Involvement of DNA mismatch repair in stationary-phase mutagenesis during prolonged starvation of Pseudomonas putida

DNA Repair

Volumn 5, Issue 4, 2006, Pages 505-514

  Saumaa, Signe ^a   Tarassova, Kairi ^a   Tark, Mariliis ^a   Tover, Andres ^a   Tegova, Radi ^a   Kivisaar, Maia ^a  

^a UNIVERSITY OF TARTU   (Estonia)

Author keywords

DNA mismatch repair; Long term starvation of bacteria; Pseudomonas putida; Stationary phase mutagenesis

Indexed keywords

DNA POLYMERASE; PROTEIN MUTL;

ARTICLE; BACTERIAL GROWTH; CELL SUBPOPULATION; COLONY FORMING UNIT; CONTROLLED STUDY; DELETION MUTANT; DNA REPAIR; DNA REPLICATION; MISMATCH REPAIR; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; STARVATION;

BASE PAIR MISMATCH; BASE PAIRING; CELL SURVIVAL; CODON, NONSENSE; DNA REPAIR; MUTAGENESIS; PSEUDOMONAS PUTIDA;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 33645346212     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2005.12.003     Document Type: Article

References (53)

1. P.L. Foster Adaptive mutation: the uses of adversity Annu. Rev. Microbiol. 47 1993 467 504
2. P.L. Foster Mechanisms of stationary phase mutation: a decade of adaptive mutation Annu. Rev. Genet. 33 1999 57 88
3. M.M. Zambrano, D.A. Siegele, M. Almiron, A. Tormo, and R. Kolter Microbial competition: Escherichia coli mutants that take over stationary phase cultures Science 259 1993 1757 1760
4. E.R. Zinser, and R. Kolter Escherichia coli evolution during stationary phase Res. Microbiol. 155 2004 328 336
5. B. Yeiser, E.D. Pepper, M.F. Goodman, and S.E. Finkel SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness Proc. Natl. Acad. Sci. U.S.A. 99 2002 8737 8741
6. B.A. Bridges Elevated mutation rate in mutT bacteria during starvation: evidence for DNA turnover? J. Bacteriol. 178 1996 2709 2711
7. B.A. Bridges, and S. Ereira DNA synthesis and viability of a mutT derivative of Escherichia coli WP2 under conditions of amino acid starvation and relation to stationary-phase (adaptive) mutation J. Bacteriol. 180 1998 2906 2910
8. I. Bjedov, O. Tenaillon, B. Gérard, V. Souza, E. Denamur, M. Radman, F. Taddei, and I. Matic Stress-induced mutagenesis in bacteria Science 300 2003 1404 1409
9. L. Loewe, V. Textor, and S. Scherer High deleterious genomic mutation rate in stationary phase of Escherichia coli Science 302 2003 1558 1560
10. B.A. Bridges Spontaneous mutation in stationary-phase Escherichia coli WP2 carrying various DNA repair alleles Mutat. Res. 302 1993 173 176
11. S. Bhamre, B.B. Gadea, C.A. Koyama, S.J. White, and R.G. Fowler An aerobic recA, umuC-dependent pathway of spontaneous base-pair substitution mutagenesis in Escherichia coli Mutat. Res. 473 2001 229 247
12. H.J. Bull, M.-J. Lombardo, and S.M. Rosenberg Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence Proc. Natl. Acad. Sci. U.S.A. 98 2001 8334 8341
13. G.J. McKenzie, P.L. Lee, M.-J. Lombardo, P.J. Hastings, and S.M. Rosenberg SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification Mol. Cell 7 2001 571 579
14. H.-M. Sung, G. Yeamans, C.A. Ross, and R.E. Yasbin Roles of YgjH and YgjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis J. Bacteriol. 185 2003 2153 2160
15. R. Tegova, A. Tover, K. Tarassova, M. Tark, and M. Kivisaar Involvement of error-prone DNA polymerase pol IV on stationary phase mutagenesis in Pseudomonas putida J. Bacteriol. 186 2004 2735 2744
16. P.L. Foster Are adaptive mutations due to decline in mismatch repair? The evidence is lacking Mutat. Res. 436 1999 179 184
17. R.S. Harris, G. Feng, K.J. Ross, R. Sidhu, C. Thulin, S. Longerich, S.K. Szigety, P.J. Hastings, M.E. Winkler, and S.M. Rosenberg Mismatch repair is diminished during stationary-phase mutation Mutat. Res. 437 1999 51 60
18. S. Longerich, A.M. Galloway, R.S. Harris, C. Wong, and S.M. Rosenberg Adaptive mutation sequences reproduced by mismatch repair deficiency Proc. Natl. Acad. Sci. U.S.A. 92 1995 12017 12020
19. G. Feng, H.-C.T. Tsui, and M.E. Winkler Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells J. Bacteriol. 178 1996 2388 2396
20. R.S. Harris, G. Feng, K.J. Ross, R. Sidhu, C. Thulin, S. Longerich, S.K. Szigety, M.E. Winkler, and S.M. Rosenberg Mismatch repair protein MutL becomes limiting during stationary-phase mutation Genes Dev. 11 1997 2426 2437
21. R.M. Schaaper, and M. Radman The extreme mutator effect of Escherichia coli mutD5 results from saturation of mismatch repair by excessive DNA replication errors EMBO J. 8 1989 3511 3516
22. S. Saumaa, A. Tover, L. Kasak, and M. Kivisaar Different spectra of stationary-phase mutations in early-arising versus late-arising mutants of Pseudomonas putida: involvement of the DNA repair enzyme MutY and stationary-phase sigma factor RpoS J. Bacteriol. 184 2002 6957 6965
23. J.H. Miller A Short Course in Bacterial Genetics 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
24. M.H. Adams Bacteriophages 1959 Interscience Publishers Inc. New York pp. 445-447
25. T. Bauchop, and S.R. Elsden The growth of micro-organisms in relation to their energy supply J. Gen. Microbiol. 23 1960 457 469
26. D. Hanahan Studies on the transformation of E. coli with plasmids J. Mol. Biol. 166 1983 577 580
27. R.C. Sharma, and R.T. Schimke Preparation of electro-competent E. coli using salt-free growth medium BioTechniques 20 1996 42 44
28. P. Carter, H. Bedouelle, and G. Winter Improved oligonucleotide site-directed mutagenesis using M13 vectors Nucl. Acids Res. 13 1985 4431 4443
29. M.I. Ramos-González, and S. Molin Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440 J. Bacteriol. 180 1998 3421 3431
30. V. de Lorenzo, M. Herrero, U. Jakubzik, and K.N. Timmis Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria J. Bacteriol. 172 1990 6568 6572
31. H. Pavel, M. Forsman, and V. Shingler An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols J. Bacteriol. 176 1994 7550 7557
32. M. Herrero, V. de Lorenzo, and K.N. Timmis Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria J. Bacteriol. 172 1990 6557 6567
33. S.A. Bayley, C.J. Duggleby, M.J. Worsey, P.A. Williams, K.G. Hardy, and P. Broda Two modes of loss of the TOL function from Pseudomonas putida mt-2 Mol. Gen. Genet. 154 1977 203 204
34. D.H. Figurski, and D.R. Helinski Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans Proc. Natl. Acad. Sci. U.S.A. 76 1979 1648 1652
35. R. Hõrak, H. Ilves, P. Pruunsild, M. Kuljus, and M. Kivisaar The ColR-ColS two-component signal transduction system is involved in regulation of Tn4652 transposition in Pseudomonas putida under starvation conditions Mol. Microbiol. 54 2004 795 807
36. L. Kasak, R. Hõrak, and M. Kivisaar Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria Proc. Natl. Acad. Sci. U.S.A. 94 1997 3134 3139
37. R.P. Haugland Assays for cells viability, proliferation and function M.T.Z. Spence Handbook of Fluorescent Probes and Research Chemicals 1996 Molecular Probes Inc. Eugene 365 398
38. J. Wagner, and T. Nohmi Escherichia coli DNA polymerase IV mutator activity: genetic requirements and mutational specificity J. Bacteriol. 182 2000 4587 4595
39. R.M. Schaaper Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli J. Biol. Chem. 268 1993 23762 23765
40. E.C. Friedberg, R. Wagner, and M. Radman Specialized DNA polymerases, cellular survival, and the genesis of mutations Science 296 2002 1627 1630
41. M.D. Sutton, and G.C. Walker Managing DNA polymerases: coordinating DNA replication, DNA repair, and DNA recombination Proc. Natl. Acad. Sci. U.S.A. 98 2001 8342 8349
42. F.J. López de Saro, and M. O'Donnell Interaction of the β sliding clamp with MutS, ligase, and DNA polymerase I Proc. Natl. Acad. Sci. U.S.A. 98 2001 8376 8380
43. F.J. López de Saro, R.E. Georgescu, M.F. Goodman, and M. O'Donnell Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair EMBO J. 22 2003 6408 6418
44. B. Dalrymple, K. Kongsuwan, G. Wijffels, N.E. Dixon, and P.A. Jennings A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems Proc. Natl. Acad. Sci. U.S.A. 98 2001 11627 11632
45. H.I.M. Boshoff, M.B. Reed, C.E. Barry III, and V. Mizrahi DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis Cell 113 2003 183 193
46. R.S. Galhardo, R.P. Rocha, M.V. Marques, and C.F.M. Menck An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus Nucl. Acids Res. 33 2005 2603 2614
47. M. Abella, I. Erill, M. Jara, G. Mazón, S. Campoy, and J. Barbé Widespread distribution of a lexA-regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum Mol. Microbiol. 54 2004 212 222
48. B.G. Hall Spontaneous point mutations that occur more often when they are advantageous than when they are neutral Genetics 126 1990 5 16
49. B.A. Bridges Hypermutation under stress Nature 387 1997 557 558
50. P.L. Foster Nonadaptive mutations occur on the F'episome during adaptive mutation conditions in Escherichia coli J. Bacteriol. 179 1997 1550 1554
51. J. Torkelson, R.S. Harris, M.-J. Lombardo, J. Nagendran, C. Thulin, and S.M. Rosenberg Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation EMBO J. 16 1997 3303 3311
52. S.E. Finkel, E.R. Zinser, and R. Kolter Long-term survival and evolution in the stationary phase G. Storz R. Hengge-Aronis Bacterial Stress Responses 2000 American Society for Microbiology Washington, DC 231 238
53. J.W. Costerton, Z. Lewandowski, D.E. Caldwell, D.R. Korber, and H.M. Lappin-Scott Microbial biofilms Annu. Rev. Microbiol. 49 1995 711 745