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. 1991 Nov;129(3):611–621. doi: 10.1093/genetics/129.3.611

Chain Bias in Chi-Stimulated Heteroduplex Patches in the λ Ren Gene Is Determined by the Orientation of λ Cos

A T Hagemann 1, S M Rosenberg 1
PMCID: PMC1204728  PMID: 1836442

Abstract

Heteroduplex patch recombinants have received information in one DNA chain but have not recombined flanking markers. Evidence regarding which chain is exchanged bears on the structure of recombination intermediates. The direction of travel along DNA of RecBCD recombinase, the central enzyme in the Escherichia coli RecBCD pathway of homologous recombination, is determined in phage λ by the orientation of the packaging origin, cos. cos is a double-chain cut site which serves as a preferred entry site for RecBCD. Using partially denaturing gels to resolve heteroduplex molecules, we have examined patch recombinants at the λ ren gene. We report that the transferred information in Chi-stimulated patches at ren can occur on either chain, but is biased to the chain ending 5' at the right of the λ map (the λ r chain) in phage carrying cos in its normal orientation. The chain bias switches in favor of the chain that ends 3' at the right (the λ l chain) when RecBCD travel direction is reversed by inverting cos. We entertain models that accommodate these and other results pertaining to the structure of RecBCD-mediated recombinants.

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Selected References

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  1. Cheng K. C., Smith G. R. Recombinational hotspot activity of Chi-like sequences. J Mol Biol. 1984 Dec 5;180(2):371–377. doi: 10.1016/s0022-2836(84)80009-1. [DOI] [PubMed] [Google Scholar]
  2. Feiss M., Widner W., Miller G., Johnson G., Christiansen S. Structure of the bacteriophage lambda cohesive end site: location of the sites of terminase binding (cosB) and nicking (cosN). Gene. 1983 Oct;24(2-3):207–218. doi: 10.1016/0378-1119(83)90081-1. [DOI] [PubMed] [Google Scholar]
  3. Goldberg A. R., Howe M. New mutations in the S cistron of bacteriophage lambda affecting host cell lysis. Virology. 1969 May;38(1):200–202. doi: 10.1016/0042-6822(69)90148-2. [DOI] [PubMed] [Google Scholar]
  4. Henderson D., Weil J. Recombination-deficient deletions in bacteriophage lambda and their interaction with chi mutations. Genetics. 1975 Feb;79(2):143–174. doi: 10.1093/genetics/79.2.143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kobayashi I., Stahl M. M., Stahl F. W. The mechanism of the chi-cos interaction in RecA-RecBC-mediated recombination in phage lambda. Cold Spring Harb Symp Quant Biol. 1984;49:497–506. doi: 10.1101/sqb.1984.049.01.056. [DOI] [PubMed] [Google Scholar]
  6. Konforti B. B., Davis R. W. 3' homologous free ends are required for stable joint molecule formation by the RecA and single-stranded binding proteins of Escherichia coli. Proc Natl Acad Sci U S A. 1987 Feb;84(3):690–694. doi: 10.1073/pnas.84.3.690. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lerman L. S., Silverstein K. Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol. 1987;155:482–501. doi: 10.1016/0076-6879(87)55032-7. [DOI] [PubMed] [Google Scholar]
  8. Lichten M., Goyon C., Schultes N. P., Treco D., Szostak J. W., Haber J. E., Nicolas A. Detection of heteroduplex DNA molecules among the products of Saccharomyces cerevisiae meiosis. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7653–7657. doi: 10.1073/pnas.87.19.7653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Matsubara K. Replication control system in lambda dv. Plasmid. 1981 Jan;5(1):32–52. doi: 10.1016/0147-619x(81)90076-7. [DOI] [PubMed] [Google Scholar]
  10. Myers R. M., Maniatis T., Lerman L. S. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 1987;155:501–527. doi: 10.1016/0076-6879(87)55033-9. [DOI] [PubMed] [Google Scholar]
  11. Rosenberg S. M. Chi-stimulated patches are heteroduplex, with recombinant information on the phage lambda r chain. Cell. 1987 Mar 13;48(5):855–865. doi: 10.1016/0092-8674(87)90082-1. [DOI] [PubMed] [Google Scholar]
  12. Rosenberg S. M., Hastings P. J. The split-end model for homologous recombination at double-strand breaks and at Chi. Biochimie. 1991 Apr;73(4):385–397. doi: 10.1016/0300-9084(91)90105-a. [DOI] [PubMed] [Google Scholar]
  13. SUSSMAN R., JACOB F. [On a thermosensitive repression system in the Escherichia coli lambda bacteriophage]. C R Hebd Seances Acad Sci. 1962 Feb 19;254:1517–1519. [PubMed] [Google Scholar]
  14. Siddiqi I., Stahl M. M., Stahl F. W. Heteroduplex chain polarity in recombination of phage lambda by the red, RecBCD, RecBC(D-) and RecF pathways. Genetics. 1991 May;128(1):7–22. doi: 10.1093/genetics/128.1.7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Smith G. R., Kunes S. M., Schultz D. W., Taylor A., Triman K. L. Structure of chi hotspots of generalized recombination. Cell. 1981 May;24(2):429–436. doi: 10.1016/0092-8674(81)90333-0. [DOI] [PubMed] [Google Scholar]
  16. Stahl F. W., Crasemann J. M., Stahl M. M. Rec-mediated recombinational hot spot activity in bacteriophage lambda. III. Chi mutations are site-mutations stimulating rec-mediated recombination. J Mol Biol. 1975 May 15;94(2):203–212. doi: 10.1016/0022-2836(75)90078-9. [DOI] [PubMed] [Google Scholar]
  17. Stahl F. W., Kobayashi I., Thaler D., Stahl M. M. Direction of travel of RecBC recombinase through bacteriophage lambda DNA. Genetics. 1986 Jun;113(2):215–227. doi: 10.1093/genetics/113.2.215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Stahl F. W., Lieb M., Stahl M. M. Does Chi give or take? Genetics. 1984 Dec;108(4):795–808. doi: 10.1093/genetics/108.4.795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stahl F. W., Stahl M. M. Recombination pathway specificity of Chi. Genetics. 1977 Aug;86(4):715–725. doi: 10.1093/genetics/86.4.715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Stahl F. W., Thomason L. C., Siddiqi I., Stahl M. M. Further tests of a recombination model in which chi removes the RecD subunit from the RecBCD enzyme of Escherichia coli. Genetics. 1990 Nov;126(3):519–533. doi: 10.1093/genetics/126.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Stahl M. M., Kobayashi I., Stahl F. W., Huntington S. K. Activation of Chi, a recombinator, by the action of an endonuclease at a distant site. Proc Natl Acad Sci U S A. 1983 Apr;80(8):2310–2313. doi: 10.1073/pnas.80.8.2310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Thaler D. S., Sampson E., Siddiqi I., Rosenberg S. M., Thomason L. C., Stahl F. W., Stahl M. M. Recombination of bacteriophage lambda in recD mutants of Escherichia coli. Genome. 1989;31(1):53–67. doi: 10.1139/g89-013. [DOI] [PubMed] [Google Scholar]
  23. Weigle J. Assembly of phage lambda in vitro. Proc Natl Acad Sci U S A. 1966 Jun;55(6):1462–1466. doi: 10.1073/pnas.55.6.1462. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wold M. S., Mallory J. B., Roberts J. D., LeBowitz J. H., McMacken R. Initiation of bacteriophage lambda DNA replication in vitro with purified lambda replication proteins. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6176–6180. doi: 10.1073/pnas.79.20.6176. [DOI] [PMC free article] [PubMed] [Google Scholar]

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