Migration of a holliday junction through a nucleosome directed by the E. coli RuvAB motor protein

Molecular Cell

Volumn 2, Issue 3, 1998, Pages 373-381

  Grigoriev, Mikhail ^a   Hsieh, Peggy ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; HELICASE; HETERODUPLEX; HISTONE; HOLLIDAY JUNCTION DNA HELICASE, E COLI; RUVB PROTEIN, BACTERIA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DNA REPAIR; ESCHERICHIA COLI; GENETIC RECOMBINATION; GENETICS; METABOLISM; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA HELICASES; DNA REPAIR; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HISTONES; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; NUCLEOSOMES; PROTEIN CONFORMATION; RECOMBINATION, GENETIC;

EID: 0032161224     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80281-6     Document Type: Article

References (43)

1. Adams, D.E., and West, S.C. (1996). Bypass of DNA heterologies during RuvAB-mediated three- and four-strand branch migration. J. Mol. Biol. 263, 582-596.
2. Adams, D.E., Tsaneva, I.R., and West, S.C. (1994). Dissociation of RecA filaments from duplex DNA by the RuvA and RuvB DNA repair proteins. Proc. Natl. Acad. Sci. USA 91, 9901-9905.
3. Ausio, J., Dong, F., and van Holde, K.E. (1989). Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome. J. Mol. Biol. 206, 451-463.
4. Bell, L., and Byers, B. (1979). Occurrence of crossed strand-exchange forms in yeast DNA during meiosis. Proc. Natl. Acad. Sci. USA 76, 3445-3449.
5. Biswas, I., Yamamoto, A., and Hsieh, P. (1998). Branch migration through DNA sequence heterology. J. Mol. Biol. 279, 795-806.
6. Bonne-Andrea, C., Wong, M.L., and Alberts, B.M. (1990). In vitro replication through nucleosomes without histone displacement. Nature 343, 719-726.
7. Camerini-Otero, R.D., and Hsieh, P. (1995). Homologous recombination proteins in prokaryotes and eukaryotes. Annu. Rev. Genet. 29, 509-552.
8. Cheng, L., and Kelly, T.J. (1989). Transcriptional activator nuclear factor I stimulates the replication of SV40 minichromosomes in vivo and in vitro. Cell 59, 541-551.
9. Egelman, E.H., Yu, X., Wild, R., Hingorani, M.M., and Patel, S.S. (1995). Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases. Proc. Natl. Acad. Sci. USA 92, 3869-3873.
10. Eggleston, A.K., O'Neill, T.E., Bradbury, E.M., and Kowalczykowski, S.C. (1995). Unwinding of nucleosomal DNA by a DNA helicase. J. Biol. Chem. 270, 2024-2031.
11. Fan, Q.-Q., and Petes, T.D. (1996). Relationship between nuclease-hypersensitive sites and meiotic recombination hot spot activity at the HIS4 locus of Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2037-2043.
12. Grigoriev, M., and Hsieh, P. (1997). A histone octamer blocks branch migration of a Holliday junction. Mol. Cell. Biol. 17, 7139-7150.
13. Haber, J.E. (1992). Mating-type gene switching in Saccharomyces cerevisiae. Trends Genet. 8, 446-452.
14. Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G., and Rafferty, J.B. (1998). Crystal structure of E. coli RuvA with bound DNA Holliday junction at 6Å resolution. Nature Struct. Biol. 5, 441-446.
15. Hiom, K., and West, S.C. (1995). Branch migration during homologous recombination: assembly of a RuvAB-Holliday junction complex in vitro. Cell 80, 787-793.
16. Holliday, R. (1964). A mechanism for gene conversion in fungi. Genet. Res. Camb. 5, 282-304.
17. Hsieh, P., and Panyutin, I.G. (1995). DNA branch migration. In Nucleic Acids and Molecular Biology, F. Eckstein and D.M.J. Lilley, eds. (Berlin: Springer-Verlag), pp. 42-65.
18. Ito, T., Tyler, J.K., and Kadonaga, J.T. (1997). Chromatin assembly factors: a dual function in nucleosome formation and mobilization? Genes Cells 2, 593-600.
19. Iype, L.E., Wood, E.A., Inman, R.B., and Cox, M.M. (1994). RuvA and RuvB proteins facilitate the bypass of heterologous DNA insertions during RecA protein-mediated DNA strand exchange. J. Biol. Chem. 269, 24967-24978.
20. Kornberg, R.D., and Lorch, Y. (1995). Interplay between chromatin structure and transcription. Curr. Opin. Cell Biol. 7, 371-375.
21. Lloyd, R.G., and Sharples, G.J. (1993). Processing of recombination intermediates by the RecG and RuvAB proteins of Escherichia coli. Nucleic Acids Res. 21, 1719-1725.
22. Lorch, Y., LaPointe, J.W., and Kornberg, R.D. (1987). Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49, 203-210.
23. Lorentz, A., Heim, L., and Schmidt, H. (1992). The switching gene swi6 affects recombination and gene expression in the mating-type region of Schizosaccharomyces pombe. Mol. Gen. Genet. 233, 436-442.
24. Mitchell, A.H., and West, S.C. (1996). Role of RuvA in branch migration reactions catalyzed by the RuvA and RuvB proteins of Escherichia coli. J. Biol. Chem. 271, 19497-19502.
25. O'Donohue, M.-F., Duband-Goulet, I., Hamiche, A., and Prunell, A. (1994). Octamer displacement and redistribution in transcription of single nucleosomes. Nucleic Acids Res. 22, 937-945.
26. Ohta, K., Shibata, T., and Nicolas, A. (1994). Changes in chromatin structure at recombination initiation sites during yeast meiosis. EMBO J. 13, 5754-5763.
27. Panyutin, I.G., and Hsieh, P. (1994). The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. USA 91, 2021-2025.
28. Ponticelli, A.S., and Smith, G.R. (1992). Chromosomal context dependence of a eukaryotic recombinational hot spot. Proc. Natl. Acad. Sci. USA 89, 227-231.
29. Potter, H., and Dressier, D. (1976). On the mechanism of genetic recombination: electron microscopic observation of recombination intermediates. Proc. Natl. Acad. Sci. USA 73, 3000-3004.
30. Ramdas, J., Mythili, E., and Muniyappa, K. (1991). Nucleosomes on linear duplex DNA allow homologous pairing but prevent strand exchange promoted by RecA protein. Proc. Natl. Acad. Sci. USA 88, 1344-1348.
31. Ramsperger, U., and Stahl, H. (1995). Unwinding of chromatin by the SV40 large T antigen DNA helicase. EMBO J. 14, 3215-3225.
32. Schwacha, A., and Kleckner, N. (1995). Identification of double Holliday junctions as intermediates in meiotic recombination. Cell 83, 783-791.
33. Shrader, T.E., and Crothers, D.M. (1989). Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA 86, 7418-7422.
34. Simpson, R.T. (1990). Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 343, 387-389.
35. Studitsky, V.M., Clark, D.J., and Felsenfeld, G. (1994). A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76, 371-382.
36. Studitsky, V.M., Kassavetis, G.A., Geiduschek, E.P., and Felsenfeld, G. (1997). Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 278, 1960-1963.
37. Tsaneva, I.R., Muller, B., and West, S.C. (1992). ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell 69, 1171-1180.
38. Valenzuela, M.S., and Inman, R.B. (1975). Visualization of a novel junction in bacteriophage lambda DNA. Proc. Natl. Acad. Sci. USA 72, 3024-3028.
39. West, S.C. (1997). Processing of recombination intermediates by the RuvABC proteins. Annu. Rev. Genet. 31, 213-244.
40. White, M.A., Dominska, M., and Petes, T.D. (1993). Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 90, 6621-6625.
41. White, M.F., Giraud-Panis, M.-J.E., Pöhler, J.R.G., and Lilley, D.M.J. (1997). Recognition and manipulation of branched DNA structure by junction-resolving enzymes. J. Mol. Biol. 269, 647-664.
42. Wolffe, A.P., Khochbin, S., and Dmiitrov, S. (1997). What do linker histones do in chromatin? BioEssays 19, 249-255.
43. Wu, T.-C., and Lichten, M. (1994). Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263, 515-518.