Analysis of the antimicrobial susceptibility of the ionizing radiation-resistant bacterium Deinococcus radiodurans: Implications for bioremediation of radioactive waste

Annals of Microbiology

Volumn 62, Issue 2, 2012, Pages 493-500

  Sghaier, Haïtham ^a   Bouchami, Ons ^b   Desler, Claus ^c   Lazim, Hadeer ^a   Saidi, Mouldi ^a   Rasmussen, Lene Juel ^c   Ben Hassen, Assia ^b  

^a Centre National des Sciences et Technologies Nucleaires Tunis   (Tunisia)

^b CENTRE NATIONAL DE GREFFE DE MOELLE OSSEUSE   (Tunisia)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Antimicrobial susceptibility; Bioremediation; Deinococcus radiodurans; Radioactive waste

Indexed keywords

BACTERIA (MICROORGANISMS); DEINOCOCCUS RADIODURANS;

EID: 84863830910     PISSN: 15904261     EISSN: 18692044     Source Type: Journal    
DOI: 10.1007/s13213-011-0281-y     Document Type: Article

References (59)

1. Agha N, Salih FM, Auda H, Al-Barwari S (1975) The effect of ionizing radiation on the antibiotic sensitivity of Micrococcus radiodurans strains RI and RII5. Int J Appl Radiat Isot 26 (6-7):387-391
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410
3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75
4. Bagwell CE, Bhat S, Hawkins GM, Smith BW, Biswas T, Hoover TR, Saunders E, Han CS, Tsodikov OV, Shimkets LJ (2008) Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. PLoS ONE 3(12):e3878
5. Bai L, Li L, Xu H, Minagawa K, Yu Y, Zhang Y, Zhou X, Floss HG, Mahmud T, Deng Z (2006) Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. Chem Biol 13(4):387-397
6. Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nuclec Acids Res 28(1):45-48 (Pubitemid 30047711)
7. Battista JR (1997) Against all odds: the survival strategies of Deinococcus radiodurans. Annu Rev Microbiol 51:203-224 (Pubitemid 27433048)
8. Bearden DT, Danziger LH (2001) Mechanism of action of and resistance to quinolones. Pharmacotherapy 21(10):224S-232S (Pubitemid 32937872)
9. Blasius M, Buob R, Shevelev IV, Hubscher U (2007) Enzymes involved in DNA ligation and end-healing in the radioresistant bacterium Deinococcus radiodurans. BMC Mol Biol 8:69
10. Bonaventura C, Johnson FM (1997) Healthy environments for healthy people: bioremediation today and tomorrow. Environ Health Perspect 105(1):5-20 (Pubitemid 27168281)
11. Brim H, McFarlan SC, Fredrickson JK, Minton KW, Zhai M, Wackett LP, Daly MJ (2000) Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments. Nat Biotechnol 18(1):85-90 (Pubitemid 30041179)
12. Brim H, Venkateswaran A, Kostandarithes HM, Fredrickson JK, Daly MJ (2003) Engineering Deinococcus geothermalis for bioremediation of high-temperature radioactive waste environments. Appl Environ Microbiol 69(8):4575-4582 (Pubitemid 36992915)
13. Brim H, Osborne JP, Kostandarithes HM, Fredrickson JK, Wackett LP, Daly MJ (2006) Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reduction. Microbiol 152(8):2469-2477 (Pubitemid 44219652)
14. Cavalier-Smith T (2006) Rooting the tree of life by transition analyses. Biol Direct 1:19
15. Challis GL, Hopwood DA (2003) Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Nat Acad Sci USA 100(2):14555-14561 (Pubitemid 37499281)
16. Chen SX, Schopfer P (1999) Hydroxyl-radical production in physiological reactions. A novel function of peroxidase. Eur J Biochem 260 (3):726-735 (Pubitemid 29148638)
17. Choi D, Yu S, Lee M (2008) The effects of inorganic ions on radiolytic decomposition of oxytetracycline. Appl Chem 12 (2):397-400
18. Daly MJ (2000) Engineering radiation-resistant bacteria for environmental biotechnology. Curr Opin Biotechnol 11(3):280-285 (Pubitemid 30326475)
19. Daly MJ (2009) A new perspective on radiation resistance based on Deinococcus radiodurans. Nat Rev 7(3):237-245
20. Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Venkateswaran A, Hess M, Omelchenko MV, Kostandarithes HM, Makarova KS, Wackett LP, Fredrickson JK, Ghosal D (2004) Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306(5698):1025-1028 (Pubitemid 39482904)
21. de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006) ScanProsite: detection of PROSITE signature matches and ProRuleassociated functional and structural residues in proteins. Nuclec Acids Res 34:362-365
22. Desler C, Suravajhala P, Sanderhoff M, Rasmussen M, Rasmussen LJ (2009) In Silico screening for functional candidates amongst hypothetical proteins. BMC Bioinform 10:289
23. Fredrickson JK, Kostandarithes HM, Li SW, Plymale AE, Daly MJ (2000) Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1. Appl Environ Microbiol 66(5):2006-2011 (Pubitemid 30253725)
24. Fredrickson JK, Zachara JM, Balkwill DL, Kennedy D, Li SM, Kostandarithes HM, Daly MJ, Romine MF, Brockman FJ (2004) Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state. Appl Environ Microbiol 70(7):4230-4241 (Pubitemid 38969771)
25. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS (2005) PSORTb v. 2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21(5):617-623 (Pubitemid 40424787)
26. Goo KS, Sim TS (2011) Designing new beta-lactams: implications from their targets, resistance factors and synthesizing enzymes. Curr Comput Aided Drug Des 7(1):53-80
27. Hawiger J, Jeljaszewicz J (1967) Antibiotic sensitivity of Micrococcus radiodurans. Appl Microbiol 15(2):304-306
28. Heinz K, Marx A (2007) Lesion bypass activity of DNA polymerase A from the extremely radioresistant organism Deinococcus radiodurans. J Biol Chem 282(15):10908-10914 (Pubitemid 47100733)
29. Izumi S, Aranishi F (2004) Relationship between gyrA mutations and quinolone resistance in Flavobacterium psychrophilum isolates. Appl Environ Microbiol 70(7):3968-3972 (Pubitemid 38969736)
30. Jacoby GA (2005) Mechanisms of resistance to quinolones. Clin Infect Dis 41(2):S120-S126 (Pubitemid 40962482)
31. Kaplan N, Sasson O, Inbar U, Friedlich M, Fromer M, Fleischer H, Portugaly E, Linial N, Linial M (2005) ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nuclec Acids Res 33:216-218
32. Kim JI, Cox MM (2002) The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proc Natl Acad Sci USA 99 (12):7917-7921 (Pubitemid 34650980)
33. Kim HY, Yu SH, Lee MJ, Kim TH, Kim SD (2009) Radiolysis of selected antibiotics and their toxic effects on various aquatic organisms. Radiat Phys Chem 78:267-272
34. Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ (2007) A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130(5):797-810 (Pubitemid 47332566)
35. Lange CC, Wackett LP, Minton KW, Daly MJ (1998) Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environments. Nat Biotechnol 16(10):929-933 (Pubitemid 28483620)
36. Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34:D257-D260
37. Li XZ, Nikaido H (2009) Efflux-mediated drug resistance in bacteria: an update. Drugs 69(12):1555-1623
38. Liochev SI, Fridovich I (1999) Superoxide and iron: partners in crime. IUBMB Life 48(2):157-161 (Pubitemid 29518805)
39. Lipton MS, Pasa-Tolic L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD (2002) Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci USA 99(17):11049-11054 (Pubitemid 34920877)
40. Liu B, Pop M (2009) ARDB-Antibiotic Resistance Genes Database. Nuclec Acids Res 37:443-447
41. Liu Y, Zhou J, Omelchenko MV, Beliaev AS, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB, Gaidamakova EK, Zhai M, Makarova KS, Koonin EV, Daly MJ (2003) Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci USA 100(7):4191-4196 (Pubitemid 36418179)
42. Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev 1(1):35-44
43. Lovley DR, Coates JD (1997) Bioremediation of metal contamination. Curr Opin Biotechnol 8(3):285-289 (Pubitemid 27277669)
44. Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavrommatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS ONE 2(9):e955
45. Mao F, Dam P, Chou J, Olman V, Xu Y (2009) DOOR: a database for prokaryotic operons. Nuclec Acids Res 37:D459-D463
46. Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D (2003) PRODORIC: prokaryotic database of gene regulation. Nuclec Acids Res 31(1):266-269 (Pubitemid 36150381)
47. Narumi I, Satoh K, Cui S, Funayama T, Kitayama S, Watanabe H (2004) PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol Microbiol 54(1):278-285 (Pubitemid 39315175)
48. Pertsemlidis A, Fondon JW, 3rd (2001) Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol 2 (10):reviews2002.1-reviews2002.10
49. Phillips RW, Wiegel J, Berry CJ, Fliermans C, Peacock AD, White DC, Shimkets LJ (2002) Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium. Int J Syst Evol Microbiol 52(3):933-938 (Pubitemid 34591222)
50. Ruiz J (2003) Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection. J Antimicrob Chemother 51(5):1109-1117 (Pubitemid 36622067)
51. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009) Database resources of the National Center for Biotechnology Information. Nuclec Acids Res 37:D5-D15
52. Sghaier H, Ghedira K, Benkahla A, Barkallah I (2008) Basal DNA repair machinery is subject to positive selection in ionizingradiation-resistant bacteria. BMC Genomics 9:297
53. Starosta AL, Karpenko VV, Shishkina AV, Mikolajka A, Sumbatyan NV, Schluenzen F, Korshunova GA, Bogdanov AA, Wilson DN (2010) Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition. Chem Biol 17(5):504-514
54. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nuclec Acids Res 22 (22):4673-4680 (Pubitemid 24354800)
55. Touati D (2000) Iron and oxidative stress in bacteria. Arch Biochem Biophys 373(1):1-6 (Pubitemid 30046483)
56. Tran JH, Jacoby GA (2002) Mechanism of plasmid-mediated quinolone resistance. Proc Natl Acad Sci USA 99(8):5638-5642 (Pubitemid 34411602)
57. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286 (5444):1571-1577
58. Yeom J, Imlay JA, Park W (2010) Iron homeostasis affects antibioticmediated cell death in Pseudomonas species. J Biol Chem 285 (29):22689-22695
59. Zhang C, Wei J, Zheng Z, Ying N, Sheng D, Hua Y (2005) Proteomic analysis of Deinococcus radiodurans recovering from gamma-irradiation. Proteomics 5(1):138-143 (Pubitemid 40189646)