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. 1991 May;128(1):7–22. doi: 10.1093/genetics/128.1.7

Heteroduplex Chain Polarity in Recombination of Phage λ by the Red, Recbcd, Recbc(d(-)) and Recf Pathways

I Siddiqi 1, M M Stahl 1, F W Stahl 1
PMCID: PMC1204455  PMID: 1829428

Abstract

We have examined the chain polarity of heteroduplex DNA in unreplicated, bacteriophage λ splice recombinants when recombination was by the RecBCD, RecBC(D(-)), or RecF pathway of Escherichia coli or the Red pathway of λ. For each of these pathways, recombination is activated by the cutting of cos that accompanies chromosome packaging, and is effected by recombination enzymes acting at the right end created by that cutting. For exchanges occurring near cos, one parent makes a lesser physical and genetic contribution than does the other. For each pathway, when the phage carried standard cos, this minority contribution was predominantly on the r chain, ending 5' at the right end of λ. When standard cos was replaced by a cloned inverted cos located centrally on the standard λ genetic map, minority contribution was predominantly on the l chain. In each case, the polarity of the overlap was usually that formed by 3' overhangs of parental information and material. These results are discussed in the context of current models of recombination for the different pathways.

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Selected References

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  1. Amundsen S. K., Taylor A. F., Chaudhury A. M., Smith G. R. recD: the gene for an essential third subunit of exonuclease V. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5558–5562. doi: 10.1073/pnas.83.15.5558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Appleyard R K. Segregation of New Lysogenic Types during Growth of a Doubly Lysogenic Strain Derived from Escherichia Coli K12. Genetics. 1954 Jul;39(4):440–452. doi: 10.1093/genetics/39.4.440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. BROWN A., ARBER W. TEMPERATURE-SENSITIVE MUTANTS OF COLIPHAGE LAMBDA. Virology. 1964 Oct;24:237–239. doi: 10.1016/0042-6822(64)90114-x. [DOI] [PubMed] [Google Scholar]
  4. Betlach M., Hershfield V., Chow L., Brown W., Goodman H., Boyer H. W. A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA. Fed Proc. 1976 Jul;35(9):2037–2043. [PubMed] [Google Scholar]
  5. Biek D. P., Cohen S. N. Identification and characterization of recD, a gene affecting plasmid maintenance and recombination in Escherichia coli. J Bacteriol. 1986 Aug;167(2):594–603. doi: 10.1128/jb.167.2.594-603.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. CAMPBELL A., DELCAMPILLO-CAMPBELL A. MUTANT OF LAMBDA BACTERIOPHAGE PRODUCING A THERMOLABILE ENDOLYSIN. J Bacteriol. 1963 Jun;85:1202–1207. doi: 10.1128/jb.85.6.1202-1207.1963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carter D. M., Radding C. M. The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease. J Biol Chem. 1971 Apr 25;246(8):2502–2512. [PubMed] [Google Scholar]
  8. Chaudhury A. M., Smith G. R. A new class of Escherichia coli recBC mutants: implications for the role of RecBC enzyme in homologous recombination. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7850–7854. doi: 10.1073/pnas.81.24.7850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cheng K. C., Smith G. R. Cutting of chi-like sequences by the RecBCD enzyme of Escherichia coli. J Mol Biol. 1987 Apr 20;194(4):747–750. doi: 10.1016/0022-2836(87)90252-x. [DOI] [PubMed] [Google Scholar]
  10. Cheng K. C., Smith G. R. Distribution of Chi-stimulated recombinational exchanges and heteroduplex endpoints in phage lambda. Genetics. 1989 Sep;123(1):5–17. doi: 10.1093/genetics/123.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. DasGupta C., Wu A. M., Kahn R., Cunningham R. P., Radding C. M. Concerted strand exchange and formation of Holliday structures by E. coli RecA protein. Cell. 1981 Aug;25(2):507–516. doi: 10.1016/0092-8674(81)90069-6. [DOI] [PubMed] [Google Scholar]
  13. Frackman S., Siegele D. A., Feiss M. A functional domain of bacteriophage lambda terminase for prohead binding. J Mol Biol. 1984 Dec 5;180(2):283–300. doi: 10.1016/s0022-2836(84)80005-4. [DOI] [PubMed] [Google Scholar]
  14. Gillen J. R., Karu A. E., Nagaishi H., Clark A. J. Characterization of the deoxyribonuclease determined by lambda reverse as exonuclease VIII of Escherichia coli. J Mol Biol. 1977 Jun 15;113(1):27–41. doi: 10.1016/0022-2836(77)90039-0. [DOI] [PubMed] [Google Scholar]
  15. Gingery R., Echols H. Mutants of bacteriophage lambda unable to integrate into the host chromosome. Proc Natl Acad Sci U S A. 1967 Oct;58(4):1507–1514. doi: 10.1073/pnas.58.4.1507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Hohn B. DNA as substrate for packaging into bacteriophage lambda, in vitro. J Mol Biol. 1975 Oct 15;98(1):93–106. doi: 10.1016/s0022-2836(75)80103-3. [DOI] [PubMed] [Google Scholar]
  18. Hradecna Z., Szybalski W. Electron micrographic maps of deletions and substitutions in the genomes of transducing coliphages lambda dg and lambda bio. Virology. 1969 Jul;38(3):473–477. doi: 10.1016/0042-6822(69)90160-3. [DOI] [PubMed] [Google Scholar]
  19. Jones M., Wagner R., Radman M. Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics. 1987 Apr;115(4):605–610. doi: 10.1093/genetics/115.4.605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Joseph J. W., Kolodner R. Exonuclease VIII of Escherichia coli. II. Mechanism of action. J Biol Chem. 1983 Sep 10;258(17):10418–10424. [PubMed] [Google Scholar]
  21. Kobayashi I., Murialdo H., Crasemann J. M., Stahl M. M., Stahl F. W. Orientation of cohesive end site cos determines the active orientation of chi sequence in stimulating recA . recBC-mediated recombination in phage lambda lytic infections. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5981–5985. doi: 10.1073/pnas.79.19.5981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Kobayashi I., Takahashi N. Double-stranded gap repair of DNA by gene conversion in Escherichia coli. Genetics. 1988 Aug;119(4):751–757. doi: 10.1093/genetics/119.4.751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kolodner R., Fishel R. A., Howard M. Genetic recombination of bacterial plasmid DNA: effect of RecF pathway mutations on plasmid recombination in Escherichia coli. J Bacteriol. 1985 Sep;163(3):1060–1066. doi: 10.1128/jb.163.3.1060-1066.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kushner S. R., Nagaishi H., Clark A. J. Isolation of exonuclease VIII: the enzyme associated with sbcA indirect suppressor. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3593–3597. doi: 10.1073/pnas.71.9.3593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kushner S. R., Nagaishi H., Templin A., Clark A. J. Genetic recombination in Escherichia coli: the role of exonuclease I. Proc Natl Acad Sci U S A. 1971 Apr;68(4):824–827. doi: 10.1073/pnas.68.4.824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lam S. T., Stahl M. M., McMilin K. D., Stahl F. W. Rec-mediated recombinational hot spot activity in bacteriophage lambda. II. A mutation which causes hot spot activity. Genetics. 1974 Jul;77(3):425–433. doi: 10.1093/genetics/77.3.425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lieb M., Allen E., Read D. Very short patch mismatch repair in phage lambda: repair sites and length of repair tracts. Genetics. 1986 Dec;114(4):1041–1060. doi: 10.1093/genetics/114.4.1041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lieb M. Specific mismatch correction in bacteriophage lambda crosses by very short patch repair. Mol Gen Genet. 1983;191(1):118–125. doi: 10.1007/BF00330898. [DOI] [PubMed] [Google Scholar]
  30. Little J. W. An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction. J Biol Chem. 1967 Feb 25;242(4):679–686. [PubMed] [Google Scholar]
  31. Lloyd R. G., Buckman C. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12. J Bacteriol. 1985 Nov;164(2):836–844. doi: 10.1128/jb.164.2.836-844.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lovett S. T., Clark A. J. Genetic analysis of the recJ gene of Escherichia coli K-12. J Bacteriol. 1984 Jan;157(1):190–196. doi: 10.1128/jb.157.1.190-196.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Luisi-DeLuca C., Lovett S. T., Kolodner R. D. Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants. Genetics. 1989 Jun;122(2):269–278. doi: 10.1093/genetics/122.2.269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. MESELSON M. ON THE MECHANISM OF GENETIC RECOMBINATION BETWEEN DNA MOLECULES. J Mol Biol. 1964 Sep;9:734–745. doi: 10.1016/s0022-2836(64)80178-9. [DOI] [PubMed] [Google Scholar]
  35. Meselson M., Yuan R. DNA restriction enzyme from E. coli. Nature. 1968 Mar 23;217(5134):1110–1114. doi: 10.1038/2171110a0. [DOI] [PubMed] [Google Scholar]
  36. Muniyappa K., Radding C. M. The homologous recombination system of phage lambda. Pairing activities of beta protein. J Biol Chem. 1986 Jun 5;261(16):7472–7478. [PubMed] [Google Scholar]
  37. Newman A. K., Rubin R. A., Kim S. H., Modrich P. DNA sequences of structural genes for Eco RI DNA restriction and modification enzymes. J Biol Chem. 1981 Mar 10;256(5):2131–2139. [PubMed] [Google Scholar]
  38. Palas K. M., Kushner S. R. Biochemical and physical characterization of exonuclease V from Escherichia coli. Comparison of the catalytic activities of the RecBC and RecBCD enzymes. J Biol Chem. 1990 Feb 25;265(6):3447–3454. [PubMed] [Google Scholar]
  39. Ponticelli A. S., Schultz D. W., Taylor A. F., Smith G. R. Chi-dependent DNA strand cleavage by RecBC enzyme. Cell. 1985 May;41(1):145–151. doi: 10.1016/0092-8674(85)90069-8. [DOI] [PubMed] [Google Scholar]
  40. Radicella J. P., Clark E. A., Fox M. S. Some mismatch repair activities in Escherichia coli. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9674–9678. doi: 10.1073/pnas.85.24.9674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Raposa S., Fox M. S. Some features of base pair mismatch and heterology repair in Escherichia coli. Genetics. 1987 Nov;117(3):381–390. doi: 10.1093/genetics/117.3.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rosenberg S. M. Chain-bias of Escherichia coli Rec-mediated lambda patch recombinants is independent of the orientation of lambda cos. Genetics. 1988 Sep;120(1):7–21. doi: 10.1093/genetics/120.1.7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]
  44. Smith G. R., Amundsen S. K., Chaudhury A. M., Cheng K. C., Ponticelli A. S., Roberts C. M., Schultz D. W., Taylor A. F. Roles of RecBC enzyme and chi sites in homologous recombination. Cold Spring Harb Symp Quant Biol. 1984;49:485–495. doi: 10.1101/sqb.1984.049.01.055. [DOI] [PubMed] [Google Scholar]
  45. 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]
  46. Stahl F. W., Fox M. S., Faulds D., Stahl M. M. Break-join recombination in phage lambda. Genetics. 1990 Jul;125(3):463–474. doi: 10.1093/genetics/125.3.463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Stahl F. W., Kobayashi I., Stahl M. M. Distance from cohesive end site cos determines the replication requirement for recombination in phage lambda. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6318–6321. doi: 10.1073/pnas.79.20.6318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. 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]
  49. Stahl F. W. Roles of double-strand breaks in generalized genetic recombination. Prog Nucleic Acid Res Mol Biol. 1986;33:169–194. doi: 10.1016/s0079-6603(08)60023-9. [DOI] [PubMed] [Google Scholar]
  50. Stahl F. W., Stahl M. M., Malone R. E., Crasemann J. M. Directionality and nonreciprocality of Chi-stimulated recombination in phage lambda. Genetics. 1980 Feb;94(2):235–248. doi: 10.1093/genetics/94.2.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Stahl F. W., Stahl M. M., Young L., Kobayashi I. Chi-stimulated recombination between phage lambda and the plasmid lambda dv. Genetics. 1982 Dec;102(4):599–613. doi: 10.1093/genetics/102.4.599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. 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]
  53. Szybalski E. H., Szybalski W. A comprehensive molecular map of bacteriophage lambda. Gene. 1979 Nov;7(3-4):217–270. doi: 10.1016/0378-1119(79)90047-7. [DOI] [PubMed] [Google Scholar]
  54. Takahashi N., Kobayashi I. Evidence for the double-strand break repair model of bacteriophage lambda recombination. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2790–2794. doi: 10.1073/pnas.87.7.2790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Taylor A. F., Schultz D. W., Ponticelli A. S., Smith G. R. RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation-dependence of the cutting. Cell. 1985 May;41(1):153–163. doi: 10.1016/0092-8674(85)90070-4. [DOI] [PubMed] [Google Scholar]
  56. 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]
  57. Thaler D. S., Stahl M. M., Stahl F. W. Double-chain-cut sites are recombination hotspots in the Red pathway of phage lambda. J Mol Biol. 1987 May 5;195(1):75–87. doi: 10.1016/0022-2836(87)90328-7. [DOI] [PubMed] [Google Scholar]
  58. Thaler D. S., Stahl M. M., Stahl F. W. Evidence that the normal route of replication-allowed Red-mediated recombination involves double-chain ends. EMBO J. 1987 Oct;6(10):3171–3176. doi: 10.1002/j.1460-2075.1987.tb02628.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Thaler D. S., Stahl M. M., Stahl F. W. Tests of the double-strand-break repair model for red-mediated recombination of phage lambda and plasmid lambda dv. Genetics. 1987 Aug;116(4):501–511. doi: 10.1093/genetics/116.4.501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. 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]
  61. White R. L., Fox M. S. On the molecular basis of high negative interference. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1544–1548. doi: 10.1073/pnas.71.4.1544. [DOI] [PMC free article] [PubMed] [Google Scholar]

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