Resolvase-Mediated Site-Specific Recombination

  • N. D. F. Grindley
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 8)


Conservative site-specific recombination involves the reciprocal exchange of DNA segments by precise breakage and rejoining processes that involve no loss or synthesis of DNA. In principle, such events can occur intermolecularly (resulting in fusion of the two recombining partners) or intramolecularly (resulting in inversion or excision of one DNA segment relative to the other), although in most biological systems this directionality is strictly controlled. Biological roles of site-specific recombination include chromosomal integration and excision of phage genomes, monomerization of plasmid chromosomes, alternation of gene expression, resolution of transposition intermediates, and fusion of gene cassettes into a functional gene.


Recombination Site Strand Exchange Synaptic Complex Crossover Site Half Twist 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Abdel-Meguid SS, Grindley NDF, Templeton NS, Steitz TA (1984) Cleavage of the site-specific recombination protein γδ resolvase; the smaller fragment binds DNA specifically. Proc Natl Acad Sci USA 81:2001–2005PubMedCrossRefGoogle Scholar
  2. Bednarz AL, Boocock MR, Sherratt DJ (1990) Determinants of correct res site alignment in site-specific recombination by Tn3 resolvase. Genes Dev 4:2366–2375PubMedCrossRefGoogle Scholar
  3. Benjamin HW, Cozzarelli NR (1986) Site-directed synapsis in recombination: slithering and random collision of sites. In: Proceedings of the Robert A. Welch Foundation Conferences on Chemical Research. XXIX. Genetic Chemistry: The Molecular Basis of Heredity. Robert A Welch Foundation, Houston, TX, pp 107–126Google Scholar
  4. Benjamin HW, Cozzarelli NR (1988) Isolation and charaterization of the Tn3 synaptic intermediate. EMBO J 7:1897–1905PubMedGoogle Scholar
  5. Benjamin HW, Cozzarelli NR (1990) Geometric arrangements of Tn3 resolvase sites. J Biol Chem 265:6441–6447PubMedGoogle Scholar
  6. Boocock MR, Brown JL, Sherratt DJ (1986) Structural and catalytic properties of specific complexes between the Tn3 resolvase and the recombination site, res. Biochem Soc Trans 14:214–216PubMedGoogle Scholar
  7. Boocock MR, Brown JL, Sherratt DJ (1987) Topological specificity of Tn3 resolvase catalysis. In: Kelly TJ, McMacken R (eds) DNA replication and recombination. Alan R Liss, New York, pp 703–718Google Scholar
  8. Chen JW, Lee J, Jayaram M (1992) DNA cleavage in trans by the active site tyrosine during Flp recombination: switching protein partners before exchanging strands. Cell 69:647–658PubMedCrossRefGoogle Scholar
  9. Chen JW, Yang SH, Jayaram M (1993) Tests for the fractional active-site model in Flp site-specific recombination. J Biol Chem 268:14417–14425PubMedGoogle Scholar
  10. Cox MM (1989) DNA inversion in the 2μm plasmid Saccharomyces cerevisiae. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, DC, pp 661–670Google Scholar
  11. Cozzarelli NR, Krasnow MA, Gerrard SP, White JH (1984) A topological treatment of recombination and topoisomerases. Cold Spring Harbor Symp Quant Biol 49:383–400PubMedGoogle Scholar
  12. Craig NL (1988) The mechanism of conservative site-specific recombination. Annu Rev Genet 22:77–105PubMedCrossRefGoogle Scholar
  13. Dodd HM, Bennett PM (1987) The R46 site-specific recombination system is a homologue of the Tn3 and γδ (Tn1000) cointegrate resolution system. J Gen Microbiol 133:2031–2039PubMedGoogle Scholar
  14. Dröge P, Hatfull GF, Grindley NDF, Cozzarelli NR (1990) The two functional domains of γδ resolvase act on the same recombination site: implications for the mechanism of strand exchange. Proc Natl Acad Sci USA 87:5336–5340PubMedCrossRefGoogle Scholar
  15. Feng J-A, Johnson RC, Dickerson RE (1994) Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. Science 263:348–355PubMedCrossRefGoogle Scholar
  16. Garnier T, Saurin W, Cole ST (1987) Molecular characterization of the resolvase gene res carried by a multicopy plasmid from Clostridium perfringens: common evolutionary origin for prokaryotic site-specific recombinases. Mol Microbiol 1:371–376PubMedCrossRefGoogle Scholar
  17. Gerlitz M, Hrabak O, Schwab H (1990) Partitioning of broad-host range plasmid RP4 is a complex system involving site specific recombination. J Bacteriol 172:6194–6203PubMedGoogle Scholar
  18. Glasgow AC, Hughes KT, Simon MI (1989) Bacterial DNA inversion systems. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, DC, pp 637–659Google Scholar
  19. Graham KS, Dervan PB (1990) Structural motif of the DNA binding domain of γδ resolvase characterized by affinity cleaving. J Biol Chem 265:16534–16540PubMedGoogle Scholar
  20. Grindley NDF (1993) Dissection of a macromolecular nucleoprotein complex: unequal roles for γδ resolvase within the synaptosome. Science 262:738–740PubMedCrossRefGoogle Scholar
  21. Hall SC, Haiford SE (1993) Specificity of DNA recognition in the nucleoprotein complex for site-specific recombination by Tn21 resolvase. Nucleic Acids Res. 21:5712–5719PubMedCrossRefGoogle Scholar
  22. Hatfull GF, Grindley NDF (1986) Analysis of γδ resolvase mutants in vitro: evidence for an interaction between serine-10 of resolvase and site I of res. Proc Natl Acad Sci USA 82:5429–5433CrossRefGoogle Scholar
  23. Hatfull GF, Grindley NDF (1988) Resolvases and DNA-invertases: a family of enzymes active in site-specific recombination. In: Kucherlapati R, Smith GR (eds) Genetic recombination. American Society for Microbiology, Washington, DC, pp 37–396Google Scholar
  24. Hatfull GF, Noble SN, Grindley NDF (1987) The γδ resolvase induces an unusual DNA structure at the recombinational crossover point. Cell 49:103–110PubMedCrossRefGoogle Scholar
  25. Hatfull GF, Salvo JJ, Falvey EE, Rimphanitchayakit V, Grindley NDF (1988) Site specific recombination by the γδ resolvase. In: Kingsman AJ, Kingsman SM, Chater KF (eds) Transposition. Society for General Microbiology Symposium 43, Cambridge University Press, Cambridge, pp 149–181Google Scholar
  26. Hatfull GF, Sanderson MR, Freemont PS, Raccuia PR, Grindley NDF, Steitz TA (1989) Preparation of heavy atom derivatives using site-directed mutagenesis: introduction of cysteine residues into γδ resolvase. J Mol Biol 208:661–667PubMedCrossRefGoogle Scholar
  27. Heichman KA, Moskowitz IPG, Johnson RC (1991) Configuration of DNA strands and mechanism of strand exchange in the Hin invertasome as revealed by analysis of recombinant knots. Genes Dev 5:1622–1634PubMedCrossRefGoogle Scholar
  28. Hughes RE, Hatfull GF, Rice P, Steitz TA, Grindley NDF (1990) Cooperativity mutants of the γδ resolvase identify an essential inter-dimer interaction. Cell 63:1331–1338PubMedCrossRefGoogle Scholar
  29. Hughes RE, Rice PA, Steitz TA, Grindley NDF (1993) Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis. EMBO J 12:1447–1458PubMedGoogle Scholar
  30. Jeltsch A, Alves J, Wolfes H, Maass G, Pingoud A (1993) Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes. Proc Natl Acad Sci USA 90:8499–8503PubMedCrossRefGoogle Scholar
  31. Johnson RC (1991) Mechanism of site-specific DNA inversion in bacteria. Curr Opinion Genet Dev 1:404–411CrossRefGoogle Scholar
  32. Kahmann R, Mertens G, Klippel A, Brauer B, Rudt F, Kock C (1987) The mechanism of G inversion. In: Kelly TJ, McMacken R (eds) DNA replication and recombination. Alan R Liss, New York, pp 681–690Google Scholar
  33. Kanaar R, van de Putte P, Cozzarelli NR (1988) Gin-mediated DNA inversion: product structure and the mechanism of strand exchange. Proc Natl Acad Sci USA 85:752–756PubMedCrossRefGoogle Scholar
  34. Kanaar R, Klippel A, Shekhtman E, Dungan JM, Kahmann R, Cozzarelli NR (1990) Processive recombination by the phage Mu Gin sytem: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62:353–366PubMedCrossRefGoogle Scholar
  35. Klippel A, Mertens G, Patschinsky T, Kahmann R (1988a) The DNA invertase Gin of phage Mu: formation of a covalent complex with DNA via a phosphoserine at amino acid position 9. EMBO J 1229–1237Google Scholar
  36. Klippel A, Cloppenborg K, Kahmann R (1988b) Isolation and characterization of unusual gin mutants. EMBO J 7:3983–3989PubMedGoogle Scholar
  37. Klippel A, Kanaar R, Kahmann R, Cozzarelli NR (1993) Analysis of strand exchange and DNA binding of enhancer-independent Gin recombinase mutants. EMBO J 12:1047–1057PubMedGoogle Scholar
  38. Krasnow MA, Cozzarelli NR (1983) Site-specific relaxation and recombination by Tn3 resolvase: recognition of the DNA path between orientated res sites. Cell 32:1313–1324PubMedCrossRefGoogle Scholar
  39. Krasnow MA, Stasiak A, Spengler SJ, Dean F, Koller T, Cozzarelli NR (1983) Determination of the absolute handedness of knots and catenanes of DNA. Nature 304:559–560PubMedCrossRefGoogle Scholar
  40. Landy A (1989) Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem 58:913–949PubMedCrossRefGoogle Scholar
  41. Mack DP, Sluka JP, Shin JA, Griffith JH, Simon MI Dervan PB (1990) Orientation of the putative recognition helix in the DNA binding domain of Hin recombinase complexed with the hix site. Biochemistry 29:6561–6567PubMedCrossRefGoogle Scholar
  42. Mazzarelli JM, Ermácora MR, Fox RO, Grindley NDF (1993) Mapping interactions between the catalytic domain of resolvase and its DNA substrate using cysteine-coupled EDTA-iron. Biochemistry 260:2979–2986CrossRefGoogle Scholar
  43. Mizuuchi K, Geliert M, Weisberg RA, Nash HA (1980) Catenation and supercoiling in the products of phage λ integrative recombination in vitro. J Mol Biol 141:485–494PubMedCrossRefGoogle Scholar
  44. Newman BJ, Grindley NDF (1984) Mutants of the γδ resolvase, a genetic analysis of the recombination function. Cell 38:463–469PubMedCrossRefGoogle Scholar
  45. Parker CN, Halford SE (1991) Dynamics of long range interactions on DNA: the speed of synapsis during site-specific recombination by resolvase. Cell 66:781–791PubMedCrossRefGoogle Scholar
  46. Reed RR, Grindley NDF (1981) Transposon-mediated site-specific recombination in vitro: DNA cleavage and protein-DNA linkage at the recombination site. Cell 25:721–728PubMedCrossRefGoogle Scholar
  47. Reed RR (1981) Transposon-mediated site-specific recombination: a defined in vitro system. Cell 25:713–719PubMedCrossRefGoogle Scholar
  48. Reed RR, Moser CD (1984) Resolvase-mediated recombination intermediates involve a serine-DNA linkage. Cold Spring Harbor Symp Quant Biol 49:245–249PubMedGoogle Scholar
  49. Rice PA, Steitz TA (1994a) Model for a DNA-mediated synaptic complex suggested by crystal packing of γδ resolvase subunits. EMBO J 13:1514–1524PubMedGoogle Scholar
  50. Rice PA, Steitz TA (1994b) Refinement of γδ resolvase reveals a striking flexible molecule. Structure (in press)Google Scholar
  51. Rimphanitchayakit V, Grindley NDF (1990) Saturation mutagenesis of the DNA site bound by the small carboxy-terminal domain of γδ resolvase. EMBO J 9:719–725PubMedGoogle Scholar
  52. Rimphanitchayakit V, Hatfull GF, Grindley NDF (1989) The 43 residue DNA binding domain of γδ resolvase binds adjacent major and minor grooves of DNA. Nucleic Acids Res 17:1035–1050PubMedCrossRefGoogle Scholar
  53. Rowland S-J, Dyke KGH (1989) Characterization of the staphylococcal β-lactamase transposon, Tn552. EMBO J 8:2761–2773PubMedGoogle Scholar
  54. Sadowski P (1986) Site-specific recombinases: changing partners and doing the twist. J Bacteriol 165:341–347PubMedGoogle Scholar
  55. Saenger W, Sandmann C, Theis K, Stainhov EB, Kostewa D, Labalim J, Grantin J (1993) Structural and functional aspects of the DNA binding protein FIS, In: Eckstein F, Lilley DMJ (eds) Nucleic Acids and Molecular Biology, vol 7. Springer, Berlin Heidelberg New York, pp 159–169Google Scholar
  56. Salvo JJ, Grindley NDF (1988) Resolvase bends the res site into a recombinogenic complex. EMBO J 7:3609–3616PubMedGoogle Scholar
  57. Sanderson MR, Freemont PS, Rice P, Goldman A, Hatfull GF, Grindley NDF, Steitz TA (1990) The crystal structure of the catalytic domain of the site-specific recombination enzyme γδ resolvase at 2.7 Å resolution. Cell 63:1323–1329PubMedCrossRefGoogle Scholar
  58. Sato T, Samori Y, Kobayashi Y (1990) The cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologous to a site-specific recombinase. J Bacteriol 172:1092–1098PubMedGoogle Scholar
  59. Sherratt D (1989) Tn3 and related transposable elements: site-specific recombination and transposition. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, DC, pp 163–184Google Scholar
  60. Sluka JP, Horvath SJ, Glasgow AC, Simon MI, Dervan PD (1990) Importance of minor groove contacts for recognition of DNA by the binding domain of Hin recombinase. Biochemistry 29:6551–6561PubMedCrossRefGoogle Scholar
  61. Stark WM, Boocock MR (1994) The linkage change of a knotting reaction catalysed by Tn3 resolvase. J Mol Biol (in press)Google Scholar
  62. Stark WM, Sherratt DJ, Boocock MR (1989a) Site-specific recombination by Tn3 resolvase. Trends Genet 5:304–309PubMedCrossRefGoogle Scholar
  63. Stark WM, Sherratt DJ, Boocock MR (1989b) Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58:779–790PubMedCrossRefGoogle Scholar
  64. Stark WM, Grindley NDF, Hatfull GF, Boocock MR (1991) Resolvase-catalysed reactions between res sites differing in the central dinucleotide of substite I. EMBO J 10:3541–3548PubMedGoogle Scholar
  65. Stark WM, Boocock MR, Sherratt DJ (1992) Catalysis by site-specific recombinases. Trends Genet 8:432–439PubMedCrossRefGoogle Scholar
  66. Stragier P, Kunkel B, Kroos L, Losick R (1989) Chromosomal rearrangement generating a composite gene for a developmental transcription factor. Science 243:507–512PubMedCrossRefGoogle Scholar
  67. Wasserman SA, Cozzarelli NR (1985) Determination of the stereo structure of the product of Tn3 resolvase by a general method. Proc Natl Acad Sci USA 82:1079–1083PubMedCrossRefGoogle Scholar
  68. Wasserman SA, Dungan JM, Cozzarelli NR (1985) Discovery of a predicted DNA knot substantiates a model for site-specific recombination. Science 229:171–174PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1994

Authors and Affiliations

  • N. D. F. Grindley
    • 1
  1. 1.Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUSA

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