The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins

Nucleic Acids Research

Volumn 36, Issue 1, 2008, Pages 94-109

  Inoue, Jin ^a,b   Honda, Masayoshi ^a,b   Ikawa, Shukuko ^a   Shibata, Takehiko ^a,b,c   Mikawa, Tsutomu ^a,b,c  

^a Japan Science and Technology Agency   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

^c RIKEN Spring 8 Center ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; BACTERIAL DNA; RECF PROTEIN; RECO PROTEIN; RECR PROTEIN; SINGLE STRANDED DNA; SINGLE STRANDED DNA BINDING PROTEIN;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DNA PROTEIN COMPLEX; ELECTRON MICROSCOPY; ENZYME INHIBITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; THERMUS THERMOPHILUS;

ADENOSINE TRIPHOSPHATASES; BACTERIAL PROTEINS; BINDING, COMPETITIVE; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; REC A RECOMBINASES; THERMUS THERMOPHILUS;

THERMUS THERMOPHILUS;

EID: 38349102456     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1004     Document Type: Article

References (42)

1. Kuzminov,A. (1999) Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev., 63, 751-813.
2. Krogh,B.O. and Symington,L.S. (2004) Recombination proteins in yeast. Annu Rev. Genet., 38, 233-271.
3. Yang,H., Li,Q., Fan,J., Holloman,W.K. and Pavletich,N.P. (2005) The BRCA2 homologue Brh2 nucleates RAD51 filament formation at a dsDNA-ssDNA junction. Nature, 433, 653-657.
4. Song,B. and Sung,P. (2000) Functional interactions among yeast Rad51 recombinase, Rad52 mediator, and replication protein A in DNA strand exchange. J. Biol. Chem., 275, 15895-15904.
5. Sugiyama,T. and Kowalczykowski,S.C. (2002) Rad52 protein associates with replication protein A (RPA)-single-stranded DNA to accelerate Rad51-mediated displacement of RPA and presynaptic complex folmation. J. Biol. Chem., 277, 31663-31672.
6. Kantake,N., Madiraju,M.V., Sugiyama,T. and Kowalczykowski,S.C. (2002) Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: A common step in genetic recombination. Proc. Natl Acad. Sci. USA, 99, 15327-15332.
7. Sugiyama,T., Kantake,N., Wu,Y. and Kowalczykowski,S.C. (2006) Rad52-mediated DNA annealing after Rad51-mediated DNA strand exchange promotes second ssDNA capture. Embo. J., 25, 5539-5548.
8. Mazloum,N., Zhou,Q. and Holloman,W.K. (2007) DNA binding, annealing, and strand exchange activities of Brh2 protein from Ustilago maydis. Biochemistry, 46, 7163-7173.
9. Petalcorin,M.I., Sandall,J., Wigley,D.B. and Boulton,S.J. (2006) CeBRC-2 stimulates D-loop formation by RAD-51 and promotes DNA single-strand annealing. J. Mol. Biol., 361, 231-242.
10. Kowalczykowski,S.C. (2000) Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci., 25 156-165.
11. Tseng,Y.C., Hung,J.L. and Wang,T.C. (1994) Involvement of RecF pathway recombination genes in postreplication repair in UV-irradiated Escherichia coli cells. Mutat. Res., 315, 1-9.
12. Rocha,E.P., Cornet,E. and Michel,B. (2005) Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet., 1, e15.
13. Morimatsu,K. and Kowalczykowski,S.C. (2003) RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: A universal step of recombinational repair. Mol. Cell, 11, 1337-1347.
14. Bork,J.M., Cox,M.M. and Inman,R.B. (2001) The RecOR proteins modulate RecA protein function at 5′ ends of single-stranded DNA. Embo. J. 20, 7313-7322.
15. Webb,B.L., Cox,M.M. and Inman,R.B. (1997) Recombinational DNA repair: the RecF and ReeR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell, 91, 347-356.
16. Shan,Q., Bork,J.M., Webb,B.L., Inman,R.B. and Cox,M.M. (1997) RecA protein filaments: End-dependent dissociation from ssDNA and stabilization, byRecO and RecR proteins. J. Mol. Biol., 265, 519-540.
17. Honda,M., Inoue,J., Yoshimasu,M., Ito,Y., Shibata,T. and Mikawa,T. (2006) Identification of the RecR Toprim domain as the binding site for both RecF and RecO. A role of RecR in RecFOR assembly at double-stranded DNA-single-stranded DNA junctions. J. Biol. Chem., 281, 18549-18559.
18. Umezu,K., Chi,N.W. and Kolodner,R.D. (1993) Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single-stranded DNA binding protein. Proc. Natl Acad. Sci. USA, 90, 3875-3879.
19. Umezu,K. and Kolodner,R.D. (1994) Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J. Biol. Chem., 269, 30005-30013.
20. Hegde,S.P., Qin,M.H., Li,X.H., Atkinson,M.A., Clark,A.J., Rajagopalan,M. and Madiraju,M.V. (1996) Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF-RecO-RecR complex in DNA repair and recombination. Proc. Natl Acad. Sci. USA, 93, 14468-14473.
21. Inoue,J., Shigemori,Y. and Mikawa,T. (2006) Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein. Nucleic Acids Res., 34, e69.
22. Honda,M., Rajesh,S., Nietlispach,D., Mikawa,T., Shibata,T. and Ito,Y. (2004) Backbone 1H, 13C, and 15N assignments of a 42 kDa RecR homodimer. J. Biomol. NMR, 28, 199-200.
23. Shigemori,Y., Mikawa,T., Shibata,T. and Oishi,M. (2005) Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products. Nucleic Acids Res., 33, e126.
24. Kuramitsu,S., Hiromi,K., Hayashi,H., Morino,Y. and Kagamiyama,H. (1990) Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry, 29, 5469-5476.
25. Menetski,J.P. and Kowalczykowski,S.C. (1985) Interaction of recA protein with single-stranded DNA. Quantitative aspects of binding affinity modulation by nucleotide cofactors. J. Mol. Biol., 181, 281-295.
26. Chrysogelos,S. and Griffith,J. (1982) Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units. Proc. Natl Acad. Sci. USA, 79, 5803-5807.
27. Cox,M M. and Lehman,I.R. (1987) Enzymes of general recombination. Annu. Rev. Biochem., 56, 229-262.
28. Timmins,J., Leiros,I. and McSweeney,S. (2007) Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding. Embo. J, 26, 3260-3271.
29. Hobbs,M.D., Sakai,A. and Cox,M.M. (2007) SSB protein limits RecOR binding onto single-stranded DNA. J. Biol. Chem., 282, 11058-11067.
30. Witte,G., Urbanke,C. and Curth,U. (2005) Single-stranded DNA-binding protein of Deinococcus radiodurans: A biophysical characterization. Nucleic Acids Res., 33, 1662-1670.
31. Eggington,J.M., Kozlov,A.G., Cox,M.M. and Lohman,T.M. (2006) Polar destabilization of DNA duplexes with single-stranded overhangs by the Deinococcus radiodurans SSB protein. Biochemistry, 45, 14490-14502.
32. Leiros,I., Timmins,J., Hall,D.R. and McSweeney,S. (2005) Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. Embo. J., 24, 906-918.
33. Makharashvili,N., Koroleva,O., Bera,S., Grandgenett,D.P. and Korolev,S. (2004) A novel structure of DNA repair protein RecO from Deinococcus radiodurans. Structure, 12, 1881-1889.
34. Bernstein,D.A., Eggington,J.M., Killoran,M.P., Misic,A.M., Cox,M.M. and Keck,J.L. (2004) Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage. Proc. Natl Acad. Sci. USA, 101, 8575-8580.
35. Murzin,A.G. (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. Embo J., 12, 861-867.
36. Yang,H., Jeffrey,P.D., Miller,J., Kinnucan,E. Sun,Y., Thoma,N.H., Zheng,N., Clien,P.L., Lee,W.H. et al. (2002) BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science 297, 1857-1848.
37. Park,M.S., Ludwig,D.L., Stigger,E. and Lee,S.H. (1996) Physical interaction between human RAD52 and RPA is required for homologous recombination in mammalian cells. J. Biol. Chem., 271, 18996-19000.
38. Raghunathan,S., Ricard,C.S., Lohman,T.M. and Waksman,G. (1997) Crystal structure of the homo-tetrameric 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. USA, 94, 6652-6657.
39. Raghunathan,S., Kozlov,A.G., Lohman,T.M. and Waksman,G. (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol., 7, 648-652.
40. Alonso,J.C., Stiege,A.C., Dobrinski,B. and Lurz,R. (1993) Purification and properties of the RecR protein from Bacillus subtilis 168. J. Biol. Chem., 268, 1424-1429.
41. Lee,B.I., Kim,K.H., Park,S.J., Eom,S.H., Song,H.K. and Suh,S.W. (2004) Ring-shaped architecture of RecR: Implications for its role in homologous recombinational DNA repair. Embo. J., 23, 2029-2038.
42. Luisi-DeLuca,C. and Kolodner,R. (1994) Purification and characterization of the Escherichia coli RecO protein. Renaturation of complementary single-stranded DNA molecules catalyzed by the RecO protein. J. Mol. Biol., 236, 124-138.