The single-stranded DNA-binding protein of Deinococcus radiodurans

BMC Microbiology

Volumn 4, Issue , 2004, Pages 1-12

  Eggington, Julie Malia ^a   Haruta, Nami ^a   Wood, Elizabeth Anne ^a   Cox, Michael Matthew ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT; CIRCULAR DNA; DIMER; DNA FRAGMENT; DOUBLE STRANDED DNA; GUANINE NUCLEOTIDE; MONOMER; OLIGOMER; OLIGONUCLEOTIDE; OLIGOSACCHARIDE; RECA PROTEIN; SINGLE STRANDED DNA BINDING PROTEIN; TETRAMER; DNA BINDING PROTEIN;

ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DEINOCOCCUS RADIODURANS; DIMERIZATION; ESCHERICHIA COLI K 12; GENE SEQUENCE; NONHUMAN; OPEN READING FRAME; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INDUCTION; PROTEIN PURIFICATION; RIBOSOMAL FRAMESHIFTING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; THERMUS AQUATICUS; THERMUS THERMOPHILUS; DEINOCOCCUS; DNA REPAIR; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); DEINOCOCCUS; DEINOCOCCUS RADIODURANS; ESCHERICHIA COLI; ESCHERICHIA COLI K12; THERMUS; THERMUS AQUATICUS; THERMUS THERMOPHILUS;

DEINOCOCCUS; DIMERIZATION; DNA REPAIR; DNA-BINDING PROTEINS; REC A RECOMBINASES;

EID: 2942642109     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-4-2     Document Type: Article

References (32)

1. Battista JR: Against all odds - the survival strategies of deinococcus radiodurans. Annu Rev Microbiol 1997, 51:203-224.
2. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ: Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 2001, 65:44-79.
3. Lohman TM, Ferrari ME: Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu Rev Biochemistry 1994, 63:527-570.
4. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin HY, Jiang LX, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fraser CM et al.: Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 1999, 286:1571-1577.
5. 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: Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A 2002, 99:11049-11054.
6. 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: Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A 2003, 100:4191-4196.
7. Dabrowski S, Olszewski M, Piatek R, Brillowska-Dabrowska A, Konopa G, Kur J: Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains. Microbiology 2002, 148:3307-3315.
8. Ma J, Campbell A, Karlin S: Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 2002, 184:5733-5745.
9. Meima R, Lidstrom ME: Characterization of the minimal replicon of a cryptic Deinococcus radiodurans SARK plasmid and development of versatile Escherichia coli-D.radiodurans shuttle vectors. Appl Environ Microbiol 2000, 66:3856-3867.
10. Meima R, Rothfuss HM, Gewin L, Lidstrom ME: Promoter cloning in the radioresistant bacterium Deinococcus radiodurans. J Bacteriol 2001, 183:3169-3175.
11. Murzin AG:OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 1993, 12:861-867.
12. Chedin F, Seitz EM, Kowalczykowski SC: Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins. Trends Biochem Sci 1998, 23:273-277.
13. Weiner JH, Bertsch LL, Kornberg A: The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication. J Biol Chem 1975, 250:1972-1980.
14. Raghunathan S, Kozlov AG, Lohman TM, Waksman G: Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat Struct Biol 2000, 7:648-652.
15. Curth U, Genschel J, Urbanke C, Greipel J: In vitro and in vivo function of the C-terminus of Escherichia coli single-stranded DNA binding protein. Nucleic Acids Res 1996, 24:2706-2711.
16. Matsumoto T, Morimoto Y, Shibata N, Kinebuchi T, Shimamoto N, Tsukihara T, Yasuoka N: Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by x-ray structure analysis. J Biochem 2000, 127:329-335.
17. Kowalczykowski SC, Krupp RA: Effects of Escherichia coli SSB protein on the single-stranded DNA-dependent ATPase activity ofEscherichia coli RecA protein. Evidence that SSB protein facilitates the binding of RecA protein to regions of secondary structure within single-stranded DNA. J Mol Biol 1987, 193:97-113.
18. Lavery PE, Kowalczykowski SC: A postsynaptic role for single-stranded DNA-binding protein in recA protein-promoted DNA strand exchange. J Biol Chem 1992, 267:9315-9320.
19. Ganesh N, Muniyappa K: Characterization of DNA strand transfer promoted by Mycobacterium smegmatis RecA reveals functional diversity with Mycobacterium tuberculosis RecA. Biochemistry 2003, 42:7216-7225.
20. Alani E, Thresher R, Griffith JD, Kolodner RD: Characterization of DNA-binding and strand-exchange stimulation properties of y-RPA, a yeast single-strand-DNA-binding protein. J Mol Biol 1992, 227:54-71.
21. Namsaraev EA, Berg P: Rad51 uses one mechanism to drive DNA strand exchange in both directions. J Biol Chem 2000, 275:3970-3976.
22. 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.
23. Lohman TM, Chao K, Green JM, Sage S, Runyon GT: Large-scale purification and characterization of the Escherichia coli rep gene product. J Biol Chem 1989, 264:10139-10147.
24. Marrione PE, Cox MM: RuvB protein-mediated ATP hydrolysis: functional asymmetry in the RuvB hexamer. Biochemistry 1995, 34:9809-9818.
25. 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.
26. Lusetti SL, Wood EA, Fleming CD, Modica MJ, Korth J, Abbott L, Dwyer DW, Roca AI, Inman RB, Cox MM: C-terminal deletions of the Escherichia coli RecA protein - Characterization of in vivo and in vitro effects. J Biol Chem 2003, 278:16372-16380.
27. Craig NL, Roberts JW: Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor. J Biol Chem 1981, 256:8039-8044.
28. Lohman TM, Overman LB: Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J Biol Chem 1985, 260:3594-3603.
29. Messing J: New M13 vectors for cloning. Methods Enzymol 1983, 101:20-78.
30. Neuendorf SK, Cox MM: Exchange of RecA protein between adjacent RecA protein-single-stranded DNA complexes. J Biol Chem 1986, 261:8276-8282.
31. Haruta N, Yu X, Yang S, Egelman EH, Cox MM: A DNA pairing-enhanced conformation of bacterial RecA proteins. J Biol Chem 2003, 278:52710-52723. (JBC papers in press - M308563200)
32. Raghunathan S, Ricard CS, Lohman TM, Waksman G: Crystal structure of the homotetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Proc Natl Acad Sci U S A 1997, 94:6652-6657.