Chi Sites and Their Consequences

  • Gerald R. Smith


Chi sites are octameric nucleotide sequences in DNA that stimulate the Rec-BCD pathway of homologous recombination in Escherichia coli. Stimulation is maximal at the Chi site, decreases approximately a factor of two for each 2–3 kb to one side, but is insignificant to the other side of Chi. Chi stimulates recombination by interaction with RecBCD enzyme, which has multiple enzymatic activities and multiple physiological roles in recombination, repair, and replication. Chi appears to be active throughout the enteric bacteria; other nucleotide sequences may similarly interact with RecBCD-like enzymes in other bacteria. This chapter reviews the properties of Chi, its interaction with RecBCD enzyme, and its occurrence on the chromosome of E. coli and other organisms.


Homologous Recombination Nuclease Activity Bacteriophage Lambda RecA Protein Homologous Pairing 
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  1. Amundsen, S. K., A. F. Taylor, A. M. Chaudhury, and G. R. Smith. 1986. recD: The gene for an essential third subunit of exonuclease V. Proc. Natl. Acad. Sci. USA 83:5558–5562.CrossRefGoogle Scholar
  2. Amundsen, S. K., A. M. Neiman, S. M. Thibodeaux, and G. R. Smith. 1990. Genetic dissection of the biochemical activities of RecBCD enzyme. Genetics 126:25–40.PubMedGoogle Scholar
  3. Asai, T., D. B. Bates, and T. Kogoma. 1994. DNA replication triggered by double-stranded breaks in E. coli: dependence on homologous recombination functions. Cell 78:1051–1061.PubMedCrossRefGoogle Scholar
  4. Biswas, I., E. Maguin, S. D. Ehrlich, and A. Gruss. 1995. A 7-base-pair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis. Proc. Natl. Acad. Sci. USA 92:2244–2248.PubMedCrossRefGoogle Scholar
  5. Blaisdell, B. E., K. E. Rudd, A. Matin, and S. Karlin. 1993. Significant dispersed recurrent DNA sequences in the Escherichia coli genome. J. Mol. Biol. 229:833–848.PubMedCrossRefGoogle Scholar
  6. Blakely, G., S. Colloms, G. May, M. Burke, and D. Sherratt. 1991. Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New. Biol. 3:789–798.PubMedGoogle Scholar
  7. Brewer, B. J. 1988. When polymerases collide: replication and the transcriptional organization of the Escherichia coli chromosome. Cell 53:679–686.PubMedCrossRefGoogle Scholar
  8. Burland, V., G. Plunkett III, D. L. Daniels, and F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: Organizational symmetry around the origin of replication. Genomics 16:551–561.PubMedCrossRefGoogle Scholar
  9. Chaudhury, A. M., and G. R. Smith. 1984. A new class of Escherichia coli recBC mutants: Implications for the role of RecBC enzyme in homologous recombination. Proc. Natl. Acad. Sci. USA, 81:7850–7854.PubMedCrossRefGoogle Scholar
  10. Cheng, K. C., and G. R. Smith. 1984. Recombinational hotspot activity of Chi-like sequences. J. Mol. Biol. 180:371–377.PubMedCrossRefGoogle Scholar
  11. Cheng, K. C., and G. R. Smith. 1989. Distribution of Chi-stimulated recombinational exchanges and heteroduplex endpoints in phage lambda. Genetics 123:5–17.PubMedGoogle Scholar
  12. Dabert, P., S. D. Ehrlich and A. Gruss. 1992. χ sequence protects against RecBCD degradation of DNA in vivo. Proc. Natl. Acad. Sci. USA 89:12073–12077.PubMedCrossRefGoogle Scholar
  13. Dabert, P. and G. R. Smith. Gene Replacement with linear DNA fragments in wild-type Escherichia coli enhancement by Chi sites. Genetics, in press.Google Scholar
  14. Dewyse, P. and W. E. C. Bradley. 1991. A very large spontaneous deletion at aprt locus in CHO cells: sequence similarities with small aprt deletions. Somatic Cell and Molecular Genetics 17:57–68.PubMedCrossRefGoogle Scholar
  15. Dixon, D. A. and S. C. Kowalczykowski. 1991. Homologous pairing in vitro stimulated by the recombination hotspot, Chi. Cell 66:361–371.PubMedCrossRefGoogle Scholar
  16. Dixon, D. A. and S. C. Kowalczykowski. 1993. The recombination hotspot χ is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell 73:87–96.PubMedCrossRefGoogle Scholar
  17. Dixon, D. A. and S. C. Kowalczykowski. 1995. Role of the Escherichia coli recombination hotspot, χ, in RecABCD-dependent homologous pairing. J. Biol. Chem. 270:16360–16370.PubMedCrossRefGoogle Scholar
  18. Dower, N. A. and F. W. Stahl. 1981. Chi activity during transduction-associated recombination. Proc. Natl. Acad. Sci. USA 78:7033–7037.PubMedCrossRefGoogle Scholar
  19. Eggleston, A. K. and S. C. Kowalczykowski. 1993. Biochemical characterization of a mutant recBCD enzyme, the recB2109 CD enzyme, which lacks χ-specific, but not nonspecific, nuclease activity. J. Mol. Biol. 231:605–620.PubMedCrossRefGoogle Scholar
  20. Faulds, D., N. Dower, M. M. Stahl, and F. W. Stahl. 1979. Orientation-dependent recombination hotspot activity in bacteriophage lambda. J. Mol. Biol. 131:681–695.PubMedCrossRefGoogle Scholar
  21. Gillen, J. R. and A. J. Clark. 1974. The RecE pathway of bacterial recombination. In Mechanisms in Recombination, R. F. Grell, ed. pp. 123–126. Plenum Press, New York.CrossRefGoogle Scholar
  22. Hagemann, A. T. and S. M. Rosenberg. 1991. Chain bias in Chi-stimulated heteroduplex patches in the lambda ren gene is determined by the orientation of lambda cos. Genetics 129:611–621.PubMedGoogle Scholar
  23. Henderson, D. and J. Weil. 1975. Recombination-deficient deletions in bacteriophage lambda and their interaction with Chi mutations. Genetics 79:143–174.PubMedGoogle Scholar
  24. Holbeck, S. L. and G. R. Smith. 1992. Chi enhances heteroduplex DNA levels during recombination. Genetics 132:879–891.PubMedGoogle Scholar
  25. Horiuchi, T., Y. Fujimura, H. Nishitani, T. Kobayashi, and M. Hidaka. 1994. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J. Bacteriol. 176:4656–4663.PubMedGoogle Scholar
  26. Jasin, M. and P. Schimmel. 1984. Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments. J. Bacteriol. 159:783–786.PubMedGoogle Scholar
  27. Kalnins, A., K. Otto, U. Ruther, and B. Muller-Hill. 1983. Sequence of the lacZ gene of Escherichia coli. EMBO J. 2:593–597.PubMedGoogle Scholar
  28. Kenter, A. L. and B. K. Birshtein. 1981. Chi, a promoter of generalized recombination in X phage, is present in immunoglobulin genes. Nature 293:402–404.PubMedCrossRefGoogle Scholar
  29. Kobayashi, I., M. M. Stahl, and F. W. Stahl. 1984. The mechanism of the Chi-cos interaction in RecA-RecBC-mediated recombination in phage lambda. Cold Spring Harbor Symp. Quant. Biol. 49:497–506.PubMedCrossRefGoogle Scholar
  30. Kobayashi, I., H. Murialdo, J. M. Crasemann, M. M. Stahl, and F. W. Stahl. 1982. 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. USA 79:5981–5985.PubMedCrossRefGoogle Scholar
  31. Köppen, A., S. Krobitsch, B. Thorns, and W. Wackernagel. 1995. Interaction with the recombination hot spot χ in vivo converts the RecBCD enzyme of Escherichia coli into a χ-independent recombinase by inactivation of the RecD subunit. Proc. Natl. Acad. Sci. USA 92:6249–6253.PubMedCrossRefGoogle Scholar
  32. Krowczynska, A. M., R. A. Rudders, and T. G. Krontiris. 1990. The human minisatellite consensus at breakpoints of oncogene translocations. Nucl. Acids Res. 18:1121–1127.PubMedCrossRefGoogle Scholar
  33. Kuzminov, A., E. Schabtach, and F. W. Stahl. 1994. χ sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease. EMBO J. 13:2764–2776.PubMedGoogle Scholar
  34. Lam, S. T., M. M. Stahl, K. D. McMilin, and F. W. Stahl. 1974. Rec-mediated recombinational hotspot activity in bacteriophage lambda. II. A mutation which causes hotspot activity. Genetics 77:425–433.PubMedGoogle Scholar
  35. Lieb, M. and S. Rehmat. 1995. Very short patch repair of T:G mismatches in vivo: Importance of context and accessory proteins. J. Bacteriol. 177:660–666.PubMedGoogle Scholar
  36. Lloyd, R. G. and C. Buckman. 1995. Conjugational recombination in Escherichia coli: Genetic analysis of recombinant formation in Hfr × F- crosses. Genetics 139:1123–1148.PubMedGoogle Scholar
  37. Lundblad, V., A. F. Taylor, G. R. Smith, and N. Kleckner. 1984. Unusual alleles of recB and recC stimulate excision of inverted repeat transposons Tn10 and Tn5. Proc. Natl. Acad. Sci. USA 81:824–828.PubMedCrossRefGoogle Scholar
  38. Malone, R. E., D. K. Chattoraj, D.H. Faulds, M. M. Stahl, and F. W. Stahl. (1978). Hotspots for generalized recombination in the Escherichia coli chromosome. J. Mol. Biol. 121:473–491.PubMedCrossRefGoogle Scholar
  39. McKittrick, N. H. and G. R. Smith. 1989. Activation of Chi recombinational hotspots by RecBCD-like enzymes from enteric bacteria. J. Mol. Biol. 210:485–495.PubMedCrossRefGoogle Scholar
  40. McMilin, K. D., M. M. Stahl, and F. W. Stahl. 1974. Rec-mediated hotspot recombinational activity in bacteriophage lambda. I. Hot spot activity associated with spi deletions and bio substitutions. Genetics 77:409–423.PubMedGoogle Scholar
  41. Myers, R. S., A. Kuzminov, and F. W. Stahl. 1995. The recombination hot spot χ activates RecBCD recombination by converting Escherichia coli to a recD mutant phenocopy. Proc. Natl. Acad. Sci. USA 92:6244–6248.PubMedCrossRefGoogle Scholar
  42. Newman, B. J. and M. Masters. 1980. The variation in frequency with which markers are transduced by phage P1 is primarily a result of discrimination during recombination. Mol. Gen. Genet. 180:585–589.PubMedCrossRefGoogle Scholar
  43. Nishitani, H., M. Hidaka, and T. Horiuchi. 1993. Specific chromosomal sites enhancing homologous recombination in Escherichia coli mutants defective in RNase H. Mol. Gen. Genet. 240:307–314.PubMedGoogle Scholar
  44. Ponticelli, A. S., D. W. Schultz, A. F. Taylor, and G. R. Smith. 1985. Chi-dependent DNA strand cleavage by RecBC enzyme. Cell 41:145–151.PubMedCrossRefGoogle Scholar
  45. Rosenberg, S. M. 1987. Chi-stimulated patches are heteroduplex, with recombinant information on the phage lambda r chain. Cell 48:855–865.PubMedCrossRefGoogle Scholar
  46. Rosenberg, S. M. 1988. Chain-bias of Escherichia coli Rec-mediated lambda patch recombinants is independent of the orientation of lambda cos. Genetics 120:7–21.PubMedGoogle Scholar
  47. Rüdiger, N. S., N. Gregersen, and M. C. Kielland-Brandt. 1995. One short well conserved region of Alu-sequences is involved in human gene rearrangements and has homology with prokaryotic chi. Nucl. Acids Res. 23:256–260.PubMedCrossRefGoogle Scholar
  48. Russell, C. B., D. S. Thaler, and F. W. Dahlquist. 1989. Chromosomal transformation of Escherichia coli recD strains with linearized plasmids. J. Bacteriol. 171:2609–2613.PubMedGoogle Scholar
  49. Sanger, F., A. R. Coulson, G. F. Hong, D. F. Hill, and G. B. Petersen. 1982. Nucleotide sequence of bacteriophage lambda DNA. J. Mol. Biol. 162:729–773.PubMedCrossRefGoogle Scholar
  50. Schultz, D. W. and G. R. Smith. 1986. Conservation of Chi cutting activity in terrestrial and marine enteric bacteria. J. Mol. Biol. 189:585–595.PubMedCrossRefGoogle Scholar
  51. Schultz, D. W., A. F. Taylor, and G. R. Smith. 1983. Escherichia coli RecBC pseudore-vertants lacking Chi recombinational hotspot activity. J. Bacteriol. 155:664–680.PubMedGoogle Scholar
  52. Shevell, D. E., A. M. Abou-Zamzam, B. Demple, and G. C. Walker. 1988. Construction of an Escherichia coli K-12 ada deletion by gene replacement in a recD strain reveals a second methyltransferase that repairs alkylated DNA. J. Bacteriol. 170:3294–3296.PubMedGoogle Scholar
  53. Siddiqi, I., M. M. Stahl, and F. W. Stahl. 1991. Heteroduplex chain polarity in recombination of phage lambda by the Red, RecBCD, RecBC(D-) and RecF pathways. Genetics 128:7–22.PubMedGoogle Scholar
  54. Smith, G. R. 1983. General recombination, in Lambda II. R. W. Hendrix, J. W. Roberts, F. W. Stahl and R. A. Weisberg, eds. pp. 175–209. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.Google Scholar
  55. Smith, G. R. 1987. Mechanism and control of homologous recombination. Escherichia coli. Annu. Rev. Genet. 21:179–201.Google Scholar
  56. Smith, G. R. 1988. Homologous recombination sites and their recognition. In The Recombination of Genetic Material. pp. 115–154. B. Low, ed. Academic Press, New York.Google Scholar
  57. Smith, G. R. 1991. Conjugational recombination in E. coli: Myths and mechanisms. Cell 64:19–27.PubMedCrossRefGoogle Scholar
  58. Smith, G. R. 1994. Hotspots of homologous recombination. Experientia 50:234–241.PubMedCrossRefGoogle Scholar
  59. Smith, G. R., C. M. Roberts, and D. W. Schultz. 1986. Activity of Chi recombinational hotspots in Salmonella typhimurium. Genetics 112:429–439.PubMedGoogle Scholar
  60. Smith, G. R., D. W. Schultz, A. F. Taylor, and K. Triman. 1981. Chi sites, RecBC enzyme, and generalized recombination. Stadler Genetics Symposium 13:25–37.Google Scholar
  61. Smith, G. R., S. K. Amundsen, A. M. Chaudhury, K. C. Cheng, A. S. Ponticelli, C. M. Roberts, D. W. Schultz, and A. F. Taylor. 1984. Roles of RecBC enzyme and Chi sites in homologous recombination. Cold Spring Harbor Symp. Cold Spring Harbor Symp. Quant Biol. 49:485–495.PubMedCrossRefGoogle Scholar
  62. Smith, G. R., S. K. Amundsen, P. Dabert, and A. F. Taylor. 1995. The initiation and control of homologous recombination in Escherichia coli. Phil. Trans. R. Soc. London 347:13–20.CrossRefGoogle Scholar
  63. Stahl, F. W. 1979. Special sites in generalized recombination. Annu. Rev. Genet. 13:7–24.PubMedCrossRefGoogle Scholar
  64. Stahl, F. W., J. M. Crasemann, and M. M. Stahl. 1975. Rec-mediated recombinational hot spot activity in bacteriophage lambda. III. Chi mutations are site-mutations stimulating Rec-mediated recombination. J. Mol. Biol. 94:203–212.PubMedCrossRefGoogle Scholar
  65. Stahl, F.W. and M. M. Stahl. 1975. Rec-mediated recombinational hot spot activity in bacteriophage lambda. IV. Effect of heterology on Chi-stimulated crossing over. Mol. Gen. Genet. 140:29–37.PubMedCrossRefGoogle Scholar
  66. Stahl, F. W. and M. M. Stahl. 1977. Recombination pathway specificity of Chi. Genetics 86:715–725.PubMedGoogle Scholar
  67. Stahl, F. W., M. M. Stahl, R. E. Malone, and J. M. Crasemann. 1980. Directionality and nonreciprocality of Chi-stimulated recombination in phage lambda. Genetics 94:235–248.PubMedGoogle Scholar
  68. Sutcliffe. J. G. 1979. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harbor Symp. Quant. Biol. 43:77–90.PubMedCrossRefGoogle Scholar
  69. Taylor, A. F. 1988. RecBCD enzyme of Escherichia coli, in Genetic Recombination, R. Kucherlapati and G. R. Smith, eds. pp. 231–263. American Society for Microbiology, Washington, DC.Google Scholar
  70. Taylor, A. F. and G. R. Smith. 1992. RecBCD enzyme is altered upon cutting DNA at a Chi recombination hotspot. Proc. Natl. Acad. Sci. USA 89:5226–5230.PubMedCrossRefGoogle Scholar
  71. Taylor, A. F. and G. R. Smith. 1995. Monomeric RecBCD enzyme binds and unwinds DNA. J. Biol. Chem. 270:24451–24458.PubMedCrossRefGoogle Scholar
  72. Taylor, A. F. and G. R. Smith. 1995b. Strand specificity of nicking of DNA at Chi sites by RecBCD enzyme: modulation by ATP and magnesium levels. J. Biol. Chem. 270:24459–24467.PubMedCrossRefGoogle Scholar
  73. Taylor, A. F., D. W. Schultz, A. S. Ponticelli, and G. R. Smith. 1985. RecBC enzyme nicking at Chi sites during DNA unwinding: Location and orientation dependence of the cutting. Cell 41:153–163.PubMedCrossRefGoogle Scholar
  74. Thaler, D. S., E. Sampson, I. Siddiqi, S. M. Rosenberg, F. W. Stahl, and M. Stahl. 1988. A hypothesis: Chi-activation of RecBCD enzyme involves removal of the RecD subunit, in Mechanisms and Consequences of DNA Damage Processing. E. Friedberg and P. Hanawalt, eds. pp. 413–422. Alan R. Liss, New York.Google Scholar
  75. Triman, K. L., D. K. Chattoraj, and G. R. Smith. 1982. Identity of a Chi site of Escherichia coli and Chi recombinational hotspots of bacteriophage lambda. J. Mol. Biol. 154:393–399.PubMedCrossRefGoogle Scholar
  76. Wahls, W. P., G. Swenson, and P. D. Moore. 1991. Two hypervariable minisatellite DNA binding proteins. Nucl. Acids Res. 19:3269–3274.PubMedCrossRefGoogle Scholar
  77. Wahls, W. P., L. J. Wallace, and P. D. Moore. 1990. Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells. Cell 60:95–103.PubMedCrossRefGoogle Scholar
  78. Weichenhan, D. and W. Wackernagel. 1989. Functional analyses of Proteus mirabilis wild-type and mutant RecBCD enzymes in Escherichia coli reveal a new mutant phenotype. Mol. Microbiol. 3:1777–1784.PubMedCrossRefGoogle Scholar
  79. Winans, S. C., S. J. Elledge, J. H. Krueger, and G. C. Walker. 1985. Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli. J. Bacteriol. 161:1219–1221.PubMedGoogle Scholar
  80. Wyatt, R. T., R. A. Rudders, A. Zelenetz, R. A. Delellis, and T. G. Krontiris. 1992. BCL2 oncogene translocation is mediated by a χ-like consensus. J. Exp. Med. 175:1575–1588.PubMedCrossRefGoogle Scholar
  81. Zaman, M. M. and T. C. Boles. 1994. Chi-dependent formation of linear plasmid DNA in exonuclease-deficient recBCD + strains of Escherichia coli. J. Bacteriol. 176:5093–5100.PubMedGoogle Scholar

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© Springer Science+Business Media New York 1998

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  • Gerald R. Smith

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