Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 737, Issue 1-2, 2012, Pages 12-24

  Tavita, Kairi ^a   Mikkel, Katren ^a   Tark Dame, Mariliis ^a   Jerabek, Hansjoerg ^b   Teras, Riho ^a   Sidorenko, Julia ^a   Tegova, Radi ^a   Tover, Andres ^a   Dame, Remus T ^c   Kivisaar, Maia ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Accessibility of chromosomal DNA; Homologous recombination in stationary phase bacteria; Nucleoid associated proteins; Phenol stress; Pseudomonas putida; Reactive oxygen species

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; CARBON; NUCLEOID ASSOCIATED PROTEIN; PHENOL; REACTIVE OXYGEN METABOLITE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BASE MISPAIRING; BINDING SITE; CARBON SOURCE; CHEMICAL STRESS; CHROMOSOMAL LOCALIZATION; COMPUTER ANALYSIS; CONTROLLED STUDY; CULTURE MEDIUM; DNA FLANKING REGION; GENE EXPRESSION; GENE STRUCTURE; HOMOLOGOUS RECOMBINATION; NONHUMAN; PHEA GENE; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN BINDING; PSEUDOMONAS PUTIDA; STARVATION;

CARBON; CHROMOSOMES, BACTERIAL; DNA MISMATCH REPAIR; DNA REPAIR ENZYMES; HOMOLOGOUS RECOMBINATION; OXIDATIVE STRESS; PHENOL; PSEUDOMONAS PUTIDA; REACTIVE OXYGEN SPECIES;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 84865515927     PISSN: 00275107     EISSN: 09218262     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2012.07.004     Document Type: Article

References (131)

1. Cox M.M. Regulation of bacterial RecA protein function. Crit. Rev. Biochem. Mol. Biol. 2007, 42:41-63.
2. Kreuzer K.N. Interplay between DNA replication and recombination in prokaryotes. Annu. Rev. Microbiol. 2005, 59:43-67.
3. Kuzminov A. DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:8461-8468.
4. Michel B., Grompone G., Flores M.J., Bidnenko V. Multiple pathways process stalled replication forks. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:12783-12788.
5. Persky N.S., Lovett S.T. Mechanisms of recombination: lessons from E. coli. Crit. Rev. Biochem. Mol. Biol. 2008, 43:347-370.
6. Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
7. Koonin E.V., Makarova K.S., Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 2001, 55:709-742.
8. Spratt B.G., Hanage W.P., Feil E.J. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 2001, 4:602-606.
9. Fraser C., Hanage W.P., Spratt B.G. Recombination and the nature of bacterial speciation. Science 2007, 315:476-480.
10. Achtman M., Wagner M. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 2008, 6:431-440.
11. van der Meer J.R., Sentchilo V. Genomic islands and the evolution of catabolic pathways in bacteria. Curr. Opin. Biotechnol. 2003, 14:248-254.
12. Johnson G.R., Jain R.K., Spain J.C. Origins of the 2,4-dinitrotoluene pathway. J. Bacteriol. 2002, 184:4219-4232.
13. Trefault N., De la Iglesia R., Molina A.M., Manzano M., Ledger T., Perez-Pantoja D., Sanchez M.A., Stuardo M., Gonzalez B. Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ. Microbiol. 2004, 6:655-668.
14. Symons Z.C., Bruce N.C. Bacterial pathways for degradation of nitroaromatics. Nat. Prod. Rep. 2006, 23:845-850.
15. Clarke P.H. The Metabolic Versatility of Pseudomonads 1982, vol. 48. Antonie Van Leeuwenhoek, pp. 105-130.
16. Timmis K.N., Pieper D.H. Bacteria designed for bioremediation. Trends Biotechnol. 1999, 17:200-204.
17. Eriksson M., Sodersten E., Yu Z., Dalhammar G., Mohn W.W. Degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils. Appl. Environ. Microbiol. 2003, 69:275-284.
18. Bordenave S., Goni-Urriza M.S., Caumette P., Duran R. Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl. Environ. Microbiol. 2007, 73:6089-6097.
19. Kim J.S., Crowley D.E. Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits. Appl. Environ. Microbiol. 2007, 73:4579-4591.
20. Pieper D.H., Reineke W. Engineering bacteria for bioremediation. Curr. Opin. Biotechnol. 2000, 11:262-270.
21. Wackett L.P. Pseudomonas putida - a versatile biocatalyst. Nat. Biotechnol. 2003, 21:136-138.
22. Cases I., de Lorenzo V. Promoters in the environment: transcriptional regulation in its natural context. Nat. Rev. Microbiol. 2005, 3:105-118.
23. Ramos J.L., Krell T., Daniels C., Segura A., Duque E. Responses of Pseudomonas to small toxic molecules by a mosaic of domains. Curr. Opin. Microbiol. 2009, 12:215-220.
24. Dominguez-Cuevas P., Gonzalez-Pastor J.E., Marques S., Ramos J.L., de Lorenzo V. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem. 2006, 281:11981-11991.
25. Santos P.M., Benndorf D., Sa-Correia I. Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 2004, 4:2640-2652.
26. Imlay J.A., Linn S. Bimodal pattern of killing of DNA-repair-defective or anoxically grown Escherichia coli by hydrogen peroxide. J. Bacteriol. 1986, 166:519-527.
27. Galitski T., Roth J.R. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium. Genetics 1997, 146:751-767.
28. Rayssiguier C., Thaler D.S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 1989, 342:396-401.
29. Worth L., Clark S., Radman M., Modrich P. Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. Proc. Natl. Acad. Sci. U.S.A. 1994, 91:3238-3241.
30. Delmas S., Matic I. Cellular response to horizontally transferred DNA in Escherichia coli is tuned by DNA repair systems. DNA Repair (Amst) 2005, 4:221-229.
31. Orren D.K., Selby C.P., Hearst J.E., Sancar A. Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I. J. Biol. Chem. 1992, 267:780-788.
32. Modrich P. Mismatch repair, genetic stability, and cancer. Science 1994, 266:1959-1960.
33. Veaute X., Delmas S., Selva M., Jeusset J., Le Cam E., Matic I., Fabre F., Petit M.A. UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. EMBO J. 2005, 24:180-189.
34. Petit M.A., Dimpfl J., Radman M., Echols H. Control of large chromosomal duplications in Escherichia coli by the mismatch repair system. Genetics 1991, 129:327-332.
35. Postow L., Hardy C.D., Arsuaga J., Cozzarelli N.R. Topological domain structure of the Escherichia coli chromosome. Genes Dev. 2004, 18:1766-1779.
36. Deng S., Stein R.A., Higgins N.P. Organization of supercoil domains and their reorganization by transcription. Mol. Microbiol. 2005, 57:1511-1521.
37. Reyes-Lamothe R., Wang X., Sherratt D. Escherichia coli and its chromosome. Trends Microbiol. 2008, 16:238-245.
38. Weiner A., Zauberman N., Minsky A. Recombinational DNA repair in a cellular context: a search for the homology search. Nat. Rev. Microbiol. 2009, 7:748-755.
39. Wiggins P.A., Cheveralls K.C., Martin J.S., Lintner R., Kondev J. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:4991-4995.
40. Umbarger M.A., Toro E., Wright M.A., Porreca G.J., Bau D., Hong S.H., Fero M.J., Zhu L.J., Marti-Renom M.A., McAdams H.H., Shapiro L., Dekker J., Church G.M. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell 2011, 44:252-264.
41. Dame R.T. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 2005, 56:858-870.
42. Dillon S.C., Dorman C.J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 2010, 8:185-195.
43. Ali Azam T., Iwata A., Nishimura A., Ueda S., Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 1999, 181:6361-6370.
44. Travers A., Muskhelishvili G. DNA supercoiling - a global transcriptional regulator for enterobacterial growth?. Nat. Rev. Microbiol. 2005, 3:157-169.
45. Amzallag G.N. Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology?. J. Theor. Biol. 2004, 229:361-369.
46. Karpinets T., Greenwood D., Pogribny I., Samatova N. Bacterial stationary-state mutagenesis and Mammalian tumorigenesis as stress-induced cellular adaptations and the role of epigenetics. Curr. Genomics 2006, 7:481-496.
47. Vora T., Hottes A.K., Tavazoie S. Protein occupancy landscape of a bacterial genome. Mol. Cell 2009, 35:247-253.
48. - strains of Escherichia coli K12. J. Mol. Biol. 1974, 83:447-457.
49. Bichara M., Pinet I., Origas M., Fuchs R.P. Inactivation of recG stimulates the RecF pathway during lesion-induced recombination in E. coli. DNA Repair (Amst) 2006, 5:129-137.
50. Hoffmann G.R. Bacterial assays for recombinagens. Mutat. Res. 1992, 284:125-146.
51. Lovett S.T., Hurley R.L., Sutera V.A., Aubuchon R.H., Lebedeva M.A. Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways. Genetics 2002, 160:851-859.
52. Baath E. Growth rates of bacterial communities in soils at varying pH: a comparison of the thymidine and leucine incorporation techniques. Microb. Ecol. 1998, 36:316-327.
53. Poulsen L.K., Licht T.R., Rang C., Krogfelt K.A., Molin S. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J. Bacteriol. 1995, 177:5840-5845.
54. Foster P.L. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu. Rev. Genet. 1999, 33:57-88.
55. Harris R.S., Longerich S., Rosenberg S.M. Recombination in adaptive mutation. Science 1994, 264:258-260.
56. Foster P.L., Trimarchi J.M., Maurer R.A. Two enzymes, both of which process recombination intermediates, have opposite effects on adaptive mutation in Escherichia coli. Genetics 1996, 142:25-37.
57. Bull H.J., Lombardo M.J., Rosenberg S.M. Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:8334-8341.
58. McKenzie G.J., Lee P.L., Lombardo M.J., Hastings P.J., Rosenberg S.M. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol. Cell 2001, 7:571-579.
59. Elez M., Radman M., Matic I. The frequency and structure of recombinant products is determined by the cellular level of MutL. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:8935-8940.
60. Lopez E., Elez M., Matic I., Blazquez J. Antibiotic-mediated recombination: ciprofloxacin stimulates SOS-independent recombination of divergent sequences in Escherichia coli. Mol. Microbiol. 2007, 64:83-93.
61. Miller J.H. A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria 1992, Cold Spring Harbour Laboratory Press, Cold Spring Harbour, NY.
62. Adams M.H. Bacteriophages 1959, Interscience Publishers Inc., NY.
63. Sharma R.C., Schimke R.T. Preparation of electrocompetent E. coli using salt-free growth medium. Biotechniques 1996, 20:42-44.
64. Herrero M., de Lorenzo V., Timmis K.N. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol. 1990, 172:6557-6567.
65. Boyer H.W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J. Mol. Biol. 1969, 41:459-472.
66. Figurski D.H., Helinski D.R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. U.S.A. 1979, 76:1648-1652.
67. Bao Y., Lies D.P., Fu H., Roberts G.P. An improved Tn7-based system for the single-copy insertion of cloned genes into chromosomes of gram-negative bacteria. Gene 1991, 109:167-168.
68. Bayley S.A., Duggleby C.J., Worsey M.J., Williams P.A., Hardy K.G., Broda P. Two modes of loss of the Tol function from Pseudomonas putida mt-2. Mol. Gen. Genet. 1977, 154:203-204.
69. Regenhardt D., Heuer H., Heim S., Fernandez D.U., Strompl C., Moore E.R., Timmis K.N. Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ. Microbiol. 2002, 4:912-915.
70. Kasak L., Hõrak R., Kivisaar M. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:3134-3139.
71. Santos P.M., Di Bartolo I., Blatny J.M., Zennaro E., Valla S. New broad-host-range promoter probe vectors based on the plasmid RK2 replicon. FEMS Microbiol. Lett. 2001, 195:91-96.
72. Sanchez-Romero J.M., Diaz-Orejas R., De Lorenzo V. Resistance to tellurite as a selection marker for genetic manipulations of Pseudomonas strains. Appl. Environ. Microbiol. 1998, 64:4040-4046.
73. Meyer R. Replication and conjugative mobilization of broad host-range IncQ plasmids. Plasmid 2009, 62:57-70.
74. Nurk A., Kasak L., Kivisaar M. Sequence of the gene (pheA) encoding phenol monooxygenase from Pseudomonas sp. EST1001: expression in Escherichia coli and Pseudomonas putida. Gene 1991, 102:13-18.
75. Kolatka K., Kubik S., Rajewska M., Konieczny I. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 2010, 64:119-134.
76. O'Toole G.A., Kolter R. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol. Microbiol. 1998, 28:449-461.
77. Tegova R., Tover A., Tarassova K., Tark M., Kivisaar M. Involvement of error-prone DNA polymerase IV in stationary-phase mutagenesis in Pseudomonas putida. J. Bacteriol. 2004, 186:2735-2744.
78. Saumaa S., Tarassova K., Tark M., Tover A., Tegova R., Kivisaar M. Involvement of DNA mismatch repair in stationary-phase mutagenesis during prolonged starvation of Pseudomonas putida. DNA Repair (Amst) 2006, 5:505-514.
79. Ojangu E.L., Tover A., Teras R., Kivisaar M. Effects of combination of different-10 hexamers and downstream sequences on stationary-phase-specific sigma factor sigma(S)-dependent transcription in Pseudomonas putida. J. Bacteriol. 2000, 182:6707-6713.
80. Saumaa S., Tover A., Kasak L., Kivisaar M. Different spectra of stationary-phase mutations in early-arising versus late-arising mutants of Pseudomonas putida: involvement of the DNA repair enzyme MutY and the stationary-phase sigma factor RpoS. J. Bacteriol. 2002, 184:6957-6965.
81. Koch B., Jensen L.E., Nybroe O. A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J. Microbiol. Methods 2001, 45:187-195.
82. Medina-Rivera A., Abreu-Goodger C., Thomas-Chollier M., Salgado H., Collado-Vides J., van Helden J. Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. 2011, 39:808-824.
83. Turatsinze J.V., Thomas-Chollier M., Defrance M., van Helden J. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc. 2008, 3:1578-1588.
84. Kivisaar M., Hõrak R., Kasak L., Heinaru A., Habicht J. Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid 1990, 24:25-36.
85. Harris R.S., Feng G., Ross K.J., Sidhu R., Thulin C., Longerich S., Szigety S.K., Winkler M.E., Rosenberg S.M. Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes Dev. 1997, 11:2426-2437.
86. Imlay J.A. Pathways of oxidative damage. Annu. Rev. Microbiol. 2003, 57:395-418.
87. Tarassova K., Tegova R., Tover A., Teras R., Tark M., Saumaa S., Kivisaar M. Elevated mutation frequency in surviving populations of carbon-starved rpoS-deficient Pseudomonas putida is caused by reduced expression of superoxide dismutase and catalase. J. Bacteriol. 2009, 191:3604-3614.
88. Kohanski M.A., DePristo M.A., Collins J.J. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol. Cell 2010, 37:311-320.
89. Touati D., Jacques M., Tardat B., Bouchard L., Despied S. Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase. J. Bacteriol. 1995, 177:2305-2314.
90. Castang S., McManus H.R., Turner K.H., Dove S.L. H-NS family members function coordinately in an opportunistic pathogen. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:18947-18952.
91. Noom M.C., Navarre W.W., Oshima T., Wuite G.J., Dame R.T. H-NS promotes looped domain formation in the bacterial chromosome. Curr. Biol. 2007, 17:R913-R914.
92. Dame R.T., Luijsterburg M.S., Krin E., Bertin P.N., Wagner R., Wuite G.J. DNA bridging: a property shared among H-NS-like proteins. J. Bacteriol. 2005, 187:1845-1848.
93. Teras R., Hõrak R., Kivisaar M. Transcription from fusion promoters generated during transposition of transposon Tn4652 is positively affected by integration host factor in Pseudomonas putida. J. Bacteriol. 2000, 182:589-598.
94. Teras R., Jakovleva J., Kivisaar M. Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652. Microbiology 2009, 155:1203-1214.
95. Kolter R., Siegele D.A., Tormo A. The stationary phase of the bacterial life cycle. Annu. Rev. Microbiol. 1993, 47:855-874.
96. Guttman D.S., Dykhuizen D.E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 1994, 266:1380-1383.
97. Ramos J.L., Duque E., Gallegos M.T., Godoy P., Ramos-Gonzalez M.I., Rojas A., Teran W., Segura A. Mechanisms of solvent tolerance in gram-negative bacteria. Annu. Rev. Microbiol. 2002, 56:743-768.
98. Heipieper H.J., Meinhardt F., Segura A. The cis-trans isomerase of unsaturated fatty acids in Pseudomonas and Vibrio: biochemistry, molecular biology and physiological function of a unique stress adaptive mechanism. FEMS Microbiol. Lett. 2003, 229:1-7.
99. Sikkema J., de Bont J.A., Poolman B. Mechanisms of membrane toxicity of hydrocarbons. Microbiol. Rev. 1995, 59:201-222.
100. Onda M., Hanada K., Kawachi H., Ikeda H. Escherichia coli mutM suppresses illegitimate recombination induced by oxidative stress. Genetics 1999, 151:439-446.
101. Steiner W.W., Kuempel P.L. Sister chromatid exchange frequencies in Escherichia coli analyzed by recombination at the dif resolvase site. J. Bacteriol. 1998, 180:6269-6275.
102. Boles B.R., Singh P.K. Endogenous oxidative stress produces diversity and adaptability in biofilm communities. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:12503-12508.
103. Fabisiewicz A., Worth L. Escherichia coli MutS, L modulate RuvAB-dependent branch migration between diverged DNA. J. Biol. Chem. 2001, 276:9413-9420.
104. Štambuk S., Radman M. Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics 1998, 150:533-542.
105. Roth J.R., Kugelberg E., Reams A.B., Kofoid E., Andersson D.I. Origin of mutations under selection: the adaptive mutation controversy. Annu. Rev. Microbiol. 2006, 60:477-501.
106. Andersson D.I., Hughes D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 2009, 43:167-195.
107. Shee C., Gibson J.L., Darrow M.C., Gonzalez C., Rosenberg S.M. Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:13659-13664.
108. Nevo E. Evolution under environmental stress at macro- and microscales. Genome Biol. Evol. 2011, 3:1039-1052.
109. Baquero F. Environmental stress and evolvability in microbial systems. Clin. Microbiol. Infect. 2009, 15(Suppl. 1):5-10.
110. Hadany L., Comeron J.M. Why are sex and recombination so common?. Ann. N. Y. Acad. Sci. 2008, 1133:26-43.
111. Prudhomme M., Attaiech L., Sanchez G., Martin B., Claverys J.P. Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science 2006, 313:89-92.
112. Itzek A., Zheng L., Chen Z., Merritt J., Kreth J. Hydrogen peroxide-dependent DNA release and transfer of antibiotic resistance genes in Streptococcus gordonii. J. Bacteriol. 2011, 193:6912-6922.
113. Lebel E.G., Masson J., Bogucki A., Paszkowski J. Stress-induced intrachromosomal recombination in plant somatic cells. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:422-426.
114. Molinier J., Ries G., Zipfel C., Hohn B. Transgeneration memory of stress in plants. Nature 2006, 442:1046-1049.
115. Kovalchuk I., Kovalchuk O., Kalck V., Boyko V., Filkowski J., Heinlein M., Hohn B. Pathogen-induced systemic plant signal triggers DNA rearrangements. Nature 2003, 423:760-762.
116. Boyko A., Hudson D., Bhomkar P., Kathiria P., Kovalchuk I. Increase of homologous recombination frequency in vascular tissue of Arabidopsis plants exposed to salt stress. Plant Cell Physiol. 2006, 47:736-742.
117. Yao Y., Kovalchuk I. Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants. Mutat. Res. 2011, 707:61-66.
118. Navarro Llorens J.M., Tormo A., Martinez-Garcia E. Stationary phase in gram-negative bacteria. FEMS Microbiol. Rev. 2010, 34:476-495.
119. Garcia-Russell N., Harmon T.G., Le T.Q., Amaladas N.H., Mathewson R.D., Segall A.M. Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements. Mol. Microbiol. 2004, 52:329-344.
120. Bartels F., Fernandez S., Holtel A., Timmis K.N., de Lorenzo V. The essential HupB and HupN proteins of Pseudomonas putida provide redundant and nonspecific DNA-bending functions. J. Biol. Chem. 2001, 276:16641-16648.
121. Boswell S., Mathew J., Beach M., Osuna R., Colon W. Variable contributions of tyrosine residues to the structural and spectroscopic properties of the factor for inversion stimulation. Biochemistry 2004, 43:2964-2977.
122. Calb R., Davidovitch A., Koby S., Giladi H., Goldenberg D., Margalit H., Holtel A., Timmis K., Sanchez-Romero J.M., de Lorenzo V., Oppenheim A.B. Structure and function of the Pseudomonas putida integration host factor. J. Bacteriol. 1996, 178:6319-6326.
123. Saumaa S., Tover A., Tark M., Tegova R., Kivisaar M. Oxidative DNA damage defense systems in avoidance of stationary-phase mutagenesis in Pseudomonas putida. J. Bacteriol. 2007, 189:5504-5514.
124. Valls M., Silva-Rocha R., Cases I., Munoz A., de Lorenzo V. Functional analysis of the integration host factor site of the sigma(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol. Microbiol. 2011, 82:591-601.
125. Tendeng C., Soutourina O.A., Danchin A., Bertin P.N. MvaT proteins in Pseudomonas spp.: a novel class of H-NS-like proteins. Microbiology 2003, 149:3047-3050.
126. Boccard F., Esnault E., Valens M. Spatial arrangement and macrodomain organization of bacterial chromosomes. Mol. Microbiol. 2005, 57:9-16.
127. Dame R.T., Kalmykowa O.J., Grainger D.C. Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria. PLoS Genet. 2011, 7:e1002123.
128. Viollier P.H., Thanbichler M., McGrath P.T., West L., Meewan M., McAdams H.H., Shapiro L. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:9257-9262.
129. Pogliano J., Ho T.Q., Zhong Z., Helinski D.R. Multicopy plasmids are clustered and localized in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:4486-4491.
130. Ho T.Q., Zhong Z., Aung S., Pogliano J. Compatible bacterial plasmids are targeted to independent cellular locations in Escherichia coli. EMBO J. 2002, 21:1864-1872.
131. Kolatka K., Witosinska M., Pierechod M., Konieczny I. Bacterial partitioning proteins affect the subcellular location of broad-host-range plasmid RK2. Microbiology 2008, 154:2847-2856.