Interaction of double-stranded DNA with polymerized PprA protein from Deinococcus radiodurans

Protein Science

Volumn 23, Issue 10, 2014, Pages 1349-1358

  Adachi, Motoyasu ^a   Hirayama, Hiroshi ^a   Shimizu, Rumi ^a   Satoh, Katsuya ^a   Narumi, Issay ^a,b   Kuroki, Ryota ^a  

^a JAPAN ATOMIC ENERGY AGENCY   (Japan)

^b TOYO UNIVERSITY   (Japan)

Author keywords

DNA binding; DNA repair; gel shift assay; polymerization; radiation

Indexed keywords

AGAROSE; AMMONIUM SULFATE; BACTERIAL PROTEIN; CALCIUM; DNA FRAGMENT; DOUBLE STRANDED DNA; MAGNESIUM; PLEIOTROPIC PROTEIN PROMOTING DNA REPAIR A; SODIUM DIHYDROGEN PHOSPHATE; STRONTIUM; UNCLASSIFIED DRUG; BACTERIAL DNA; DNA SUPERCOILING; INORGANIC SALT; RECOMBINANT PROTEIN;

ARTICLE; ASSAY; CENTRIFUGATION; DEINOCOCCUS RADIODURANS; DISSOCIATION CONSTANT; ELUTION; ESCHERICHIA COLI; GEL FILTRATION; GEL SHIFT ASSAY; HILL COEFFICIENT; LIGHT SCATTERING; MOLECULAR WEIGHT; MULTIANGLE LASER LIGHT SCATTERING; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN PURIFICATION; RADIATION ABSORPTION; ULTRAVIOLET SPECTROPHOTOMETRY; BINDING SITE; DEINOCOCCUS; DNA REPAIR; DNA SUPERCOILING; GEL MOBILITY SHIFT ASSAY; GENETICS; METABOLISM; RADIATION DOSE; SINGLE STRANDED DNA BREAK;

DEINOCOCCUS RADIODURANS; ESCHERICHIA COLI;

BACTERIAL PROTEINS; BINDING SITES; DEINOCOCCUS; DNA BREAKS, SINGLE-STRANDED; DNA REPAIR; DNA, BACTERIAL; DNA, SUPERHELICAL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI; RADIATION TOLERANCE; RECOMBINANT PROTEINS; SALTS;

EID: 84928886520     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2519     Document Type: Article

References (36)

1. Anderson AW, Nordan HC, Cain RF, Parrish G, Duggan D, (1956) Studies on radioresistant micrococcus. I. Isolation, morphology, cultural characteristics and resistance to gamma radiation. Food Technol 10: 575-582.
2. Battista JR, (1997) Against all odds: the survival strategies of Deinococcus radiodurans. Annu Rev Microbiol 51: 203-224.
3. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ, (2001) Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 65: 44-79.
4. Narumi I, (2003) Unlocking radiation resistance mechanisms: still a long way to go. Trends Microbiol 11: 422-425.
5. Cox MM, Battista JR, (2005) Deinococcus radiodurans-the consummate survivor. Nat Rev Microbiol 3: 882-892.
6. Blasius M, Sommer S, Hübscher U, (2008) Deinococcus radiodurans: what belongs to the survival kit Crit Rev Biochem Mol Biol 43: 221-238.
7. Slade D, Radman M, (2011) Oxidative stress resistance in Deinococcus radiodurans. Microbiol Mol Biol Rev 75: 133-191.
8. Moseley BE, Copland HJ, (1975) Isolation and properties of a recombination-deficient mutant of Micrococcus radiodurans. J Bacteriol 121: 422-428.
9. Dean CJ, Feldschreiber P, Lett JT, (1966) Repair of x-ray damage to the deoxyribonucleic acid in Micrococcus radiodurans. Nature 209: 49-52.
10. Mattimore V, Battista JR, (1996) Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. J Bacteriol 178: 633-637.
11. Moseley BE, Mattingly A, (1971) Repair of irradiated transforming deoxyribonucleic acid in wild type and a radiation-sensitive mutant of Micrococcus radiodurans. J Bacteriol 105: 976-983.
12. Krasin F, Hutchinson F, (1977) Repair of DNA double-strand breaks in Escherichia coli, which requires recA function and the presence of a duplicate genome. J Mol Biol 116: 81-98.
13. 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: 1571-1577.
14. 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: 278-285.
15. Hua Y, Narumi I, Gao G, Tian B, Satoh K, Kitayama S, Shen B, (2003) PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem Biophys Res Commun 306: 354-360.
16. Ohba H, Satoh K, Sghaier H, Yanagisawa T, Narumi I, (2009) Identification of PprM: a modulator of the PprI-dependent DNA damage response in Deinococcus radiodurans. Extremophiles 13: 471-479.
17. Satoh K, Ohba H, Sghaier H, Narumi I, (2006) Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans. Microbiology 152: 3217-3226.
18. Sheng D, Jao J, Li M, Xu P, Zhang J, (2009) RecX is involved in the switch between DNA damage response and normal metabolism in D. radiodurans. J Biochem 146: 337-342.
19. Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavromatis 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: e955.
20. de Groot A, Dulermo R, Ortet P, Blanchard L, Guérin P, Fernandez B, Vacherie B, Dossat C, Jolivet E, Siguier P, Chandler M, Barakat M, Dedieu A, Barbe V, Heulin T, Sommer S, Achouak W, Armengaud J, (2009) Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet 5: e1000434.
21. Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, (2011) Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Stand Genomic Sci 4: 163-172.
22. Yuan M, Chen M, Zhang W, Lu W, Wang J, Yang M, Zhao P, Tang R, Li X, Hao Y, Zhou Z, Zhan Y, Yu H, Teng C, Yan Y, Ping S, Wang Y, Lin M, (2012) Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations. PLoS One 7: e34458.
23. 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: 11049-11054.
24. 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: 4191-4196.
25. Ohba H, Satoh K, Yanagisawa T, Narumi I, (2005) The radiation responsive promoter of the Deinococcus radiodurans pprA gene. Gene 363: 133-141.
26. Zhang C, Wei J, Zheng Z, Ying N, Sheng D, Hua Y, (2005) Proteomic analysis of Deinococcus radiodurans recovering from γ-irradiation. Proteomics 5: 138-143.
27. Basu B, Apte SK, (2011) Gamma radiation-induced proteome of Deinococcus radiodurans primarily targets DNA repair and oxidative stress alleviation. Mol Cell Proteomics 11: M111.011734.
28. Murakami M, Narumi I, Satoh K, Furukawa A, Hayata I, (2006) Analysis of interaction between DNA and Deinococcus radiodurans PprA protein by atomic force microscopy. Biochim Biophys Acta 1764: 20-23.
29. Kota S, Kamble VA, Rajpurohit YS, Misra HS, (2010) ATP-type DNA ligase requires other proteins for its activity in vitro and its operon components for radiation resistance in Deinococcus radiodurans in vivo. Biochem Cell Biol 88: 783-790.
30. Kota S, Misra HS, (2006) PprA: a protein implicated in radioresistance of Deinococcus radiodurans stimulates catalase activity in Escherichia coli. Appl Microbiol Biotechnol 72: 790-796.
31. Devigne A, Mersaoui S, Bouthier-de-la-Tour C, Sommer S, Servant P, (2013) The PprA protein is required for accurate cell division of γ-irradiated Deinococcus radiodurans bacteria. DNA Repair 12: 265-272.
32. Kota S, Charaka VK, Ringgaard S, Waldor MK, Misra HS, (2014) PprA contributes to Deinococcus radiodurans resistance to nalidixic acid, genome maintenance after DNA damage and interacts with deinococcal topoisomerases. PLoS One 9: e85288.
33. Grove A, Wilkinson SP, (2005) Differential DNA binding and protection by dimeric and dodecameric forms of the ferritin homolog Dps from Deinococcus radiodurans. J Mol Biol 347: 495-508.
34. Harpaz Y, Gerstein M, Chothia C, (1994) Volume changes on protein folding. Structure 2: 641-649.
35. Chen Z, Yang H, Pavletich NP, (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature 453: 489-494.
36. Zahradka K, Slade D, Bailone A, Sommer S, Averbeck D, Petranovic M, Lindner AB, Radman M, (2006) Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443: 569-573.