Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate

Journal of Molecular Biology

Volumn 289, Issue 3, 1999, Pages 503-515

  Jones, Jessica M ^a   Nakai, Hiroshi ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

in vitro DNA replication; Phage Mu; PriA helicase; Primosome

Indexed keywords

DNA BINDING PROTEIN; DOUBLE STRANDED DNA; HELICASE;

ARTICLE; BACTERIOPHAGE MU; CHROMOSOME REPLICATION; DNA REPLICATION; DNA STRUCTURE; ESCHERICHIA COLI; GENETIC RECOMBINATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY;

ENTEROBACTERIA PHAGE MU; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0033546121     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2783     Document Type: Article

References (62)

1. Adzuma, K. & Mizuuchi, K. (1988). Target immunity of Mu transposition reflects a differential distribution of Mu B protein. Cell, 53, 257-266.
2. Arai, K. & Kornberg, A. (1981). Unique primed start of phage φX174 DNA replication and mobility of the primosome in a direction opposite chain synthesis. Proc. Natl Acad. Sci. USA, 78, 69-73.
3. Asai, T. & Kogoma, T. (1994). D-loops and R-loops: Alternate mechanisms for the initiation of chromosome replication in Escherichia coli. J. Bacteriol. 176, 1807-1812.
4. Asai, T., Bates, D. & Kogoma, T. (1994). DNA replication triggered by double-strand breaks in E. coli: Dependence on homologous recombination functions. Cell, 78, 1051-1061.
5. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1992). CurRent Protocols in Molecular Biology, Jacob Wiley & Sons, New York.
6. Baker, T. A., Sekimizu, K., Funnell, B. E. & Kornberg, A. (1986). Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the orgin of the Escherichia coli chromosome. Cell, 45, 53-64.
7. Bierne, H. & Michel, B. (1994). When replication forks stop. Mol. Microbiol. 13, 17-23.
8. Bramhill, D. & Kornberg, A. (1988). Duplex opening by DnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell, 52, 743-755.
9. Bujalowski, W. & Jezewska, M. J. (1995). Interactions of Escherichia coli primary replicative helicase DnaB protein with single-stranded DNA. The nucleic acid does not wrap around the protein hexamer. BioChemistry, 34, 8513-8519.
10. Courcelle, J., Carswell-Crumpton, C. & Hanawalt, P. C. (1997). recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli. Proc. Natl Acad. Sci. USA, 94, 3714- 3719.
11. Craigie, R. & Mizuuchi, K. (1985). Mechanism of transposition of bacteriophage Mu: Structure of a transposition intermediate. Cell, 41, 867-876.
12. Craigie, R. & Mizuuchi, K. (1987). Transposition of Mu DNA: Joining of Mu to target DNA can be uncoupled from cleavage at the ends of Mu. Cell, 51, 493-501.
13. Craigie, R., Mizuuchi, M. & Mizuuchi, K. (1984). Site- Specific recognition of the bacteriophage Mu ends by the Mu A protein. Cell, 39, 387-394.
14. Craigie, R., Arndt-Jovin, D. J. & Mizuuchi, K. (1985). A defined system for the DNA strand-transfer reaction at the initiation of bacteriophage Mu transposition: Protein and DNA substrate requirements. Proc. Natl Acad. Sci. USA, 82, 7570-7574.
15. Funnell, B. E., Baker, T. A. & Kornberg, A. (1987). In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J. Biol. Chem. 262, 10327-10334.
16. Jones, J. M. & Nakai, H. (1997). The φX174-type primosome promotes replisome assembly at the site of recombination in bacteriophage Mu transposition. EMBO J. 16, 6886-6895.
17. Kogoma, T. (1996). Recombination by replication. Cell, 85, 625-627.
18. Kogoma, T. (1997). Stable DNA replication: Interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev. 61, 212-238.
19. Kogoma, T., Cadwell, G. W., Barnard, K. G. & Asai, T. (1996). The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair. J. Bacteriol. 178, 1258- 1264.
20. Kruklitis, R. & Nakai, H. (1994). Participation of bacteriophage Mu A protein and host factors in initiation of Mu DNA synthesis in vitro. J. Biol. Chem. 269, 16469-16477.
21. Kruklitis, R., Welty, D. J. & Nakai, H. (1996). ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. EMBO J. 15, 935- 944.
22. Kuo, C.-F., Zou, A., Jayaram, M., Getzoff, E. & Harshey, R. (1991). DNA-protein complexes during attachment-site synapsis in Mu DNA transposition. EMBO J. 10, 1585-1591.
23. Kuzminov, A. (1995). Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16, 373-384.
24. Lasken, R. S. & Kornberg, A. (1988). The primosomal protein n' of Escherichia coli is a DNA helicase. J. Biol. Chem. 263, 5512-5518.
25. Lavoie, B. D. & Chaconas, G. (1990). Immunoelectron microscopic analysis of the A, B, and HU protein content of bacteriophage Mu transpososomes. J. Biol. Chem. 265, 1623-1627.
26. Lavoie, B. D. & Chaconas, G. (1993). Site-specific HU binding in the Mu transpososome: Conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev. 7, 2510-2519.
27. Lavoie, B. D. & Chaconas, G. (1994). A second high affinity HU binding site in the phage Mu transpososome. J. Biol. Chem. 269, 15571-15576.
28. Lavoie, B. D., Chan, B. S., Allison, R. G. & Chaconas, G. (1991). Structural aspects of a higher order nucleoprotein complex: Induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 10, 3051-3059.
29. Learn, B. A., Um, S. J., Huang, L. & McMacken, R. (1997). Cryptic single-stranded-Dna binding activities of the phage lambda P and Escherichia coli DnaC replication initiation proteins facilitate the transfer of E. coli DnaB helicase onto DNA. Proc. Natl Acad. Sci. USA, 94, 1154-1159.
30. LeBowitz, J. H. & McMacken, R. (1986). The Escherichia coli DnaB replication protein is a DNA helicase. J. Biol. Chem. 261, 4738-4748.
31. Lee, E. H. & Kornberg, A. (1991). Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n' protein. Proc. Natl Acad. Sci. USA, 88, 3029-3032.
32. Lee, E. H., Masai, H., Allen, G. C. & Kornberg, A. (1990). The priA gene encoding the primosomal replicative n' protein of Escherichia coli. Proc. Natl Acad. Sci. USA, 87, 4620-4624.
33. Lee, M. S. & Marians, K. J. (1987). Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase. Proc. Natl Acad. Sci. USA, 84, 8345-8349.
34. Lee, M. S. & Marians, K. J. (1989). The Escherichia coli primosome can translocate actively in either direction along the DNA strand. J. Biol. Chem. 264, 14531-14542.
35. Levchenko, I., Luo, L. & Baker, T. A. (1995). Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev. 9, 2399-2408.
36. Liu, J., Nurse, P. & Marians, K. J. (1996). The ordered assembly of the φX174-type primosome: PriB facilitates complex formation between PriA and DnaT. J. Biol. Chem. 271, 15656-15661.
37. Marians, K. J. (1995). φX174-type primosomal proteins: Purification and assay. Methods Enzymol. 262, 507- 521.
38. Masai, H., Asai, T., Kubota, Y., Arai, K. & Kogoma, T. (1994). Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO J. 13, 5338-5345.
39. McGlynn, P., Al-Deib, A. A., Liu, J., Marians, K. J. & Lloyd, R. G. (1997). The DNA replication protein PriA and the recombination protein RecG bind D-Loops. J. Mol. Biol. 270, 212-221.
40. Minden, J. S. & Marians, K. J. (1985). Replication of pBR322 DNA in vitro with purified proteins. J. Biol. Chem. 260, 9316-9325.
41. Mizuuchi, M., Baker, T. A. & Mizuuchi, K. (1992). Assembly of the active form of the transposase-Mu DNA complex: A critical control point in Mu transposition. Cell, 70, 303-311.
42. Nakai, H. & Kruklitis, R. (1995). Disassembly of the bacteriophage Mu transposase for the initiation of Mu DNA replication. J. Biol. Chem. 270, 19591-19598.
43. Ng, J. Y. & Marians, K. J. (1996a). The ordered assembly of the φX174-type primosome: Isolation and identification of intermediate protein-DNA complexes. J. Biol Chem. 271, 15642-15648.
44. Ng, J. Y. & Marians, K. J. (1996b). The ordered assembly of the φX174-type primosome: Preservation of primosome composition from assembly through replication. J. Biol Chem. 271, 15649-15655.
45. Nurse, P., Zavitz, K. H. & Marians, K. J. (1991). Inactivation of the Escherichia coli PriA DNA replication protein induces the SOS response. J. Bacterial. 173, 6686-6693.
46. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. (1995). How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423.
47. Rupp, W. D. & Howard-Flanders, P. (1968). Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation. J. Mol Biol 31, 291-304.
48. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). MolecuLar Cloning, A Laboratory Manual, 2nd Edit., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
49. Sandler, S. J., Samra, H. S. & Clark, A. J. (1996). Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC. Genetics, 143, 5-13.
50. Sassanfar, M. & Roberts, J. W. (1990). Nature of the SOS-inducing signal in Escherichia coli: The involvement of DNA replication. J. Mol. Biol. 212, 79-96.
51. Shlomai, J. & Kornberg, A. (1980a). An Escherichia coli replication protein that recognizes a unique sequence hairpin within a region of φX174 DNA. Proc. Natl Acad. Sci. USA, 77, 799-803.
52. Shlomai, J. & Kornberg, A. (1980b). A prepriming DNA replication enzyme of Escherichia coli. I. Purification of protein n': A sequence-specific, DNA-dependent ATPase. J. Biol. Chem. 255, 6789-6783.
53. Surette, M. G., Buch, S. J. & Chaconas, G. (1987). Transpososomes: Stable protein-DNA complexes involved in the in vitro transposition of bacteriophage Mu DNA. Cell, 49, 253-262.
54. Svoboda, D. L. & Vos, J. H. (1995). Differential replication of a single, UV-induced lesion in the leading or lagging strand by a human cell extract: Fork uncoupling or gap formation. Proc. Natl Acad. Sci. USA, 92, 11975-11979.
55. Tougo, K., Peng, H. & Marians, K. J. (1994). Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork. J. Biol. Chem. 269, 4675-4682.
56. Wahle, E., Lasken, R. S. & Kornberg, A. (1989a). The DnaB-DnaC replication protein complex of Escherichia coli. II. Role of the complex in mobilizing dnaB functions. J. Biol. Chem. 264, 2469-2475.
57. Wahle, E., Lasken, R. S. & Kornberg, A. (1989b). The DnaB-DnaC replication protein complex of Escherichia coli. I. Formation and properties. J. Biol. Chem. 264, 2463-2468.
58. Wickner, S. & Hurwitz, J. (1974). Conversion of φX174 viral DNA to double-stranded form by purified Escherichia coli proteins. Proc. Natl Acad. Sci. USA, 71, 4120-4124.
59. Yuzhakov, A., Turner, J. & O'Donnell, M. (1996). Replisome assembly reveals the basis for asymmetric function in leading and lagging strand replication. Cell, 86, 877-886.
60. Zavitz, K. H. & Marians, K. J. (1992). ATPase-deficient mutants of the Escherichia coli DNA replication protein PriA are capable of catalyzing the assembly of active primosomes. J. Biol. Chem. 267, 6933-6940.
61. Zipursky, S. L. & Marians, K. J. (1980). Identification of two Escherichia coli factor Y effector sites near the origins of replication of plasmids ColE1 and pBR322. Proc. Natl Acad. Sci. USA, 77, 6521-6525.
62. Zipursky, S. L. & Marians, K. J. (1981). Escherichia coli factor Y sites of plasmid pBR322 can function as origins of DNA replication. Proc. Natl Acad. Sci. USA, 78, 6111-6115.