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Chapter 12 : Reinitiation of DNA Replication

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Abstract:

This chapter highlights the current knowledge of replication restart in and T4-infected . T4 uses homologous recombination to initiate most of its DNA replication. Soon after phage gene expression commences, DNA replication is initiated from internal replication origins, and the forks so generated travel toward the ends of the infecting genome. UvsW is an RNA-DNA helicase that disrupts the origin R-loop, an essential intermediate in origin replication. Many rounds of recombination-dependent DNA replication (RDR) convert the intracellular form of T4 DNA into a long concatemer. Investigations of phage T4 hotspots for marker rescue recombination provided a dramatic demonstration of the coupling between replication, DNA damage, and recombination. The hotspots were first detected as regions of the genome where genetic markers could be rescued by homologous recombination from UV-irradiated phage at an inflated frequency. The coordinated action of several proteins-PriA, PriB, PriC, DnaT, and DnaC--is required for replication reinitiation at nonorigin sequences in . PriA is the key protein in assembly of the primosome complex, the base of the scaffold that leads to the loading of DnaB. In addition to its primosome assembly activity, PriA has an ssDNA-dependent ATPase activity, which is also dependent on primosome assembly site (PAS) sites in the presence of single-strand binding protein (SSB). RecG strongly prefers forks with a single-strand gap on the leading strand; this and other results argue for a special role of RecG in the replication of damaged DNA.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Figures

Image of Figure 1.
Figure 1.

The T4 genome is terminally redundant and circularly permuted. (A) Every packaged genomic DNA molecule of phage T4 has the same sequence at the two ends of the duplex. (B) DNA packaging in T4 occurs by sequential headful packaging. Since the phage head holds slightly more than 100% of the unique genomic sequence, each packaged DNA is terminally redundant. In addition, since packaging is sequential from concatemeric DNA, different packaged molecules have different end sequences (circular permutation).

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 2.
Figure 2.

DNA replication in phage T4 infections. As described in the text, origin replication leads to unreplicated 30 ends in the daughter molecules (steps A and B). Each single-stranded 30 end can undergo a strand-invasion reaction with the opposite end of one of the daughter molecules (C), leading to the assembly of a new replication fork (D). When two or more phage infect the same cell, D-loop formation can occur with homologous DNA in more central regions of the genome (E), but the consequences are very similar.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 3.
Figure 3.

Proposed pathway for T4 RDR. The proposed steps in T4 RDR are depicted, including 5′-end resection (A), D-loop formation (B), D-loop stabilization (C), and replication fork assembly and function (D). See text for further description.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 4.
Figure 4.

Two modes of DNA synthesis from a D-loop. (A) In the absence of a replicative helicase, T4 replication proteins can catalyze bubble-migration synthesis, in which only one product strand (equivalent to leading strand) is generated. (B) When the replicative helicase is successfully loaded, bubble-migration synthesis is suppressed in favor of normal semiconservative replication.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 5.
Figure 5.

Model for the assembly of PriA-dependent primosome at a D-loop structure. The PriA protein (diamond) first recognizes the D-loop. Binding of PriB (oval) and DnaT (triangle) stabilizes the complex. In the last step, DnaC (closed circle) loads DnaB (open circles). Full lines represent template DNA strands, and dashed lines represent the invading strand in the D-loop. Adapted from reference .

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 6.
Figure 6.

Replication fork collapse model. Encounter of the replication fork with a gap or nick leads to the generation of a double-stranded end. Reincorporation of the broken chromosome end into the homologue sister is mediated by RecBCD-RecA homologous recombination. Resolution of the recombination intermediate and assembly of replication proteins leads to the reconstitution of a replication fork. Adapted from reference 67.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 7.
Figure 7.

RFR model. In the first step (A), the replication fork is arrested and the two newly synthesized strands anneal, forming a Holliday junction. In the second step (B), the junction is stabilized by RuvAB binding. In recombination-proficient strains, RecBCD binds to the double-stranded end (C1); degradation takes place until the first recognized w site (w is an octameric sequence that switches RecBCD from an exonuclease to a recombinase enzyme), which facilitates a genetic exchange mediated by RecA (C2); finally, RuvC resolves Holliday junctions bound by RuvAB (C3). In this manner, recombination enzymes reconstitute the replication fork. Alternatively, RecBCD-mediated degradation of the tail progresses up to the RuvABbound Holliday junction (D). Replication can restart when RecBCD has displaced the RuvAB complex. This pathway can take place in recombination-proficient strains if RecBCD reaches RuvAB before encountering a w site; it is the only pathway that leads to a viable chromosome in recA and mutants. In the absence of RecBCD, RuvC resolves the RuvAB-bound Holliday junction, which leads to the RuvABC-dependent DSBs observed in \mutants (E). The gray circles represent RuvAB, and the partial circles represent RecBCD. Continuous and discontinuous lines represent the template and the newly synthesized strand of the chromosome, respectively; the arrowheads indicate the 3′ end of the growing strands. Adapted from references 93 and 123.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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Image of Figure 8.
Figure 8.

Two models for the role of RFR in response to DNA damage. When the fork is arrested by damage on the leading strand, the lagging strand polymerase may replicate somewhat beyond the region of the damage. RFR can thereby extrude the two product strands, moving the site of DNA damage back into parental duplex DNA. In the model on the left, DNA polymerase extends the nascent leading strand product using the nascent lagging strand as template ( ). Upon readvance of the fork by branch migration, the leading strand product has been extended past the damage, allowing the replication fork to be reestablished. In the model on the right, excision repair (or other conventional repair pathways) corrects the leading strand template lesion (see references and ). This repair is possible only after the lesion has branch migrated back into duplex parental DNA via the RFR reaction. The replication fork can be reestablished after the fork is readvanced by branch migration.

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
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References

/content/book/10.1128/9781555817640.chap12
1. Allen, G. C.,, and A. Kornberg. 1991. The priB gene encoding the primosomal replication N-protein of Escherichia coli. J. Biol. Chem. 266: 11610 11613.
2. Appasani, K.,, D. S. Thaler,, and E. B. Goldberg. 1999. Bacteriophage T4 gp2 interferes with cell viability and with bacteriophage lambda red recombination. J. Bacteriol. 181: 1352 1355.
3. Asai, T.,, and T. Kogoma. 1994. D-loops and R-loops: alternative mechanisms for the initiation of chromosome replication in Escherichia coli. J. Bacteriol. 176: 1807 1812.
4. Asai, T.,, S. Sommer,, A. Bailone,, and T. Kogoma. 1993. Homologous recombination-dependent initiation of DNA replication from DNA damage-inducible origins in Escherichia coli. EMBO J. 12: 3287 3295.
5. Barcena, M.,, T. Ruiz,, L. E. Donate,, S. E. Brown,, N. E. Dixon,, W. Radermacher,, and J. M. Carazo. 2001. The DnaB-DnaC complex: a structure based on dimers assembled around an occluded channel. EMBO J. 20: 1462 1468.
6. Barry, J.,, and B. Alberts. 1994. Purification and characterization of bacteriophage T4 gene 59 protein. A DNA helicase assembly protein involved in DNA replication. J. Biol. Chem. 269: 33049 33062.
7. Beernink, H. T.,, and S. W. Morrical. 1999. RMPs: recombination/ replication mediator proteins. Trends Biochem. Sci. 24: 385 389.
8. Bernstein, C. 1981. Deoxyribonucleic acid repair in bacteriophage. Microbiol. Rev. 45: 72 98.
9. Bishop, A. J. R.,, and R. H. Schiestl. 2000. Homologous recombination as a mechanism for genome rearrangements: environmental and genetic effects. Hum. Mol. Genet. 9: 2427 2434.
10. Black, L. W.,, and M. K. Showe,. 1983. Morphogenesis of the T4 head, p. 219 245. In C. K. Mathews,, E. M. Kutter,, G. Mosig,, and P. B. Berget (ed.), Bacteriophage T4. American Society for Microbiology, Washington, D.C.
11. Bleuit, J. S.,, H. Xu,, Y. Ma,, T. Wang,, J. Liu,, and S.W. Morrical. 2001. Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNAreplication and repair. Proc. Natl. Acad. Sci. USA 98: 8298 8305.
12. Bruand, C.,, S. D. Ehrlich,, and L. Jannie`re. 1995. Primosome assembly site in Bacillus subtilis. EMBO J. 14: 2642 2650.
13. Bruand, C.,, M. Farache,, S. McGovern,, S. D. Ehrlich,, and P. Polard. 2001 DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Mol. Microbiol. 42: 245 255.
14. Bull, H. J.,, M. J. Lombardo,, and S. M. Rosenberg. 2001. Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence. Proc. Natl. Acad. Sci. USA 98: 8334 8341.
15. Campbell, D. A. 1969. On the Mechanism of the Recombinant Increase in X-Irradiated Bacteriophage T4D. Ph.D. thesis. University of Washington, Seattle.
16. Carles-Kinch, K.,, J. W. George,, and K. N. Kreuzer. 1997. Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair, and the regulation of DNA replication origins. EMBO J. 16: 4142 4151.
17. Chakraverty, R. K.,, and I. D. Hickson. 1999. Defending genome integrity during DNA replication: a proposed role for RecQ family helicases. Bioessays 21: 286 294.
18. Clyman, J.,, S. Quirk,, and M. Belfort,. 1994. Mobile introns in the T-even phages, p. 83 88. In J. D. Karam (ed. in chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
19. Colasanti, J.,, and D. T. Denhardt. 1987. The Escherichia coli rep mutation. Consequences of increased and decreased Rep protein levels. Mol. Gen. Genet. 209: 382 390.
20. Cox, M. M. 2001. Recombinational repair of damaged replication forks in Escherichia coli. Annu. Rev. Genet. 35: 53 82.
21. Cunningham, R. P.,, and H. Berger. 1977. Mutations affecting genetic recombination in bacteriophage T4D. I. Pathway analysis. Virology 80: 67 82.
22. Derr, L. K.,, and K. N. Kreuzer. 1990. Expression and function of the uvsW gene of bacteriophage T4. J. Mol. Biol. 214: 643 656.
23. Doan, P. L.,, K. G. Belanger,, and K. N. Kreuzer. 2001. Two types of recombination hotspots in bacteriophage T4: one requires DNA damage and a replication origin and the other does not. Genetics 157: 1077 1087.
24. Doe, C. L.,, J. Dixon,, F. Osman,, and M. C. Whitby. 2000. Partial suppression of the fission yeast rqh1(-) phenotype by expression of the bacterial Holliday junction resolvase. EMBO J. 19: 2751 2762.
25. Dudas, K. C.,, and K. N. Kreuzer. 2001. UvsW protein regulates bacteriophage T4 origin-dependent replication by unwinding R-loops. Mol. Cell. Biol. 21: 2706 2715.
26. Edgar, R. S.,, G. H. Denhardt,, and R. H. Epstein. 1964. A comparative study of conditional lethal mutations of bacteriophage T4D. Genetics 49: 635 648.
27. Ferguson, D. O.,, and W. K. Holloman. 1996. Recombinational repair of gaps in DNA is asymmetric in Ustilago maydis and can be explained by a migrating D-loop model. Proc. Natl. Acad. Sci. USA 93: 5419 5424.
28. Flores, M. J.,, S. D. Ehrlich,, and B. Michel. 2002. Primosome assembly requirement for replication restart in the Escherichia coli holD G10 replication mutant. Mol. Microbiol. 44: 783 792.
29. Flores, M. J.,, H. Bierne,, S. D. Ehrlich,, and B. Michel. 2001. Impairment of lagging strand synthesis triggers the formation of a RuvABC substrate at replication forks. EMBO J. 20: 619 629.
30. Formosa, T.,, and B. M. Alberts. 1986. Purification and characterization of the T4 bacteriophage uvsX protein. J. Biol. Chem. 261: 6107 6118.
31. Formosa, T.,, and B. M. Alberts. 1986. DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified T4 proteins. Cell 47: 793 806.
32. Friedberg, E. C.,, G. C. Walker,, and W. Siede. 1995. DNA Repair and Mutagenesis. ASM Press, Washington, D.C.
33. George, J. W.,, and K. N. Kreuzer. 1996. Repair of doublestrand breaks in bacteriophage T4 by a mechanism that involves extensive DNA replication. Genetics 143: 1507 1520.
34. George, J. W.,, B. A. Stohr,, D. J. Tomso,, and K. N. Kreuzer. 2001. The tight linkage betweenDNAreplication and doublestrand break repair in bacteriophage T4. Proc. Natl. Acad. Sci. USA 98: 8290 8297.
35. Goodman, M. F. 2000. Coping with replication "train Wrecks" in Escherichia coli using Pol V, Pol II and RecA proteins. Trends Biochem. Sci. 25: 189 195.
36. Goodman, M. F.,, and B. Tippin. 2000. Sloppier copier DNA polymerases involved in genome repair. Curr. Opin. Genet. Dev. 10: 162 168.
37. Gorbalenya, A. E.,, and E. V. Koonin. 1993. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3: 419 429.
38. Gregg, A. V.,, P. McGlynn,, R. P. Jaktaji,, and R. G. Lloyd. 2002. Direct rescue of stalled replication forks via the combined action of PriA and RecG helicase activities. Mol. Cell 9: 241 251.
39. Gross, J. D.,, D. Karamata,, and P. G. Hempstead. 1968. Temperature sensitive mutants of Bacillus subtilis defective in DNA synthesis. Cold Spring Harbor Symp. Quant. Biol. 33: 307 312.
40. Gruber, M.,, R. E. Wellinger,, and J. M. Sogo. 2000. Architecture of the replication fork stalled at the 30 end of yeast ribosomal genes. Mol. Cell. Biol. 20: 5777 5787.
41. Hamlett, N. V.,, and H. Berger. 1975. Mutations altering genetic recombination and repair of DNA in bacteriophage T4. Virology 63: 539 567.
42. Harris, L. D.,, and J. D. Griffith. 1989. UvsY protein of bacteriophage T4 is an accessory protein for in vitro catalysis of strand exchange. J. Mol. Biol. 206: 19 27.
43. Higgins, N. P.,, K. Kato,, and B. Strauss. 1976. A model for replication repair in mammalian cells. J. Mol. Biol. 101: 417 425.
44. Hong, G.,, and K. N. Kreuzer. 2000. An antitumor druginduced topoisomerase cleavage complex blocks a bacteriophage T4 replication fork in vivo. Mol. Cell. Biol. 20: 594 603.
45. Horiuchi, T.,, and Y. Fujimura. 1995. Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate. J. Bacteriol. 177: 783 791.
46. Hosoda, J.,, E. Mathews,, and B. Jansen. 1971. Role of genes 46 and 47 in bacteriophage T4 reproduction. J. Virol. 8: 372 387.
47. Hyrien, O. 2000. Mechanisms and consequences of replication fork arrest. Biochimie 82: 5 17.
47a.. Imai, Y.,, N. Ogasawara,, D. Ishigo-oka,, R. Kadoya,, T. Daito,, and S. Moriya. 2000. Subcellular localization of DNAinitiation proteins in Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids. Mol. Microbiol. 36: 1037 1048.
48. Jones, C. E.,, T. C. Mueser,, K. C. Dudas,, K. N. Kreuzer,, and N. G. Nossal. 2001. Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination. Proc. Natl. Acad. Sci. USA 98: 8312 8318.
49. Jones, C. E.,, T. C. Mueser,, and N. G. Nossal. 2000. Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other, and with fork, flap, and cruciform DNA. J. Biol. Chem. 275: 27145 27154.
50. Jones, J. M.,, and H. Nakai. 1997. The fX174-type primosome promotes replisome assembly at the site of recombination in bacteriophage Mu transposition. EMBO J. 16: 6886 6895.
51. Jones, J. M.,, and H. Nakai. 1999. Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. J. Mol. Biol. 289: 503 516.
52. Jones, J. M.,, and H. Nakai. 2000. PriA and phage T4 gp59: factors that promote DNA replication on forked substrates. Mol. Microbiol. 36: 519 527.
53. Jones, J. M.,, and H. Nakai. 2001. Escherichia coli PriA helicase: fork binding orients the helicase to unwind the lagging strand side of arrested replication forks. J. Mol. Biol. 312: 935 947.
54. Karamata, D.,, and J. D. Gross. 1970. Isolation and genetic analysis of temperature sensitive mutants of B. subtilis defective in DNA synthesis. Mol. Gen. Genet. 108: 277 287.
55. Kelman, Z.,, and M. O’ Donnell. 1995. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64: 171 200.
56. Kim, S.,, H. G. Dallmann,, C. S. McHenry,, and K. J. Marians. 1996. Coupling of a replicative polymerase and helicase: a tau-DnaB interaction mediates rapid replication fork movement. Cell 84: 643 650.
57. Kodadek, T.,, D. C. Gan,, and K. Stemke-Hale. 1989. The phage T4 uvsY recombination protein stabilizes presynaptic filaments. J. Biol. Chem. 264: 16451 16457.
58. Kogoma, T. 1996. Recombination by replication. Cell 85: 625 627.
59. Kogoma, T. 1997. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev. 61: 212 238.
60. Kogoma, T.,, G. W. Cadwell,, K. G. Barnard,, and T. Asai. 1996. The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair. J. Bacteriol. 178: 1258 1264.
61. Koonin, E. V. 1992. A new group of putative RNA helicases. Trends Biochem. Sci. 17: 495 497.
62. Kornberg, R. D.,, and T. Baker. 1992. DNA Replication. W. H. Freeman & Co., New York, N.Y.
63. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25: 156 165.
64. Kreuzer, K. N.,, and S. W. Morrical,. 1994. Initiation of DNA replication, p. 28 42. In J. D. Karam (ed. in chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
65. Kreuzer, K. N.,, and J. W. Drake,. 1994. Repair of lethal DNA damage, p. 89 97. In J. D. Karam (ed. in chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
66. Kreuzer, K. N. 2000. Recombination-dependent DNA replication in phage T4. Trends Biochem. Sci. 25: 165 173.
67. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16: 373 384.
68. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63: 751 813.
69. Kuzminov, A. 2001. Single-strand interruptions in replicating chromosomes cause double-strand breaks. Proc. Natl. Acad. Sci. USA 98: 8241 8246.
70. Kuzminov, A.,, and F. W. Stahl. 1999. Double-strand end repair via the RecBC pathway in Escherichia coli primes DNA replication. Genes Dev. 13: 345 356.
71. Lark, C. A.,, J. Riazi,, and K. G. Lark. 1978. dnaT, dominant conditional-lethal mutation affecting DNA replication in Escherichia coli. J. Bacteriol. 136: 1008 1017.
72. Lee, D. G.,, and S. P. Bell. 2000. ATPase switches controlling DNA replication initiation. Curr.Opin. Cell Biol. 12: 280 285.
73. Lee, E. H.,, and A. Kornberg. 1991. Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n0-protein. Proc. Natl. Acad. Sci. USA 88: 3029 3032.
74. Lee, E. H.,, H. Masai,, G. C. Allen,, and A. Kornberg. 1990. The priA gene encoding the primosomal replicative n0 protein of Escherichia coli. Proc. Natl. Acad. Sci. USA 87: 4620 4624.
75. Levy, J. N. 1975. Effects of radiophosphorus decay in bacteriophage T4D. II. The mechanism of marker rescue. Virology 68: 14 26.
76. Liu, J.,, and K. J. Marians. 1999. PriA-directed assembly of a primosome on D loop DNA. J. Biol. Chem. 274: 25033 25041.
77. Liu, J.,, P. Nurse,, and K. J. Marians. 1996. The ordered assembly of the fX174-type primosome. 3. PriB facilitates complex formation between PriA and DnaT. J. Biol. Chem. 271: 15656 15661.
78. Liu, J. I.,, L. W. Xu,, S. J. Sandler,, and K. J. Marians. 1999. Replication fork assembly at recombination intermediates is required for bacterial growth. Proc. Natl. Acad. Sci. USA 96: 3552 3555.
79. Luria, S. 1947. Reactivation of irradiated bacteriophage by transfer of self-reproducing units. Proc. Natl. Acad. Sci. USA 33: 253 264.
80. Maisnier-Patin, S.,, K. Nordstrom,, and S. Dasgupta. 2001. Replication arrests during a single round of replication of the Escherichia coli chromosome in the absence of DnaC activity. Mol. Microbiol. 42: 1371 1382.
81. Marians, K. J. 1992. Prokaryotic DNA replication. Annu. Rev. Biochem. 61: 673 719.
82. Marians, K. J. 2000. PriA-directed replication fork restart in Escherichia coli. Trends Biochem. Sci. 25: 185 189.
83. Marsin, S.,, S. McGovern,, S. D. Ehrlich,, C. Bruand,, and P. Polard. 2001. Early steps of Bacillus subtilis primosome assembly. J. Biol. Chem. 276: 45818 45825.
84. Masai, H.,, and K. Arai. 1988. Operon structure of dnaT and dnaC genes essential for normal and stable DNA replication of Escherichia coli chromosome. J. Biol. Chem. 263: 15083 15093.
85. Masai, H.,, T. Asai,, Y. Kubota,, K. Arai,, and T. Kogoma. 1994. Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO J. 13: 5338 5345.
86. Masai, H.,, M. W. Bond,, and K. Arai. 1986. Cloning of the Escherichia coli gene for primosomal protein i: the relationship to dnaT, essential for chromosomal DNA replication. Proc. Natl. Acad. Sci. USA 83: 1256 1260.
87. McCool, J. D.,, and S. J. Sandler. 2001. Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2:kan mutant. Proc. Natl. Acad. Sci. USA 98: 8203 8210.
88. McGlynn, P.,, and R. G. Lloyd. 2000. Modulation of RNA polymerase by (P)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 101: 35 45.
89. McGlynn, P.,, and R. G. Lloyd. 2001. Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc. Natl. Acad. Sci. USA 98: 8227 8234.
90. McGlynn, P.,, A. A. Al-Deib,, J. Liu,, K. J. Marians,, and R. G. Lloyd. 1997. The DNA replication protein PriA and the recombination protein RecG bind D-loops. J. Mol. Biol. 270: 212 221.
91. McGlynn, P.,, R. G. Lloyd,, and K. J. Marians. 2001. Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled. Proc. Natl. Acad. Sci. USA 98: 8235 8240.
92. Melamede, R. J.,, and S. S. Wallace. 1977. Properties of the nonlethal recombinational repair x and y mutants of bacteriophage T4. II. DNA synthesis. J. Virol. 24: 28 40.
93. Michel, B. 2000. Replication fork arrest and DNA recombination. Trends Biochem. Sci. 25: 173 178.
94. Michel, B.,, M. J. Flores,, E. Viguera,, G. Grompone,, M. Seigneur,, and V. Bidnenko. 2001. Rescue of arrested replication forks by homologous recombination. Proc. Natl. Acad. Sci. USA 98: 8181 8188.
95. Mickelson, C.,, and J. S. Wiberg. 1981. Membrane-associated DNase activity controlled by genes 46 and 47 of bacteriophage T4D and elevated DNase activity associated with the T4 das mutation. J. Virol. 40: 65 77.
96. Mizuuchi, K.,, B. Kemper,, J. Hays,, and R. A. Weisberg. 1982. T4 endonuclease VII cleaves Holliday structures. Cell 29: 357 365.
97. Mosig, G., 1983. Relationship of T4 DNA replication and recombination, p. 120 130. In C. K. Mathews,, E. M. Kutter,, G. Mosig,, and P. B. Berget (ed.), Bacteriophage T4. American Society for Microbiology, Washington, D.C.
98. Mosig, G., 1994. Homologous recombination, p. 54 82. In J. D. Karam (ed. in chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
99. Mosig, G.,, J. Gewin,, A. Luder,, N. Colowick,, and D. Vo. 2001. Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer. Proc. Natl. Acad. Sci. USA 98: 8306 8311.
100. Motamedi, M. R.,, S. K. Szigety,, and S. M. Rosenberg. 1999. Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes Dev. 13: 2889 2903.
101. Mueller, J. E.,, T. Clyman,, Y. J. Huang,, M. M. Parker,, and M. Belfort. 1996. Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways. Genes Dev. 10: 351 364.
102. Mueser, T. C.,, C. E. Jones,, N. G. Nossal,, and C. C. Hyde. 2000. Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 Å resolution crystal structure reveals a novel a-helical two-domain fold. J. Mol. Biol. 296: 597 612.
103. Mukherjee, A.,, C. Cao,, and J. Lutkenhaus. 1998. Inhibition of FtsZ polymerization by SulA, an inhibitor of septation in Escherichia coli. Proc. Natl. Acad. Sci. USA 95: 2885 2890.
104. Nassif, N.,, J. Penney,, S. Pal,, W. R. Engels,, and G. B. Gloor. 1994. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol. Cell. Biol. 14: 1613 1625.
105. Ng, J. Y.,, and K. J. Marians. 1996. The ordered assembly of the fX174-type primosome. 1. Isolation and identification of intermediate protein-DNA complexes. J. Biol. Chem. 271: 15642 15648.
106. Ng, J. Y.,, and K. J. Marians. 1996. The ordered assembly of the fX174-type primosome. 2. Preservation of primosome composition from assembly through replication. J. Biol. Chem. 271: 15649 15655.
107. Nilsen, T.,, and C. Baglioni. 1979. Unusual base-pairing of newly synthesized DNA in HeLa cells. J. Mol. Biol. 133: 319 338.
108. Nossal, N. G., 1994. The bacteriophage T4 DNA replication fork, p. 43 53. In J. D. Karam (ed. in chief), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
109. Nossal, N. G.,, K. C. Dudas,, and K. N. Kreuzer. 2001. Bacteriophage T4 proteins replicate plasmids with a preformed R loop at the T4 ori(uvsY) replication origin in vitro. Mol. Cell 7: 31 41.
110. Nurse, P.,, J. Liu,, and K. J. Marians. 1999. Two modes of PriA binding to DNA. J. Biol. Chem. 274: 25026 25032.
111. Nurse, P.,, R. J. DiGate,, K. H. Zavitz,, and K. J. Marians. 1990. Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y. Proc. Natl. Acad. Sci. USA 87: 4615 4619.
112. Nurse, P.,, K. H. Zavitz,, and K. J. Marians. 1991. Inactivation of the Escherichia coli PriA DNA replication protein induces the SOS response. J. Bacteriol. 173: 6686 6693.
113. Polard, P.,, S. Marsin,, S. McGovern,, M. Velten,, D. Wigley,, S. D. Ehrlich,, and C. Bruand. 2002. Restart of DNA replication in Gram-positive bacteria: functional characterisation of the Bacillus subtilis PriA initiator. Nucleic Acids Res. 30: 1593 1605.
114. Postow, L.,, N. J. Crisona,, B. J. Peter,, C. D. Hardy,, and N. R. Cozzarelli. 2001. Topological challenges to DNA replication: conformations at the fork. Proc. Natl. Acad. Sci. USA 98: 8219 8226.
115. Robu, M. E.,, R. B. Inman,, and M. M. Cox. 2001. RecA protein promotes the regression of stalled replication forks in vitro. Proc. Natl. Acad. Sci. USA 98: 8211 8218.
116. Rothstein, R.,, B. Michel,, and S. Gangloff. 2000. Replication fork pausing and recombination or "gimme a break." Genes Dev. 14: 1 10.
117. Sandler, S. J.,, J. D. McCool,, and R. Johansen. 2001. PriA mutations that affect PriA-PriC function during replication restart. Mol. Microbiol. 41: 697 704.
118. Sandler, S. J. 2000. Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12. Genetics 155: 487 497.
119. Sandler, S. J.,, and K. J. Marians. 2000. Role of PriA in replication fork reactivation in Escherichia coli. J. Bacteriol. 182: 9 13.
120. Sandler, S. J.,, K. J. Marians,, K. H. Zavitz,, J. Coutu,, M. A. Parent,, and A. J. Clark. 1999. dnaC mutations suppress defects in DNA replication- and recombination-associated functions in priB and priC double mutants in Escherichia coli K-12. Mol. Microbiol. 34: 91 101.
121. Sandler, S. J.,, H. S. Samra,, and A. J. Clark. 1996. Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC. Genetics 143: 5 13.
122. Schlomai, J.,, and A. Kornberg. 1980. An Escherichia coli replication protein that recognizes a unique sequence within a hairpin region in fX174 DNA. Proc. Natl. Acad. Sci. USA 77: 799 803.
123. Seigneur, M.,, V. Bidnenko,, S. D. Ehrlich,, and B. Michel. 1998. RuvAB acts at arrested replication forks. Cell 95: 419 430.
124. Seigneur, M.,, S. D. Ehrlich,, and B. Michel. 2000. RuvABCdependent double-strand breaks in dnaBts mutants require RecA. Mol. Microbiol. 38: 565 574.
125. Sharples, G. J. 2001. The X philes: structure-specific endonucleases that resolve Holliday junctions. Mol. Microbiol. 39: 823 834.
126. Sharples, G. J.,, and D. R. F. Leach. 1995. Structural and functional similarities between the SbcCD proteins of Escherichia coli and the RAD50 and MRE11 (RAD32) recombination and repair proteins of yeast. Mol. Microbiol. 17: 1215 1220.
127. Singleton, M. R.,, S. Scaife,, and D. B. Wigley. 2001. Structural analysis of DNA replication fork reversal by RecG. Cell 107: 79 89.
128. Smith, G. R. 1991 Conjugational recombination in E. coli— myths and mechanisms. Cell 64: 19 27.
129. Sung, P. 1997. Function of yeast Rad52 protein as a mediator between replication protein A and the Rad51 recombinase. J. Biol. Chem. 272: 28194 28197.
130. Sweezy, M. A.,, and S. W. Morrical. 1999. Biochemical interactions within a ternary complex of the bacteriophage T4 recombination proteins uvsY and gp32 bound to singlestranded DNA. Biochemistry 38: 936 944.
131. Szostak, J. W.,, T. L. Orr-Weaver,, R. J. Rothstein,, and F. W. Stahl. 1983. The double-strand-break repair model for recombination. Cell 33: 25 35.
132. Tatsumi, K.,, and B. Strauss. 1978. Production of DNA bifilarly substituted with bromodeoxyuridine in the first round of synthesis: branch migration during isolation of cellular DNA. Nucleic Acids Res. 5: 331 347.
133. Tougu, K.,, H. Peng,, and K. J. Marians. 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.
134. Turner, J.,, M. M. Hingorani,, Z. Kelman,, and M. O’Donnell. 1999. The internal workings of a DNA polymerase clamploading machine. EMBO J. 18: 771 783.
135. Umezu, K.,, and R. D. Kolodner. 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.
136. Wechsler, J. A. 1975. Genetic and phenotypic characterization of dnaC mutations. J. Bacteriol. 121: 594 599.
137. West, S. C. 1997. Processing of recombination intermediates by the RuvABC proteins. Annu. Rev. Genet. 31: 213 244.
138. Whitby, M. C.,, G. J. Sharples,, and R. G. Lloyd. 1995. The RuvAB and RecG proteins of Escherichia coli. Nucleic Acids Mol. Biol. 9: 66 83.
139. Williams, K. R.,, and W. H. Konigsberg,. 1983. Structure-function relationships in the T4 single-stranded DNA binding protein, p. 82 89. In C. K. Mathews,, E. M. Kutter,, G. Mosig,, and P. B. Berget (ed.), Bacteriophage T4. American Society for Microbiology, Washington, D.C.
140. Withers, H. L.,, and R. Bernander. 1998. Characterization of dnaC2 and dnaC28 mutants by flow cytometry. J. Bacteriol. 180: 1624 1631.
141. Womack, F. C. 1965. Cross reactivation differences in bacteriophage T4D. Virology 26: 758 761.
142. Xu, L. W.,, and K. J. Marians. 2000. Purification and characterization of DnaC810, a primosomal protein capable of bypassing PriA function. J. Biol. Chem. 275: 8196 8205.
143. Yap, W. Y.,, and K. N. Kreuzer. 1991. Recombination hotspots in bacteriophage T4 are dependent on replication origins. Proc. Natl. Acad. Sci. USA 88: 6043 6047.
144. Yonesaki, T.,, and T. Minagawa. 1985. T4 phage gene uvsX product catalyzes homologous DNA pairing. EMBO J. 4: 3321 3327.
145. Yonesaki, T.,, and T. Minagawa. 1989. Synergistic action of three recombination gene products of bacteriophage T4, uvsX, uvsY, and gene 32 proteins. J. Biol. Chem. 264: 7814 7820.
146. Zavitz, K. H.,, R. J. Digate,, and K. J. Marians. 1991. The PriB and PriC replication proteins of Escherichia coli genes, DNA sequence, overexpression, and purification. J. Biol. Chem. 266: 13988 13995.
147. Zavitz, K. H.,, and K. J. Marians. 1991. Dissecting the functional role of PriA protein-catalysed primosome assembly in Escherichia coli DNA replication. Mol. Microbiol. 5: 2869 2873.
148. Zavitz, K. H.,, and K. J. Marians. 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.
149. Zavitz, K. H.,, and K. J. Marians. 1993. Helicase-deficient cysteine to glycine substitution mutants of Escherichia coli replication protein PriA retain single-stranded DNAdependent ATPase activity. Zn2þ stimulation of mutant PriA helicase and primosome assembly activities. J. Biol. Chem. 268: 4337 4346.

Tables

Generic image for table
Table 1.

Proteins implicated in replication restart in phage T4 and

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12
Generic image for table
Table 2.

Terminology used in this chapter

Citation: Kreuzer K, Michel B. 2005. Reinitiation of DNA Replication, p 229-250. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch12

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