RecA Proteins from Deinococcus geothermalis and Deinococcus murrayi - Cloning, Purification and Biochemical Characterisation

BMC Molecular Biology

Volumn 12, Issue , 2011, Pages

  Wanarska, Marta ^a   Krawczyk, Beata ^a   Hildebrandt, Piotr ^a   Kur, Józef ^a  

^a GDANSK UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; MAGNESIUM ION; OLIGOMER; RECA PROTEIN; BACTERIAL PROTEIN; SINGLE STRANDED DNA;

ARTICLE; DEINOCOCCUS; DEINOCOCCUS GEOTHERMALIS; DEINOCOCCUS MURRAYI; DEINOCOCCUS RADIODURANS; DNA BINDING; DNA REPAIR; ESCHERICHIA COLI; GAMMA RADIATION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN HYDROLYSIS; PROTEIN ISOLATION; PROTEIN PURIFICATION; RADIOSENSITIVITY; THERMOPHILIC BACTERIUM; THERMOSTABILITY; AMINO ACID SEQUENCE; BACTERIAL GENE; GENE EXPRESSION; GENETICS; HEAT; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN STABILITY; SEQUENCE ALIGNMENT;

DEINOCOCCUS GEOTHERMALIS; DEINOCOCCUS MURRAYI; DEINOCOCCUS RADIODURANS; DEINOCOCCUS SP.; ESCHERICHIA COLI;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CLONING, MOLECULAR; DEINOCOCCUS; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STABILITY; REC A RECOMBINASES; SEQUENCE ALIGNMENT;

EID: 79955042508     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-12-17     Document Type: Article

References (54)

1. Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MS. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 1997, 47:939-947. 10.1099/00207713-47-4-939, 9336890.
2. Väisänen OM, Weber A, Bennasar A, Rainey FA, Busse HJ, Salkinoja-Salonen MS. Microbial communities of printing paper machines. J Appl Microbiol 1998, 84:1069-1084. 10.1046/j.1365-2672.1998.00447.x, 9717292.
3. Kolari M, Nuutinen J, Salkinoja-Salonen MS. Mechanisms of biofilm formation in paper machine by Bacillus species: the role of Deinococcus geothermalis. J Ind Microbiol Biotechnol 2001, 27:343-351. 10.1038/sj.jim.7000201, 11773998.
4. Peltola M, Kanto Öqvist C, Ekman J, Kosonen M, Jokela S, Kolari M, Korhonen P, Salkinoja-Salonen M. Quantitative contributions of bacteria and of Deinococcus geothermalis to deposits and slimes in paper industry. J Ind Microbiol Biotechnol 2008, 35:1651-1657. 10.1007/s10295-008-0409-7, 18726625.
5. Zahradka K, Slade D, Bailone A, Sommer S, Averbeck D, Petranovic M, Lindner AB, Radman M. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 2006, 443:569-573.
6. Slade D, Lindner AB, Paul G, Radman M. Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans. Cell 2009, 136:1044-1055. 10.1016/j.cell.2009.01.018, 19303848.
7. Repar J, Cvjetan S, Slade D, Radman M, Zahradka D, Zahradka K. RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans. DNA Repair 2010, 9:1151-1161. 10.1016/j.dnarep.2010.08.003, 20817622.
8. Shigenobu S, Watanabe H, Masahira Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 2000, 407:81-86. 10.1038/35024074, 10993077.
9. Gil R, Silva FJ, Zientz E, Delmotte F, González-Candelas F, Latorre A, Rausell C, Kamerbeek J, Gadau J, Hölldobler B, van Ham RCHJ, Gross R, Moya A. The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci USA 2003, 100:9388-9393. 10.1073/pnas.1533499100, 170928, 12886019.
10. Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 2002, 32:402-407. 10.1038/ng986, 12219091.
11. Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Shinro Nishi S, Maiko Harada M, Kazuyo Matsuyama K, Takishita K, Kawato M, Uematsu K, Fujiwara Y, Sato T, Kato C, Kitagawa M, Kato I, Maruyama T. Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr Biol 2007, 17:881-886. 10.1016/j.cub.2007.04.039, 17493812.
12. Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 2007, 315:998-1000. 10.1126/science.1138438, 17303757.
13. Kuwahara H, Takaki Y, Yoshida T, Shimamura S, Takishita K, Reimer JD, Kato C, Maruyama T. Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. Extremophiles 2008, 12:365-374. 10.1007/s00792-008-0141-2, 18305898.
14. Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC. RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. Genes Dev 1998, 12:1248-1253. 10.1101/gad.12.9.1248, 316774, 9573041.
15. Ogawa T, Yu X, Shinohara A, Egelman EH. Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 1993, 259:1896-1899. 10.1126/science.8456314, 8456314.
16. Benson FE, Stasiak A, West SC. Purification and characterization of the human Rad51 protein, an analogue of E. coli RecA. Embo J 1994, 13:5764-5771. 395542, 7988572.
17. Fujisawa H, Yonesaki T, Minagawa T. Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli. Nucleic Acids Res 1985, 13:7473-7481. 10.1093/nar/13.20.7473, 322056, 2932679.
18. Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 1994, 58:401-465. 372975, 7968921.
19. Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage λ. Microbiol Mol Biol Rev 1999, 63:751-813. 98976, 10585965.
20. Lusetti SL, Cox MM. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu Rev Biochem 2002, 71:71-100. 10.1146/annurev.biochem.71.083101.133940, 12045091.
21. Little JW. Mechanism of specific LexA cleavage - autodigestion and the role of RecA coprotease. Biochimie 1991, 73:411-421. 10.1016/0300-9084(91)90108-D, 1911941.
22. Shinagawa H. SOS response as an adaptative response to DNA damage in prokaryotes. EXS 1996, 77:221-235.
23. Burckhardt SE, Woodgate R, Scheuremann RH, Echols H. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci USA 1988, 85:1811-1815. 10.1073/pnas.85.6.1811, 279869, 3279417.
24. Nohmi T, Battista JR, Dodson LA, Walker GC. RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci USA 1988, 85:1816-1820. 10.1073/pnas.85.6.1816, 279870, 3279418.
25. Shinagawa H, Iwasaki T, Kato T, Nakata A. RecA-protein dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci USA 1988, 85:1806-1810. 10.1073/pnas.85.6.1806, 279868, 3126496.
26. Bruck I, Woodgate R, McEntee K, Goodman MF. Purification of a soluble UmuD'C complex from Escherichia coli: cooperative binding of UmuD'C to single-stranded DNA. J Biol Chem 1996, 271:10767-10774. 10.1074/jbc.271.18.10767, 8631887.
27. Tang M, Shen X, Frank EG, O'Donnell M, Woodgate R, Goodman MF. UmuD'2C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci USA 1999, 96:8919-8924. 10.1073/pnas.96.16.8919, 17708, 10430871.
28. Jiang Q, Karata K, Woodgate R, Cox MM, Goodman MF. The active form of DNA polymerase V is UmuD'2C-RecA-ATP. Nature 2009, 460:359-363. 10.1038/nature08178, 2731490, 19606142.
29. Egelman EH, Stasiak A, . Structure of helical RecA-DNA complexes Complexes formed in the presence of ATP-gamma-S or ATP. J Mol Biol 1986, 191:677-697. 10.1016/0022-2836(86)90453-5, 2949085, Structure of helical RecA-DNA complexes.
30. Di Capua E, Schnarr M, Ruigrok RWH, Lindner P, Timmins PA. Complexes of RecA protein in solution. A study by small angle neutron scattering. J Mol Biol 1990, 214:557-570. 10.1016/0022-2836(90)90198-U, 2380987.
31. Nordén B, Elvingson C, Kubista M, Sjöberg B, Ryberg H, Ryberg M, Mortensen K, Takahashi M. Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J Mol Biol 1992, 226:1175-1191. 10.1016/0022-2836(92)91060-3, 1518050.
32. Yu X, Egelman EH. Structural data suggest that the active and inactive forms of the RecA filament are not simply interconvertible. J Mol Biol 1992, 227:334-346. 10.1016/0022-2836(92)90702-L, 1522597.
33. Weinstock GM, McEntee K, Lehman IR. Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Characterization of ATP hydrolysis. J Biol Chem 1981, 256:8829-8834.
34. Arenson TA, Tsodikov OV, Cox MM. Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA. J Mol Biol 1999, 288:391-401. 10.1006/jmbi.1999.2705, 10329149.
35. Honigberg SM, Gonda DK, Flory J, Radding CM. The pairing activity of stable nucleoprotein filaments made from recA protein, single-stranded DNA, and adenosine 5'-(gamma-thio)triphosphate. J Biol Chem 1985, 260:11845-11851.
36. Menetski JP, Bear DG, Kowalczykowski SC. Stable DNA heteroduplex formation catalyzed by the Escherichia coli RecA protein in the absence of ATP hydrolysis. Proc Natl Acad Sci USA 1990, 87:21-25. 10.1073/pnas.87.1.21, 53191, 2404275.
37. Cox MM, Lehman IR. RecA protein-promoted DNA strand exchange. Stable complexes of recA protein and single-stranded DNA formed in the presence of ATP and single-stranded DNA binding protein. J Biol Chem 1982, 257:8523-8532.
38. Chow SA, Chiu SK, Wong BC. RecA protein-promoted homologous pairing and strand exchange between intact and partially single-stranded duplex DNA. J Mol Biol 1992, 223:79-93. 10.1016/0022-2836(92)90717-X, 1530979.
39. Jain SK, Cox MM, Inman RB. On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. III. Unidirectional branch migration and extensive hybrid DNA formation. J Biol Chem 1994, 269:20653-20661.
40. Kim JI, Cox MM, Inman RB. On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. I. Bypassing a short heterologous insert in one DNA substrate. J Biol Chem 1992, 267:16438-16443.
41. Shan Q, Cox MM, Inman RB. DNA strand exchange promoted by RecA K72R. Two reaction phases with different Mg2+ requirements. J Biol Chem 1996, 271:5712-5724. 10.1074/jbc.271.10.5712, 8621437.
42. Kim JI, Cox MM, Inman RB. On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. II. Four-strand exchanges. J Biol Chem 1992, 67:16444-16449.
43. Kim JI, Cox MM. The RecA protein of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proc Natl Acad Sci USA 2002, 99:7917-7921. 10.1073/pnas.122218499, 122995, 12048253.
44. Filipkowski P, Duraj-Thatte A, Kur J. Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis. Arch Microbiol 2006, 186:129-137. 10.1007/s00203-006-0128-2, 16802171.
45. Brenner SL, Zlotnick A, Griffith JD. RecA protein self-assembly. Multiple discrete aggregation states. J Mol Biol 1988, 204:959-972. 10.1016/0022-2836(88)90055-1, 3065521.
46. Brenner SL, Zlotnick A, Stafford WF. RecA protein self-assembly. II. Analytical equilibrium ultracentrifugation studies of the entropy-driven self-association of RecA. J Mol Biol 1990, 216:949-964. 10.1016/S0022-2836(99)80013-8, 2266565.
47. Yu X, Angov E, Camerini-Otero RD, Egelman EH. Structural polymorphism of the RecA protein from the thermophilic bacterium Thermus aquaticus. Biophys J 1995, 69:2728-2738. 10.1016/S0006-3495(95)80144-X, 1236510, 8599679.
48. Masui R, Mikawa T, Kato R, Kuramitsu S. Characterization of the oligomeric states of RecA protein: monomeric RecA protein can form a nucleoprotein filament. Biochemistry 1998, 37:14788-14797. 10.1021/bi981296c, 9778353.
49. Kim JI, Sharma AK, Abbott SN, Wood EA, Dwyer DW, Jambura A, Minton KW, Inman RB, Daly MJ, Cox MM. RecA protein from the extremely radioresistant bacterium Deinococcus radiodurans: expression, purification, and characterization. J Bacteriol 2002, 184:1649-1660. 10.1128/JB.184.6.1649-1660.2002, 134872, 11872716.
50. Kim JI. Analysis of double stranded DNA-dependent activities of Deinococcus radiodurans RecA protein. J Microbiol 2006, 44:508-514.
51. Kato R, Kuramitsu S. Characterization of thermostable RecA protein and analysis of its interaction with single-stranded DNA. Eur J Biochem 1999, 259:592-601.
52. Sghaier H, Satoh K, Ohba H, Narumi I. Assessing the role of RecA protein in the radioresistant bacterium Deinococcus geothermalis. Afr J Bichem Res 2010, 4:111-118.
53. Bentchikou E, Servant P, Coste G, Sommer S. A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genetics 2010, 6:e1000774. 10.1371/journal.pgen.1000774, 2806897, 20090937.
54. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976, 72:248-254. 10.1016/0003-2697(76)90527-3, 942051.