:5558-5562.
3. Ayora S., et al. Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol. Rev. 2011, 35:1055-1081.
4. Cairns J., Overbaugh J., Miller S. The origin of mutants. Nature 1988, 335:142-145.
5. Chedin F., Noirot P., Blaudet V., Ehrlich S.D. A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis. Mol. Microbiol. 1998, 29:1369-1377.
6. Dale C., Wang B., Moran N., Ochman H. Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration. Mol. Biol. Evol. 2003, 20:1188-1194.
7. Drake J.W. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. U. S. A. 1991, 88:7160-7164.
8. Drake J.W., Charlesworth B., Charlesworth D., Crow J.F. Rates of spontaneous mutation. Genetics 1998, 148:1667-1686.
9. Dufresne A., Garczarek L., Partensky F. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 2005, 6:R14.
10. Garcia-Gonzalez A., Rivera-Rivera R., Massey S.E. The presence of the DNA repair genes mutM, mutY, mutL and mutS is related to proteome size in bacterial genomes. Front. Evol. Genomic Microbiol. 2012, 3:3.
11. Gong C., et al. Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C. Nat. Struct. Mol. Biol. 2005, 12:304-312.
12. Harris R.S., Ross K.J., Rosenberg S.M. Opposing roles of the Holliday junction processing system of Escherichia coli in recombination-dependent adaptive mutation. Genetics 1996, 142:681-691.
13. He A.S., Rohatgi P.R., Hersh M.N., Rosenberg S.M. Roles of E. coli double-strand-break-repair proteins in stress-induced mutation. DNA Repair 2006, 5:258-273.
14. Hershberg R., Petrov D.A. Evidence that mutation is universally biased toward AT in bacteria. PLoS Genet. 2010, 6:e1001115.
15. Hildebrand F., Meyer A., Eyre-Walker A. Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 2010, 6:e1001107.
16. Jolivet-Gougeon A., et al. Bacterial hypermutation: clinical implications. J. Med. Microbiol. 2011, 60:563-573.
17. King J.L., Jukes T.H. Non-Darwinian evolution. Science 1969, 164:788-798.
18. Klasson L., Andersson S.G.E. Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. Mol. Biol. Evol. 2006, 23:1031-1039.
19. Lee H., Popodi E., Tang H., Foster P.L. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:E2774-E2783.
20. Lind P.A., Andersson D.A. Whole-genome mutational biases in bacteria. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:17878-17883.
21. Lynch M. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 1996, 13:209-220.
22. Massey S.E. The proteomic constraint and its role in molecular evolution. Mol. Biol. Evol. 2008, 25:2557-2565.
23. Massey S.E. Proteome size as the major factor determining mutation rates. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:E858-E859.
24. Massey S.E., Garey J.R. A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs. J. Mol. Evol. 2007, 64:399-410.
25. McCutcheon J.P., Moran N.A. Extreme genome reduction in symbiotic bacteria. Nat. Rev. Microbiol. 2011, 10:13-26.
26. McGregor N., et al. The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage. Structure 2005, 13:1341-1351.
27. Moran N.A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:2873-2878.
28. O'Rourke E.J., et al. Pathogen DNA as target for host-generated oxidative stress: role for repair of bacterial DNA damage in Helicobacter pylori colonization. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:2789-2794.
29. Palmeira L., Gueguen L., Lobry J.R. UV-targeted dinucleotides are not depleted in light-exposed prokaryotic genomes. Mol. Biol. Evol. 2006, 23:2214-2219.
30. Partensky F., Garczarek L. Prochlorococcus: advantages and limits of minimalism. Ann. Rev. Mar. Sci. 2010, 2:305-331.
31. Pavankumar T.L., Sinha A.K., Ray M.K. All three subunits of RecBCD enzyme are essential for DNA repair and low-temperature growth in the Antartic Pseudomonas syringae Lz4W. PLoS One 2010, 5:e9412.
32. R Development Core Team R: a language and environment for statistical computing 2011, R Foundation for Statistical Computing, Vienna, Austria, (http://www.R-project.org/).
33. Raghavan R., Kelkar Y.D., Ochman H. A selective force favoring increased G+C content in bacterial genes. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:14504-14507.
34. Rocha E.P.C., Cornet E., Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PloS Genet. 2005, 1:e15.
35. Seigneur M., Ehrlich S.D., Michel B. RuvABC-dependent double-strand breaks in dnaBts mutants require recA. Mol. Microbiol. 2000, 38:565-574.
36. Shuman S., Glickman M.S. Bacterial DNA repair by non-homologous end joining. Nat. Rev. Microbiol. 2007, 5:852-861.
37. Stephanou N.C., et al. Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks. J. Bacteriol. 2007, 189:5237-5246.
38. Sueoka N. Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein. Proc. Natl. Acad. Sci. U. S. A. 1961, 47:1141-1149.
39. Sung W., Ackerman M.S., Miller S.F., Doak T.G., Lynch M. Drift-barrier hypothesis and mutation-rate evolution. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:18488-18492.
40. Sung W., Tucker A.E., Doak T.G., Choi E., Thomas W.K., Lynch M. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:19339-19344.
41. van Leuven J.T., McCutcheon J.P. An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. Genome Biol. Evol. 2012, 4:24-27.
42. Viklund J., Ettema T.J.G., Andersson S.G.E. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 2012, 29:599-615.
43. Vink C., Rudenko G., Seifert H.S. Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiol. Rev. 2011, 36:917-948.
44. Wernegreen J.J., Moran N.A. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol. Biol. Evol. 1999, 16:83-97.
45. West S.C. The RuvABC proteins and Holliday junction processing in Escherichia coli. J. Bacteriol. 1996, 178:1237-1241.
46. West S.C., Connolly B. Biological roles of the Escherichia coli RuvA, RuvB and RuvC proteins revealed. Mol. Microbiol. 1992, 6:2755-2759.
47. Yu X.-J., Walker D.H., Liu Y., Zhang L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol. 2009, 9:514-517.