Pleiotropic effects of RecQ in Deinococcus radiodurans

Genomics

Volumn 94, Issue 5, 2009, Pages 333-340

  Chen, Huan ^a,b   Huang, Lifen ^a,c   Hua, Xiaoting ^a   Yin, Longfei ^a   Hu, Yihuai ^a,d,e   Wang, Chao ^a   Chen, Weiwei ^a   Yu, Xiaomin ^f   Xu, Zhenjian ^a   Tian, Bing ^a   Hu, Songnian ^f   Hua, Yuejin ^a  

^a Key Laboratory for Nuclear Agricultural Sciences   (China)

^b Zhejiang Institute of Microbiology   (China)

^c YANGZHOU UNIVERSITY   (China)

^d ZHEJIANG UNIVERSITY   (China)

^e HUAIYIN INSTITUTE OF TECHNOLOGY   (China)

^f Chinese Academy of Sciences   (China)

Author keywords

Deinococcus radiodurans; Manganese iron; Microarray; Reactive oxygen species; RecQ

Indexed keywords

COMPLEMENTARY DNA; HYDROGEN PEROXIDE; IRON; MANGANESE; MUTANT PROTEIN; REACTIVE OXYGEN METABOLITE; RECQ HELICASE;

ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DEINOCOCCUS RADIODURANS; DNA DAMAGE; DNA MICROARRAY; GENE EXPRESSION; GENE FUNCTION; IRON METABOLISM; NONHUMAN; OXIDATIVE STRESS; PLEIOTROPY; PRIORITY JOURNAL; PROTEIN FUNCTION; PULSED FIELD GEL ELECTROPHORESIS; WILD TYPE;

BACTERIAL PROTEINS; DEINOCOCCUS; DNA DAMAGE; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; HEAT-SHOCK RESPONSE; HYDROGEN PEROXIDE; IRON; MANGANESE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATIVE STRESS; REACTIVE OXYGEN SPECIES; RECQ HELICASES;

DEINOCOCCUS RADIODURANS;

EID: 70349835414     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.08.001     Document Type: Article

References (43)

1. Khakhar R.R., Cobb J.A., Bjergbaek L., Hickson I.D., and Gasser S.M. RecQ helicases: multiple roles in genome maintenance. Trends Cell Biol. 13 (2003) 493-501
2. Morozov V., Mushegian A.R., Koonin E.V., and Bork P. A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. Trends Biochem. Sci. 22 (1997) 417-418
3. Opresko P.L., Cheng W.H., and Bohr V.A. Junction of RecQ helicase biochemistry and human disease. J. Biol. Chem. 279 (2004) 18099-18102
4. Muftuoglu M., Kusumoto R., Speina E., Beck G., Cheng W.H., and Bohr V.A. Acetylation regulates WRN catalytic activities and affects base excision DNA repair. PLoS ONE 3 (2008) e1918
5. Mohaghegh P., and Hickson I.D. DNA helicase deficiencies associated with cancer predisposition and premature ageing disorders. Human Mol. Gen. 10 (2001) 741
6. Von Kobbe C., May A., Grandori C., and Bohr V.A. Werner syndrome cells escape hydrogen peroxide-induced cell proliferation arrest. FASEB J. 18 (2004) 1970-1972
7. Bachrati C.Z., and Hickson I.D. RecQ helicases: suppressors of tumorigenesis and premature aging. Biochem. J. 374 (2003) 577-606
8. Cobb J.A., Bjergbaek L., and Gasser S.M. RecQ helicases: at the heart of genetic stability. FEBS Lett. 529 (2002) 43-48
9. Fry R.C., Sambandan T.G., and Rha C. DNA damage and stress transcripts in Saccharomyces cerevisiae mutant sgs1. Mech. Ageing Dev. 124 (2003) 839-846
10. Makarova K.S., Aravind L., Wolf Y.I., Tatusov R.L., Minton K.W., Koonin E.V., and Daly M.J. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65 (2001) 44-79
11. Killoran M.P., and Keck J.L. Three HRDC domains differentially modulate Deinococcus radiodurans RecQ DNA helicase biochemical activity. J. Biol. Chem. 281 (2006) 12849-12857
12. Huang L.F., Hua X.T., Lu H.M., Gao G.J., Tian B., Shen B.H., and Hua Y.J. Functional analysis of helicase and three tandem HRDC domains of RecQ in Deinococcus radiodurans. J. Zhejiang Univ. Sci. B 7 (2006) 373-376
13. Huang L., Hua X., Lu H., Gao G., Tian B., Shen B., and Hua Y. Three tandem HRDC domains have synergistic effect on the RecQ functions in Deinococcus radiodurans. DNA Repair (Amst) 6 (2007) 167-176
14. Huang L.F., Zhang S.W., Hua X.T., Gao G.J., and Hua Y.J. Construction of the recQ double mutants and analysis of adversity in Deinococcus radiodurans. Wei Sheng Wu Xue Bao 46 (2006) 205-209
15. Qiu X., Daly M.J., Vasilenko A., Omelchenko M.V., Gaidamakova E.K., Wu L., Zhou J., Sundin G.W., and Tiedje J.M. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J. Bacteriol. 188 (2006) 1199-1204
16. Chen H., Xu G., Zhao Y., Tian B., Lu H., Yu X., Xu Z., Ying N., Hu S., and Hua Y. A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans. PLoS ONE 3 (2008) e1602
17. Boyd J., Oza M.N., and Murphy J.R. Molecular cloning and DNA sequence analysis of a diphtheria tox iron-dependent regulatory element (dtxR) from Corynebacterium diphtheriae. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 5968-5972
18. Glasfeld A., Guedon E., Helmann J.D., and Brennan R.G. Structure of the manganese-bound manganese transport regulator of Bacillus subtilis. Nat. Struct. Biol. 10 (2003) 652-657
19. Tanaka M., Earl A.M., Howell H.A., Park M.J., Eisen J.A., Peterson S.N., and Battista J.R. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics 168 (2004) 21-33
20. Andrews S.C., Robinson A.K., and Rodriguez-Quinones F. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27 (2003) 215-237
21. White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L., Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M., Vamathevan J.J., Lam P., McDonald L., Utterback T., Zalewski C., Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D., Ketchum K.A., Nelson K.E., Salzberg S., Smith H.O., Venter J.C., and Fraser C.M. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286 (1999) 1571-1577
22. Ratledge C., and Dover L.G. Iron metabolism in pathogenic bacteria. Annu. Rev. Microbiol. 54 (2000) 881-941
23. Liu Y., Zhou J., Omelchenko M.V., Beliaev A.S., Venkateswaran A., Stair J., Wu L., Thompson D.K., Xu D., Rogozin I.B., Gaidamakova E.K., Zhai M., Makarova K.S., Koonin E.V., and Daly M.J. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 4191-4196
24. Chen H., Xu Z.J., Tian B., Chen W.W., Hu S.N., and Hua Y.J. Transcriptional profile in response to ionizing radiation at low dose in Deinococcus radiodurans. Progress in Natural Science 17 (2007) 525-536
25. Ghosal D., Omelchenko M.V., Gaidamakova E.K., Matrosova V.Y., Vasilenko A., Venkateswaran A., Zhai M., Kostandarithes H.M., Brim H., Makarova K.S., Wackett L.P., Fredrickson J.K., and Daly M.J. How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress. FEMS Microbiol. Rev. 29 (2005) 361-375
26. Seaver L.C., and Imlay J.A. Are respiratory enzymes the primary sources of intracellular hydrogen peroxide?. J. Biol. Chem. 279 (2004) 48742-48750
27. Imlay J.A. Cellular defenses against superoxide and hydrogen peroxide. Annu. Rev. Biochem. (2008)
28. Markillie L.M., Varnum S.M., Hradecky P., and Wong K.K. Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants. J. Bacteriol. 181 (1999) 666-669
29. Kim S.G., Bhattacharyya G., Grove A., and Lee Y.H. Crystal structure of Dps-1, a functionally distinct Dps protein from Deinococcus radiodurans. J. Mol. Biol. 361 (2006) 105-114
30. Cuypers M.G., Mitchell E.P., Romao C.V., and McSweeney S.M. The crystal structure of the Dps2 from Deinococcus radiodurans reveals an unusual pore profile with a non-specific metal binding site. J. Mol. Biol. 371 (2007) 787-799
31. Daly M.J., Gaidamakova E.K., Matrosova V.Y., Vasilenko A., Zhai M., Venkateswaran A., Hess M., Omelchenko M.V., Kostandarithes H.M., Makarova K.S., Wackett L.P., Fredrickson J.K., and Ghosal D. Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306 (2004) 1025-1028
32. Gao W., Liu Y., Giometti C.S., Tollaksen S.L., Khare T., Wu L., Klingeman D.M., Fields M.W., and Zhou J. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. BMC Genomics 7 (2006) 76
33. Ma J.F., Ochsner U.A., Klotz M.G., Nanayakkara V.K., Howell M.L., Johnson Z., Posey J.E., Vasil M.L., Monaco J.J., and Hassett D.J. Bacterioferritin A modulates catalase A (KatA) activity and resistance to hydrogen peroxide in Pseudomonas aeruginosa. J. Bacteriol. 181 (1999) 3730-3742
34. Crack J.C., Green J., Le Brun N.E., and Thomson A.J. Detection of sulfide release from the oxygen-sensing [4Fe-4S] cluster of FNR. J. Biol. Chem. 281 (2006) 18909-18913
35. Jakubovics N.S., and Jenkinson H.F. Out of the iron age: new insights into the critical role of manganese homeostasis in bacteria. Microbiology 147 (2001) 1709-1718
36. Daly M.J., Gaidamakova E.K., Matrosova V.Y., Vasilenko A., Zhai M., Leapman R.D., Lai B., Ravel B., Li S.M., Kemner K.M., and Fredrickson J.K. Protein oxidation implicated as the primary determinant of bacterial radioresistance. PLoS Biol. 5 (2007) e92
37. Mattimore V., Udupa K.S., Berne G.A., and Battista J.R. Genetic characterization of forty ionizing radiation-sensitive strains of Deinococcus radiodurans: linkage information from transformation. J. Bacteriol. 177 (1995) 5232-5237
38. Xu D., Li G., Wu L., Zhou J., and Xu Y. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18 (2002) 1432-1437
39. Smyth G.K. Limma: linear models for microarray data. In: Gentlemen R., Carey V., Dudoit S., Irizarry R., and Huber W. (Eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor (2005), Springer, New York 397-420
40. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., and Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30 (2002) e15
41. Smyth G.K., Michaud J., and Scott H.S. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21 (2005) 2067-2075
42. Gong K.Z., Zhang Z.G., Li A.H., Huang Y.F., Bu P., Dong F., and Liu J. ROS-mediated ERK activation in delayed protection from anoxic preconditioning in neonatal rat cardiomyocytes. Chin. Med. J. (Engl.) 117 (2004) 395-400
43. Keyer K., and Imlay J.A. Superoxide accelerates DNA damage by elevating free-iron levels. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 13635-13640