Site‐specific Recombination in Chromosome Function


Site‐specific recombination leads to the integration, deletion or inversion of defined DNA segments by conservative breakage–rejoining reactions at defined recombination sites. It functions to integrate and excise extrachromosomal elements into and out of genomes, to maintain circular replicons at the correct copy number in a monomeric state, and to mediate inversion gene switches.

Keywords: site‐specific recombination; resolvase; invertase; integrase

Figure 1.

(a) Schematic of the recombination core sites of a serine and tyrosine recombinase (not to scale). The 2‐bp and 6–8‐bp central (overlap) regions lie between the sites of recombinase‐mediated cleavage (arrows). Recombinase molecules are depicted as ovoids containing their respective nucleophiles. (b) Organization of the bacteriophage λ attP and attB recombination sites. Recombinase‐binding sites are indicated by arrows (solid lines for core binding and dashed lines for binding to the accessory sequence arms P and P′; different regions of the recombinases contact these different types of site). Binding sites for the accessory proteins IHF, FIS and Xis are also indicated. Recombination between attP and attB generates attL (P′ plus core) and attR (P plus core).

Figure 2.

Outcomes of site‐specific recombination.

Figure 3.

Role of accessory sequences and proteins in resolution and inversion selectivity. (a) The recombination site for Tn3 and γδ resolvase contains a core site (site I) and two adjacent accessory sites (sites II and III). All three sites bind two molecules of resolvase. Recombination occurs at site I, and resolvase bound at sites II and III acts as an accessory protein that entraps three plectonemic supercoils. Intramolecular recombination between two directly repeated (DR) sites forms a −2 catenane recombinant product. The specific geometry of the synapse restricts recombination to intramolecular events between directly repeated molecules. (b) Schematic of synapsed directly repeated (DR) cer sites, the substrate for recombination by XerCD. In this case the accessory sequences (AS) are bound by ArgR and PepA. A −4 catenane results from recombination. In reality, the recombination sites may synapse in a close to antiparallel orientation, making an extra node entrapped between the recombination sites in addition to the three shown. (c) Schematic of synapsed inverted (IR) gix sites, the substrate for Gin invertase. Binding of the accessory protein, FIS to a distant enhancer site (E), entraps two negative supercoils, and thereby ensures inversion selectivity.

Figure 4.

(a) Reaction pathway for serine recombinases. (b) Reaction pathway for tyrosine recombinases. (c) Chemistry of serine recombinase‐mediated site‐specific recombination. (d) Chemistry of tyrosine recombinase‐mediated site‐specific recombination.

Figure 5.

Three strategies for Hin, Gin and Fim invertase‐mediated gene switches. Inverted recombination sites are shown as horizontal arrows. Promoters and their transcripts are shown by p (promoter) followed by a zig‐zag line indicating the transcript.



Cox MM, Goodman MF, Kreuzer KN et al. (2000) The importance of repairing stalled replication forks. Nature 404: 37–41.

Futcher AB (1986) Copy number amplification of the 2 micron plasmid of Saccharomyces cerevisiae. Journal of Theoretical Biology 119: 197–204.

Gopaul DN and Van Duyne G (1999) Structure and mechanism in site‐specific recombination. Current Opinion in Structural Biology 9: 14–20.

Guo F, Gopaul DN and Van Guyne GD (1997) Structure of Cre recombinase complexed with DNA in a site‐specific recombination synapse. Nature 389: 40–46.

Hall RM, Collis CM, Kim M‐J et al. (1999) Mobile gene cassettes and integrons in evolution. Annals of the New York Academy of Sciences 870: 68–80.

Haselkorn R (1992) Developmentally regulated gene rearrangements in prokaryotes. Annual Review of Genetics 26: 113–130.

Landy A (1989) Dynamic, structural and regulatory aspects of lambda site‐specific recombination. Annual Review of Biochemistry 58: 913–949.

Shapiro JA (1979) Molecular model for the transposition of bacteriophage Mu and other transposable elements. Proceedings of the National Academy of Sciences of the USA 76: 1933–1937.

Sherratt DJ and Wigley DB (1998) Conserved themes but novel activities in recombinases and topoisomerases. Cell 93: 149–152.

Sherratt DJ, Arciszewska LK, Blakely G et al. (1995) Site‐specific recombination and circular chromosome segregation. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 347: 37–42.

Stark WM and Boocock MR (1995 Topological selectivity in site‐specific recombination. In: Sherratt DJ (ed.) Mobile Genetic Elements, pp. 101–1129. Oxford: IRL.

Thorpe H and Smith MCM (1998) In vitro site‐specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proceedings of the National Academy of Sciences of the USA 95: 5505–5510.

Yang W and Steitz TA (1995) Crystal structure of the site‐specific recombinase resolvase complexed with a 34 bp cleavage site. Cell 82: 193–207.

Further Reading

Hallet B and Sherratt DJ (1997) Transposition and site‐specific recombination: adapting DNA cut‐and‐paste mechanisms to a variety of genetic rearrangements. FEMS Microbiology Reviews 21: 157–178.

Nash HA (1996) Site‐specific recombination: integration, excision, resolution, and inversion of defined DNA segments. In: Neidhart FE, Curtiss III R, Ingraham JL et al. (eds) Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology, pp. 2363–2376. Washington DC: ASM Press.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Sherratt, David J(Apr 2001) Site‐specific Recombination in Chromosome Function. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0001499]