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. 2002 Nov;162(3):1019–1030. doi: 10.1093/genetics/162.3.1019

Coordination of DNA ends during double-strand-break repair in bacteriophage T4.

Bradley A Stohr 1, Kenneth N Kreuzer 1
PMCID: PMC1201557  PMID: 12454052

Abstract

The extensive chromosome replication (ECR) model of double-strand-break repair (DSBR) proposes that each end of a double-strand break (DSB) is repaired independently by initiating extensive semiconservative DNA replication after strand invasion into homologous template DNA. In contrast, several other DSBR models propose that the two ends of a break are repaired in a coordinated manner using a single repair template with only limited DNA synthesis. We have developed plasmid and chromosomal recombinational repair assays to assess coordination of the broken ends during DSBR in bacteriophage T4. Results from the plasmid assay demonstrate that the two ends of a DSB can be repaired independently using homologous regions on two different plasmids and that extensive replication is triggered in the process. These findings are consistent with the ECR model of DSBR. However, results from the chromosomal assay imply that the two ends of a DSB utilize the same homologous repair template even when many potential templates are present, suggesting coordination of the broken ends during chromosomal repair. This result is consistent with several coordinated models of DSBR, including a modified version of the ECR model.

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Selected References

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  1. Anderson D. E., Trujillo K. M., Sung P., Erickson H. P. Structure of the Rad50 x Mre11 DNA repair complex from Saccharomyces cerevisiae by electron microscopy. J Biol Chem. 2001 Jul 24;276(40):37027–37033. doi: 10.1074/jbc.M106179200. [DOI] [PubMed] [Google Scholar]
  2. Belfort M. Phage T4 introns: self-splicing and mobility. Annu Rev Genet. 1990;24:363–385. doi: 10.1146/annurev.ge.24.120190.002051. [DOI] [PubMed] [Google Scholar]
  3. Bell-Pedersen D., Quirk S. M., Aubrey M., Belfort M. A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4. Gene. 1989 Oct 15;82(1):119–126. doi: 10.1016/0378-1119(89)90036-x. [DOI] [PubMed] [Google Scholar]
  4. Bell-Pedersen D., Quirk S., Clyman J., Belfort M. Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications. Nucleic Acids Res. 1990 Jul 11;18(13):3763–3770. doi: 10.1093/nar/18.13.3763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berger H., Pardoll D. Evidence that mismatched bases in heteroduplex T4 bacteriophage are recognized in vivo. J Virol. 1976 Nov;20(2):441–445. doi: 10.1128/jvi.20.2.441-445.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bleuit J. S., Xu H., Ma Y., Wang T., Liu J., Morrical S. W. Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8298–8305. doi: 10.1073/pnas.131007498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cromie G. A., Connelly J. C., Leach D. R. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell. 2001 Dec;8(6):1163–1174. doi: 10.1016/s1097-2765(01)00419-1. [DOI] [PubMed] [Google Scholar]
  8. Doan P. L., Belanger K. G., Kreuzer K. N. Two types of recombination hotspots in bacteriophage T4: one requires DNA damage and a replication origin and the other does not. Genetics. 2001 Mar;157(3):1077–1087. doi: 10.1093/genetics/157.3.1077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. EDGAR R. S., DENHARDT G. H., EPSTEIN R. H. A COMPARATIVE GENETIC STUDY OF CONDITIONAL LETHAL MUTATIONS OF BACTERIOPHAGE T4D. Genetics. 1964 Apr;49:635–648. doi: 10.1093/genetics/49.4.635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. George J. W., Kreuzer K. N. Repair of double-strand breaks in bacteriophage T4 by a mechanism that involves extensive DNA replication. Genetics. 1996 Aug;143(4):1507–1520. doi: 10.1093/genetics/143.4.1507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. George J. W., Stohr B. A., Tomso D. J., Kreuzer K. N. The tight linkage between DNA replication and double-strand break repair in bacteriophage T4. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8290–8297. doi: 10.1073/pnas.131007598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Huang Y. J., Parker M. M., Belfort M. Role of exonucleolytic degradation in group I intron homing in phage T4. Genetics. 1999 Dec;153(4):1501–1512. doi: 10.1093/genetics/153.4.1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hunter N., Kleckner N. The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination. Cell. 2001 Jul 13;106(1):59–70. doi: 10.1016/s0092-8674(01)00430-5. [DOI] [PubMed] [Google Scholar]
  14. Kreuzer K. N., Alberts B. M. A defective phage system reveals bacteriophage T4 replication origins that coincide with recombination hot spots. Proc Natl Acad Sci U S A. 1985 May;82(10):3345–3349. doi: 10.1073/pnas.82.10.3345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kreuzer K. N., Engman H. W., Yap W. Y. Tertiary initiation of replication in bacteriophage T4. Deletion of the overlapping uvsY promoter/replication origin from the phage genome. J Biol Chem. 1988 Aug 15;263(23):11348–11357. [PubMed] [Google Scholar]
  16. Malkova A., Ivanov E. L., Haber J. E. Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7131–7136. doi: 10.1073/pnas.93.14.7131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Morrow D. M., Connelly C., Hieter P. "Break copy" duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics. 1997 Oct;147(2):371–382. doi: 10.1093/genetics/147.2.371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Mueller J. E., Smith D., Belfort M. Exon coconversion biases accompanying intron homing: battle of the nucleases. Genes Dev. 1996 Sep 1;10(17):2158–2166. doi: 10.1101/gad.10.17.2158. [DOI] [PubMed] [Google Scholar]
  19. Nassif N., Penney J., Pal S., Engels W. R., Gloor G. B. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol Cell Biol. 1994 Mar;14(3):1613–1625. doi: 10.1128/mcb.14.3.1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Pâques F., Haber J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1999 Jun;63(2):349–404. doi: 10.1128/mmbr.63.2.349-404.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Rattray A. J., McGill C. B., Shafer B. K., Strathern J. N. Fidelity of mitotic double-strand-break repair in Saccharomyces cerevisiae: a role for SAE2/COM1. Genetics. 2001 May;158(1):109–122. doi: 10.1093/genetics/158.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Seigneur M., Bidnenko V., Ehrlich S. D., Michel B. RuvAB acts at arrested replication forks. Cell. 1998 Oct 30;95(3):419–430. doi: 10.1016/s0092-8674(00)81772-9. [DOI] [PubMed] [Google Scholar]
  23. Selick H. E., Kreuzer K. N., Alberts B. M. The bacteriophage T4 insertion/substitution vector system. A method for introducing site-specific mutations into the virus chromosome. J Biol Chem. 1988 Aug 15;263(23):11336–11347. [PubMed] [Google Scholar]
  24. Sharples G. J., Leach D. R. 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. 1995 Sep;17(6):1215–1217. doi: 10.1111/j.1365-2958.1995.mmi_17061215_1.x. [DOI] [PubMed] [Google Scholar]
  25. Shcherbakov V. P., Chirkov G. P., Plugina L. A., Kudriashova E. A., Sizova S. T. Vklad korrektsii v geneticheskuiu rekombinatsiiu u faga T4, izmeriaemyi po éffektu suzheniia karty. Genetika. 1978;14(1):122–128. [PubMed] [Google Scholar]
  26. Shcherbakov V. P., Plugina L. A., Kudryashova E. A., Efremova O. I., Sizova S. T., Toompuu O. G. Marker-dependent recombination in T4 bacteriophage. I. Outline of the phenomenon and evidence suggesting a mismatch repair mechanism. Genetics. 1982 Dec;102(4):615–625. doi: 10.1093/genetics/102.4.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Shinedling S., Singer B. S., Gayle M., Pribnow D., Jarvis E., Edgar B., Gold L. Sequences and studies of bacteriophage T4 rII mutants. J Mol Biol. 1987 Jun 5;195(3):471–480. doi: 10.1016/0022-2836(87)90176-8. [DOI] [PubMed] [Google Scholar]
  28. Shinedling S., Walker L. T., Gold L. Cloning the complete rIIB gene of bacteriophage T4 and some observations concerning its middle promoters. J Virol. 1986 Nov;60(2):787–792. doi: 10.1128/jvi.60.2.787-792.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Solaro P. C., Birkenkamp K., Pfeiffer P., Kemper B. Endonuclease VII of phage T4 triggers mismatch correction in vitro. J Mol Biol. 1993 Apr 5;230(3):868–877. doi: 10.1006/jmbi.1993.1207. [DOI] [PubMed] [Google Scholar]
  30. Stohr B. A., Kreuzer K. N. Repair of topoisomerase-mediated DNA damage in bacteriophage T4. Genetics. 2001 May;158(1):19–28. doi: 10.1093/genetics/158.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  32. Woods J. P., Dempsey J. F., Kawula T. H., Barritt D. S., Cannon J. G. Characterization of the neisserial lipid-modified azurin bearing the H.8 epitope. Mol Microbiol. 1989 May;3(5):583–591. doi: 10.1111/j.1365-2958.1989.tb00205.x. [DOI] [PubMed] [Google Scholar]
  33. de Jager M., van Noort J., van Gent D. C., Dekker C., Kanaar R., Wyman C. Human Rad50/Mre11 is a flexible complex that can tether DNA ends. Mol Cell. 2001 Nov;8(5):1129–1135. doi: 10.1016/s1097-2765(01)00381-1. [DOI] [PubMed] [Google Scholar]

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