nfxB as a Novel Target for Analysis of Mutation Spectra in Pseudomonas aeruginosa

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Monti, Mariela R ^a   Morero, Natalia R ^a   Miguel, Virginia ^a   Argaraña, Carlos E ^a  

^a UNIVERSIDAD NACIONAL DE CÓRDOBA   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL GENE; BACTERIAL MUTATION; BACTERIAL STRAIN; CONTROLLED STUDY; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; MUTATIONAL ANALYSIS; MUTATOR GENE; MUTM GENE; MUTS GENE; MUTT GENE; MUTY GENE; NFXB GENE; NONHUMAN; OPEN READING FRAME; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS; WILD TYPE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; CIPROFLOXACIN; DNA-BINDING PROTEINS; DRUG RESISTANCE, BACTERIAL; GENES, REPORTER; LUMINESCENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENS; MUTATION; MUTATION RATE; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 84878769207     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066236     Document Type: Article

References (63)

1. Maki H, (2002) Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses. Annu Rev Genet 36: 279-303.
2. Miller JH, (1996) Spontaneous mutators in bacteria: insights into pathways of mutagenesis and repair. Annu Rev Microbiol 50: 625-643.
3. Peix A, Ramirez-Bahena MH, Velazquez E, (2009) Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 9: 1132-1147.
4. Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW, (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 35: 652-680.
5. Driscoll JA, Brody SL, Kollef MH, (2007) The epidemiology, pathogenesis and treatment of Pseudomonas aeruginosa infections. Drugs 67: 351-368.
6. Coggan KA, Wolfgang MC, (2012) Global regulatory pathways and cross-talk control Pseudomonas aeruginosa environmental lifestyle and virulence phenotype. Curr Issues Mol Biol 14: 47-70.
7. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci U S A 103: 8487-8492.
8. Ciofu O, Riis B, Pressler T, Poulsen HE, Hoiby N, (2005) Occurrence of hypermutable Pseudomonas aeruginosa in cystic fibrosis patients is associated with the oxidative stress caused by chronic lung inflammation. Antimicrob Agents Chemother 49: 2276-2282.
9. Oliver A, (2010) Mutators in cystic fibrosis chronic lung infection: Prevalence, mechanisms, and consequences for antimicrobial therapy. Int J Med Microbiol 300: 563-72.
10. Oliver A, Baquero F, Blazquez J, (2002) The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants. Mol Microbiol 43: 1641-1650.
11. Ciofu O, Mandsberg LF, Bjarnsholt T, Wassermann T, Hoiby N, (2010) Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants. Microbiology 156: 1108-1119.
12. Kasak L, Horak R, Kivisaar M, (1997) 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: 3134-3139.
13. Tegova R, Tover A, Tarassova K, Tark M, Kivisaar M, (2004) Involvement of error-prone DNA polymerase IV in stationary-phase mutagenesis in Pseudomonas putida. J Bacteriol 186: 2735-2744.
14. Conibear TC, Collins SL, Webb JS, (2009) Role of mutation in Pseudomonas aeruginosa biofilm development. PLoS One 4: e6289.
15. Jatsenko T, Tover A, Tegova R, Kivisaar M, (2010) Molecular characterization of Rif(r) mutations in Pseudomonas aeruginosa and Pseudomonas putida. Mutat Res 683: 106-114.
16. Juurik T, Ilves H, Teras R, Ilmjarv T, Tavita K, et al. (2012) Mutation frequency and spectrum of mutations vary at different chromosomal positions of Pseudomonas putida. PLoS One 7: e48511.
17. Shiba T, Ishiguro K, Takemoto N, Koibuchi H, Sugimoto K, (1995) Purification and characterization of the Pseudomonas aeruginosa NfxB protein, the negative regulator of the nfxB gene. J Bacteriol 177: 5872-5877.
18. Poole K, Gotoh N, Tsujimoto H, Zhao Q, Wada A, et al. (1996) Overexpression of the mexC-mexD-oprJ efflux operon in nfxB-type multidrug-resistant strains of Pseudomonas aeruginosa. Mol Microbiol 21: 713-724.
19. Okazaki T, Iyobe S, Hashimoto H, Hirai K, (1991) Cloning and characterization of a DNA fragment that complements the nfxB mutation in Pseudomonas aeruginosa PAO. FEMS Microbiol Lett 63: 31-35.
20. Sali A, Blundell TL, (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
21. Bellinzoni M, Buroni S, Schaeffer F, Riccardi G, De Rossi E, et al. (2009) Structural plasticity and distinct drug-binding modes of LfrR, a mycobacterial efflux pump regulator. J Bacteriol 191: 7531-7537.
22. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ, (1998) JPred: a consensus secondary structure prediction server. Bioinformatics 14: 892-893.
23. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.
24. O'Neil KT, DeGrado WF, (1990) A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250: 646-651.
25. Morgan C, Lewis PD, (2006) iMARS-mutation analysis reporting software: an analysis of spontaneous cII mutation spectra. Mutat Res 603: 15-26.
26. Wong A, Kassen R, (2011) Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. Microbiology 157: 937-944.
27. Morero NR, Monti MR, Argarana CE, (2011) Effect of ciprofloxacin concentration on the frequency and nature of resistant mutants selected from Pseudomonas aeruginosa mutS and mutT hypermutators. Antimicrob Agents Chemother 55: 3668-3676.
28. Choi KH, Schweizer HP, (2006) mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc 1: 153-161.
29. Blázquez J, Couce A, Rodríguez-Beltrán J, Rodríguez-Rojas A, (2012) Antimicrobials as promoters of genetic variation. Curr Opin Microbiol. 15: 561-569.
30. Kivisaar M, (2010) Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads. FEMS Microbiol Lett 312: 1-14.
31. Foster PL, Trimarchi JM, (1995) Adaptive reversion of an episomal frameshift mutation in Escherichia coli requires conjugal functions but not actual conjugation. Proc Natl Acad Sci U S A 92: 5487-5490.
32. Rodriguez C, Tompkin J, Hazel J, Foster PL, (2002) Induction of a DNA nickase in the presence of its target site stimulates adaptive mutation in Escherichia coli. J Bacteriol 184: 5599-5608.
33. Campo Esquisabel AB, Rodriguez MC, Campo-Sosa AO, Rodriguez C, Martinez-Martinez L, (2011) Mechanisms of resistance in clinical isolates of Pseudomonas aeruginosa less susceptible to cefepime than to ceftazidime. Clin Microbiol Infect 17: 1817-1822.
34. Kiser TH, Obritsch MD, Jung R, MacLaren R, Fish DN, (2010) Efflux pump contribution to multidrug resistance in clinical isolates of Pseudomonas aeruginosa. Pharmacotherapy 30: 632-638.
35. Jalal S, Wretlind B, (1998) Mechanisms of quinolone resistance in clinical strains of Pseudomonas aeruginosa. Microb Drug Resist 4: 257-261.
36. Okazaki T, Hirai K, (1992) Cloning and nucleotide sequence of the Pseudomonas aeruginosa nfxB gene, conferring resistance to new quinolones. FEMS Microbiol Lett 76: 197-202.
37. Chuanchuen R, Beinlich K, Hoang TT, Becher A, Karkhoff-Schweizer RR, et al. (2001) Cross-resistance between triclosan and antibiotics in Pseudomonas aeruginosa is mediated by multidrug efflux pumps: exposure of a susceptible mutant strain to triclosan selects nfxB mutants overexpressing MexCD-OprJ. Antimicrob Agents Chemother 45: 428-432.
38. Jalal S, Ciofu O, Hoiby N, Gotoh N, Wretlind B, (2000) Molecular mechanisms of fluoroquinolone resistance in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Antimicrob Agents Chemother 44: 710-712.
39. Poole K, Gotoh N, Tsujimoto H, Zhao Q, Wada A, et al. (1996) Overexpression of the mexC-mexD-oprJ efflux operon in nfxB-type multidrug-resistant strains of Pseudomonas aeruginosa. Mol Microbiol 21: 713-724.
40. Garibyan L, Huang T, Kim M, Wolff E, Nguyen A, et al. (2003) Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome. DNA Repair (Amst) 2: 593-608.
41. Schaaper RM, Dunn RL, (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc Natl Acad Sci U S A 84: 6220-6224.
42. Maki H, Sekiguchi M, (1992) MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature 355: 273-275.
43. Oliver A, Sanchez JM, Blazquez J, (2002) Characterization of the GO system of Pseudomonas aeruginosa. FEMS Microbiol Lett 217: 31-35.
44. Michaels ML, Miller JH, (1992) The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol 174: 6321-6325.
45. Sanders LH, Sudhakaran J, Sutton MD, (2009) The GO system prevents ROS-induced mutagenesis and killing in Pseudomonas aeruginosa. FEMS Microbiol Lett 294: 89-96.
46. Ono T, Negishi K, Hayatsu H, (1995) Spectra of superoxide-induced mutations in the lacI gene of a wild-type and a mutM strain of Escherichia coli K-12. Mutat Res 326: 175-183.
47. Pitsikas P, Patapas JM, Cupples CG, (2004) Mechanism of 2-aminopurine-stimulated mutagenesis in Escherichia coli. Mutat Res 550: 25-32.
48. Yarema KJ, Lippard SJ, Essigmann JM, (1995) Mutagenic and genotoxic effects of DNA adducts formed by the anticancer drug cis-diamminedichloroplatinum(II). Nucleic Acids Res 23: 4066-4072.
49. Burnouf D, Duane M, Fuchs RP, (1987) Spectrum of cisplatin-induced mutations in Escherichia coli. Proc Natl Acad Sci U S A 84: 3758-3762.
50. Jackson AL, Loeb LA, (2000) Microsatellite instability induced by hydrogen peroxide in Escherichia coli. Mutat Res 447: 187-198.
51. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W, (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775-780.
52. Brouwer J, van de Putte P, Fichtinger-Schepman AM, Reedijk J, (1981) Base-pair substitution hotspots in GAG and GCG nucleotide sequences in Escherichia coli K-12 induced by cis-diamminedichloroplatinum (II). Proc Natl Acad Sci U S A 78: 7010-7014.
53. Jacobs MA, Alwood A, Thaipisuttikul I, Spencer D, Haugen E, et al. (2003) Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 100: 14339-14344.
54. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
55. Luria SE, Delbruck M, (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28: 491-511.
56. Sarkar S, Ma WT, Sandri GH, (1992) On fluctuation analysis: a new, simple and efficient method for computing the expected number of mutants. Genetica 85: 173-179.
57. Zheng Q, (2002) Statistical and algorithmic methods for fluctuation analysis with SALVADOR as an implementation. Math Biosci 176: 237-252.
58. Lobley A, Sadowski MI, Jones DT, (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 25: 1761-1767.
59. Benkert P, Tosatto SC, Schomburg D, (2008) QMEAN: A comprehensive scoring function for model quality assessment. Proteins 71: 261-277.
60. Heinig M, Frishman D, (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32: W500-502.
61. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
62. Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, et al. (2011) A series of PDB related databases for everyday needs. Nucleic Acids Res 39: D411-419.
63. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:: 33-38, 27-38.