Skip to main content

Part of the book series: Topics in Current Genetics ((TCG,volume 17))

Abstract

Site-specific recombination is a reaction in which a pair of genetically defined sites undergoes reciprocal exchange (“crossing-over”) via a recombinase-mediated DNA breakage and joining process. Such reactions have a wide range of biological outcomes, from integration and excision of virus genomes into and out of host chromosomes, to acquisition of novel genes and drug resistance, and even facilitating bacterial chromosome segregation. Two distinct families of recombinases exist, designated by their active site residues. In both these families recombination is carried out by a core of four recombinase monomers acting at two synapsed DNA sites. In many cases additional recombinase monomers and/or accessory proteins act at adjacent DNA sites to facilitate synapsis and often play a critical role in determining reaction topology. Here, the mechanism of site-specific recombination reactions is examined for both site-specific recombinase families, as well as for related proteins that mediate variant reactions, such as integrons and the integrases of conjugative transposons.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abbani M, Iwahara M, Clubb RT (2005) The structure of the excisionase (Xis) protein from conjugative transposon Tn916 provides insights into the regulation of heterobiva-lent tyrosine recombinases. J Mol Biol 347:11–25

    Article  CAS  PubMed  Google Scholar 

  • Abremski K, Hoess R (1984) Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J Biol Chem 259:1509–1514

    CAS  PubMed  Google Scholar 

  • Akopian A, He J, Boocock MR, Stark WM (2003) Chimeric recombinases with designed DNA sequence recognition. Proc Natl Acad Sci USA 100:8688–8691

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Arciszewska LK, Grainge I, Sherratt DJ (1997) Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J 16:731–743

    Article  Google Scholar 

  • Arnold PH, Blake DG, Grindley NDF, Boocock MR, Stark WM (1999) Mutants of Tn3 resolvase, which do not require accessory binding sites for recombination activity. EMBO J 18:1407–1414

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Azaro MA, Landy A (1997) The isomeric preference of Holliday junctions influences resolution bias by lambda integrase. EMBO J 16:3744–3755

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Azaro MA, Landy A (2002) The integration/excision cycle of lambda and other bacteriophages. In, NL Craig, R Craigie, M Gellert, A Lambowitz (eds.), Mobile DNA II. ASM Press, Washington, DC, pp. 117–148

    Google Scholar 

  • Baba T, Ara T, Okumura Y, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 inframe, single-gene knockout mutants-the Keio collection. Mol Syst Biol doi:10.1038/msb4100050

    Google Scholar 

  • Burgess SM, Kleckner N (1999) Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. Genes Dev 13:1871–1883

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bigot S, Saleh OA, Lesterlin C, Pages C, El Karoui M, Dennis C, Grigoriev M, Allemand JF, Barre FX, Cornet F (2005) KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase. EMBO J 24:3770–3780

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger, T (2005) A structural basis for allosteric control of DNA recombination by lambda integrase. Nature 435:1059–1066

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Blakely G, Colloms S, May G, Burke M, Sherratt D (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol 3:789–798

    CAS  PubMed  Google Scholar 

  • Bode J, Schlake T, Iber M, Schubeler D, Seibler J, Snezhkov E, Nikolaev L (2000) The transgeneticist’s toolbox: novel methods for the targeted modification of eukaryotic genomes. Biol Chem 381:801–813

    Article  CAS  PubMed  Google Scholar 

  • Boocock MR, Zhu X, Grindley ND (1995) Catalytic residues of gamma delta resolvase act in cis. EMBO J 14:5129–5140

    CAS  PubMed Central  PubMed  Google Scholar 

  • Buchholz F, Angrand PO, Stewart AF (1998) Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat Biotechnol 16:657–662

    Article  CAS  PubMed  Google Scholar 

  • Burns LS, Smith SG, Dorman CJ (2000) Interaction of the FimB integrase with the fimS invertible DNA element in Escherichia coli in vivo and in vitro. J Bacteriol 82:2953–2959

    Article  Google Scholar 

  • Chen Y, Narendra U, Iype L E, Cox MM, Rice PA (2000) Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol Cell 6:885–897

    CAS  PubMed  Google Scholar 

  • Chen Y, Rice P (2003) New insight into site-specific recombination from Flp recombinase-DNA structures. Annu Rev Biophys Biomol Struct 32:135–159

    Article  CAS  PubMed  Google Scholar 

  • Cheng C, Kussie P, Pavletich N, Shuman S (1998) Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92:841–850

    Article  CAS  PubMed  Google Scholar 

  • Collis CM, Kim MJ, Stokes HW, Hall RM (1998) Binding of the purified integron DNA integrase Intl1 to integron-and cassette associated recombination sites. Mol Microbiol 29:477–490

    Article  CAS  PubMed  Google Scholar 

  • Cornet F, Mortier I, Patte J, Louarn JM (1994) Plasmid pSC101 harbors a recombination site, psi, which is able to resolve plasmid multimers and to substitute for the analogous chromosomal Escherichia coli site dif. J Bacteriol 176:3188–195

    CAS  PubMed Central  PubMed  Google Scholar 

  • Crellin PK, Rood JI (1997) The resolvase/invertase domain of the site-specific recombinase TnpX is functional and recognizes a target sequence that resembles the junction of the circular form of the Clostridium perfringens transposon Tn4451. J Bacteriol 179:5148–5156

    CAS  PubMed Central  PubMed  Google Scholar 

  • Dhar G, Sanders ER, Johnson RC (2004) Architecture of the Hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands. Cell 119:33–45

    Article  CAS  PubMed  Google Scholar 

  • Esposito D, Scocca JJ (1997) The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res 25:3605–3614

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Espeli O, Lee C, Marians KJ (2003) A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. J Biol Chem 278:44639–44644

    Article  CAS  PubMed  Google Scholar 

  • Francia MV, Zabala JC, de la Cruz F, Garcia-Lobo JM (1999) The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site. J Bacteriol 181:6844–6849

    CAS  PubMed Central  PubMed  Google Scholar 

  • Futcher AB (1986) Copy number amplification of the 2 micron circle plasmid of Saccharomyces cerevisiae. J Theor Biol 119:197–204

    Article  CAS  PubMed  Google Scholar 

  • Gally DL, Leathart J, Blomfield IC (1996) Interaction of FimB and FimE with the fim switch that controls the phase variation of type 1 fimbriae in Escherichia coli K-12. Mol Microbiol 21:725–738

    Article  CAS  PubMed  Google Scholar 

  • Golic, MM, Golic KG (1996) A quantitative measure of the mitotic pairing of alleles in Drosophila melanogaster and the influence of structural heterozygosity. Genetics 143:385–400

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gopaul DN, Guo F, Van Duyne GD (1998) Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J 17:4175–4187

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Guo F, Gopaul DN, van Duyne GD (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389:40–46

    Article  CAS  PubMed  Google Scholar 

  • Gravel A, Fournier B, Roy PH (1998) DNA complexes obtained with the integron integrase IntI1 at the attI1 site. Nucleic Acids Res 26:4347–4355

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hall RM, Collis CM (1995) Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 15:593–600

    Article  CAS  PubMed  Google Scholar 

  • Hickman AB, Waninger S, Scocca JJ, Dyda F (1997) Molecular organization in sitespecific recombination: the catalytic domain of bacteriophage HP1 integrase at 2. 7 A resolution. Cell 89:227–237

    Article  CAS  PubMed  Google Scholar 

  • Hildebrandt ER, Cozzarelli NR (1995) Comparison of recombination in vitro and in E. coli cells: Measure of the effective concentration of DNA in vivo. Cell 81:331–340

    Article  CAS  PubMed  Google Scholar 

  • Hoess R, Ziese M, Sternberg N (1982) P1 Site-specific recombination: nucleotide sequence of the recombining sites. Proc Natl Acad Sci USA 79:3398–3402

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Huang WM, Joss L, Hsieh T, Casjens S (2004) Protelomerase uses a topoisomerase IB/Yrecombinase type mechanism to generate DNA hairpin ends. J Mol Biol 337:77–92

    Article  CAS  PubMed  Google Scholar 

  • Huber KE, Waldor MK (2002) Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417:656–659

    Article  CAS  PubMed  Google Scholar 

  • Ip SC, Bregu M, Barre FX, Sherratt DJ (2003) Decatenation of DNA circles by FtsK-dependent Xer site-specific recombination. EMBO J 22:6399–6407

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kersulyte D, Mukhopadhyay AK, Shirai M, Nakazawa T, Berg DE (2000) Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J Bacteriol 182:5300–5305

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kobryn K, Chaconas G (2001) The circle is broken: telomere resolution in linear replicons. Curr Opin Microbiol 4:558–564

    Article  CAS  PubMed  Google Scholar 

  • Kobryn K, Chaconas G (2002) ResT, a telomere resolvase encoded by the Lyme disease spirochete Mol Cell 9:195–201

    Article  CAS  PubMed  Google Scholar 

  • Kobryn K, Burgin AB, Chaconas G (2005) Uncoupling the chemical steps of telomere resolution by ResT. J Biol Chem 280:26788–26795

    Article  CAS  PubMed  Google Scholar 

  • Kuempel PL, Henson JM, Dircks L, Tecklenburg M, Lim DF (1991) dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli. New Biol 3:799–811

    CAS  PubMed  Google Scholar 

  • Kwon HJ, Tirumalai R, Landy A, Ellenberger T (1997) Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science 276:126–131

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lee J, Whang I, Lee J, Jayaram M (1994) Directed protein replacement in recombination full sites reveals trans-horizontal DNA cleavage by Flp recombinase. EMBO J 13:5346–5354

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee J, Jayaram M (1995) Role of partner homology in DNA recombination. Complementary base pairing orients the 5’-hydroxyl for strand joining during Flp sitespecific re-combination. J Biol Chem 270:4042–4052

    Article  CAS  PubMed  Google Scholar 

  • Lee J, Jayaram M, Grainge I (1999) Wild-type Flp recombinase cleaves DNA in trans. EMBO J 18:784–791

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, Bustamante C, Cozzarelli NR (2005) Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci USA 102:17618–17623

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Letzelter C, Duguet M, Serre M (2004) Mutational analysis of the archaeal tyrosine recombinase SSV1 untegrase suggests a mechanism of DNA cleavage in trans. J Biol Chem 279:28936–28944

    Article  CAS  PubMed  Google Scholar 

  • Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (2005) Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs. Science 309:1210–1215

    Article  CAS  PubMed  Google Scholar 

  • McCulloch R, Coggins LW, Colloms SD, Sherratt DJ (1994) Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo. EMBO J 13:1844–1855

    CAS  PubMed Central  PubMed  Google Scholar 

  • McIlwraith MJ, Boocock MR, Stark WM (1997) Tn3 resolvase catalyses multiple recombination events without intermediate rejoining of DNA ends. J Mol Biol 266:108–121

    Article  CAS  PubMed  Google Scholar 

  • Merickel SK, Haykinson MJ, Johnson RC (1998) Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion. Genes Dev 12:2803–2816

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nöllman M, He J, Byron O, Stark WM (2004) Solution structure of the Tn3 resolvasecrossover site synaptic complex. Mol Cell 16:127–137

    Article  Google Scholar 

  • Nünes-Duby SE, Azaro MA, Landy A (1995) Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr Biol 5:139–148

    Article  PubMed  Google Scholar 

  • Pease PJ, Levy O, Cost GJ, Gore J, Ptacin JL, Sherratt D, Bustamante C, Cozzarelli NR (2005) Sequence-directed DNA translocation by purified FtsK. Science 307:586–590

    Article  CAS  PubMed  Google Scholar 

  • Radman-Livaja M, Biswas T, Ellenberger T, Landy A, Aihara H (2006) DNA arms do the legwork to ensure the directionality of lambda site-specific recombination. Curr Opin Struct Biol 16: in press

    Google Scholar 

  • Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279:1504–1513

    Article  CAS  PubMed  Google Scholar 

  • Rowe-Magnus DA, Guerout A-M, Ploncard P, Dychinco B, Davies J, Mazel D (2001) The evolutionary history of chromosomal super-integrons provides an ancestry for multi-resitant integrons. Proc Natl Acad Sci USA 98:652–657

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sauer B (1998) Inducible gene targeting in mice using the Cre/lox system. Methods Enzymol 14:381–392

    Article  CAS  Google Scholar 

  • Senecoff JF, Cox MM (1986) Directionality in FLP protein-promoted site-specific recombination is mediated by DNA-DNA pairing. J Biol Chem 261:7380–7386

    CAS  PubMed  Google Scholar 

  • Sherratt DJ, Arciszewska LK, Blakely G, Colloms S, Grant K, Leslie N, McCulloch R (1995) Site-specific recombination and circular chromosome segregation. Philos Trans R Soc Lond B Biol Sci 347:37–42

    Article  CAS  PubMed  Google Scholar 

  • Smith MCM, Thorpe HM (2002) Diversity in the serine recombinases. Mol Micro 44:299–307

    Article  CAS  Google Scholar 

  • Smith SG, Dorman CJ (1999) Functional analysis of the FimE integrase of Escherichia coli K-12: isolation of mutant derivatives with altered DNA inversion preferences. Mol Microbiol 34:965–979

    Article  CAS  PubMed  Google Scholar 

  • Stark WM, Boocock MR, Sherratt DJ (1989) Site-specific recombination by Tn3 resolvase. Trends Genet 5:304–309

    Article  CAS  PubMed  Google Scholar 

  • Stark M, Grindley ND, Hatfull GF, Boocock MR (1991) Resolvase-catalysed reactions between res sites differing in the central dinucleotide of subsite I. EMBO J 10:3541–3548

    CAS  PubMed Central  PubMed  Google Scholar 

  • Staczek P, Higgins NP (1998) Gyrase and Topo IV modulate chromosome domain size in vivo. Mol Microbiol 29:1435–1448

    Article  CAS  PubMed  Google Scholar 

  • Subramanya HS, Arciszewska LK, Baker RA, Bird LE, Sherratt DJ, Wigley DB (1997) Crystal structure of the site-specific recombinase, XerD. EMBO J 16:5178–187

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Summers DK, Sherratt DJ (1984) Multimerization of high copy number plasmids causes instability: CoIE1 encodes a determinant essential for plasmid monomerization and stability. Cell 36:1097–1103

    Article  CAS  PubMed  Google Scholar 

  • Thorpe HM, Smith MCM (1998) In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proc Natl Acad Sci USA 95:5505–5510

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Val ME, Bouvier M, Campos J, Sherratt D, Cornet F, Mazel D, Barre FX (2005) The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae. Mol Cell 19:559–566

    Article  CAS  PubMed  Google Scholar 

  • van de Putte P, Goosen N (1992) DNA inversions in phages and bacteria. Trends Genet 8:457–462

    Article  PubMed  Google Scholar 

  • Wang H, Mullany P (2000) The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. J Bacte-riol 182:6577–6583

    Article  CAS  Google Scholar 

  • Wojciak JM, Connolly KM, Clubb RT (1999) NMR structure of the Tn916 integrase-DNA complex. Nat Struct Biol 6:366–373

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Grainge, I., Sherratt, D.J. (2007). Site-specific recombination. In: Aguilera, A., Rothstein, R. (eds) Molecular Genetics of Recombination. Topics in Current Genetics, vol 17. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71021-9_15

Download citation

Publish with us

Policies and ethics