Book contents
- Frontmatter
- Contents
- List of Contributors
- PART 1 Basic Mechanisms of Genome Rearrangement in Bacteria
- 1 Mechanisms of homologous recombination in bacteria
- 2 Introduction to site-specific recombination
- 3 Site-specific recombination by the serine recombinases
- 4 Mobile introns and retroelements in bacteria
- PART 2 Horizontal Gene Transfer and Genome Plasticity
- PART 3 Biological Consequences of the Mobile Genome
- Index
- Plate Section
- References
2 - Introduction to site-specific recombination
Published online by Cambridge University Press: 06 August 2009
Edited by
Book contents
- Frontmatter
- Contents
- List of Contributors
- PART 1 Basic Mechanisms of Genome Rearrangement in Bacteria
- 1 Mechanisms of homologous recombination in bacteria
- 2 Introduction to site-specific recombination
- 3 Site-specific recombination by the serine recombinases
- 4 Mobile introns and retroelements in bacteria
- PART 2 Horizontal Gene Transfer and Genome Plasticity
- PART 3 Biological Consequences of the Mobile Genome
- Index
- Plate Section
- References
Summary
Recombination provides a means for creating genetic variety. Exchange of information within gene pools expands their diversity and enhances the choices available for natural selection to act on. Recombination can be broadly divided into two classes: the highly pervasive “homologous” recombination and the more specialized “site-specific recombination.”
HOMOLOGOUS RECOMBINATION
Before we discuss site-specific recombination, a brief overview of general (or homologous) recombination is useful for an appreciation of the distinctions between the two systems. Homologous recombination is a nearly universal mechanism employed by living organisms to reshuffle their genetic information. Within a cell, recombination can occur between two homologous chromosomes, between two sister chromatids formed by DNA replication, and between extrachromosomal elements such as plasmids or viral genomes. In eukaryotes, the rate of recombination during mitosis is relatively low and is markedly increased during meiosis. In fact, genetic exchange between homologs and chiasma formation appear to be a prerequisite for the proper reductional segregation of chromosomes and the generation of haploid gametes. The consequences of the resulting genetic configuration and the corresponding fitness contribution to an individual will be manifested directly, and almost immediately, in a haploid organism. For a diploid organism, the expression of the novel genetic makeup must await the fusion between the male and female gametes to produce a zygote. Recombination is therefore one of the forces that drive Darwinian evolution.
- Type
- Chapter
- Information
- The Dynamic Bacterial Genome , pp. 33 - 82Publisher: Cambridge University PressPrint publication year: 2005
References
, , , and (1986). Bacteriophage P1 Cre-loxP site-specific recombination. Site-specific DNA topoisomerase activity of the Cre recombination protein. J Biol Chem 261, 391–396Google ScholarPubMed
, , , and (2000). Coordinated control of XerC and XerD catalytic activities during Holliday junction resolution. J Mol Biol 299, 391–403CrossRefGoogle ScholarPubMed
Azaro, M. A., and Landy, A. (2002). Lambda Integrase and the lambda Int family. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 118–148CrossRefGoogle Scholar
Baker, T. A., and Mizuuchi, K. (2002). Chemical mechanisms for mobilizing DNA. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 12–23CrossRefGoogle Scholar
Barre, F.-X., and Sherratt, D. J. (2002). Xer site-specific recombination: Promoting chromosome segregation. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 149–161CrossRefGoogle Scholar
Belfort, M., Derbyshire, V., Parker, M., Cousineau, B., and Lambowitz, A. M. (2002). Mobile introns: Pathways and proteins. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 761–783CrossRefGoogle Scholar
, and (1997). Homing endonucleases: Keeping the house in order. Nucleic Acids Res 25, 3379–3388CrossRefGoogle ScholarPubMed
, and (1996). Cis and trans in site-specific recombination. Mol Microbiol 20, 234–237CrossRefGoogle ScholarPubMed
, , and (1995). Catalytic residues of gamma delta resolvase act in cis. EMBO J 14, 5129–5140Google ScholarPubMed
, and (1991). Circular DNA plasmids of yeasts: The molecular biology of the yeast Saccharomyces. Genome dynamics, protein synthesis and energetics. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 279–331Google Scholar
, , and (1998). Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat Biotechnol 16, 657–662CrossRefGoogle ScholarPubMed
, , and (1995). Programmed DNA rearrangement of a cyanobacterial hupL gene in heterocysts. Proc Natl Acad Sci U S A 92, 791–795CrossRefGoogle ScholarPubMed
, (1990). Self-splicing of group I introns. Annu Rev Biochem, 59, 543–568CrossRefGoogle ScholarPubMed
, , and (1992). DNA cleavage in trans by the active site tyrosine during Flp recombination: Switching protein partners before exchanging strands. Cell 69, 647–658CrossRefGoogle ScholarPubMed
, , , , and (2000). Crystal structure of a Flp recombinase-Holliday junction complex: Assembly of an active oligomer by helix swapping. Mol Cell 6, 885–897Google ScholarPubMed
, and (1998). A catalytic domain of eukaryotic DNA topoisomerase I. J Biol Chem 273, 11589–11595CrossRefGoogle ScholarPubMed
Churchward, G. (2002). Conjugative transposons and related mobile elements. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 177–191CrossRefGoogle Scholar
, , and (1997). Topological selectivity in Xer site-specific recombination. Cell 88, 855–864CrossRefGoogle ScholarPubMed
, , and (1997). Xer recombination in Escherichia coli. Site-specific DNA topoisomerase activity of the XerC and XerD recombinases. J Biol Chem 272, 21927–21931CrossRefGoogle ScholarPubMed
Cozzarelli, N. R., Boles, T. C., and White, J. H. (1990). In and , eds. Primer on the topology and geometry of DNA supercoiling. In DNA topology and its biological effects (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 140–184Google Scholar
, , , and (1984). A topological treatment of recombination and topoisomerases. Cold Spring Harb Symp Quant Biol 49, 383–400CrossRefGoogle ScholarPubMed
Craig, N. L. (2002a). Mobile DNA: An introduction. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 1–11CrossRefGoogle Scholar
Craig, N. L. (2002b). Tn7. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 423–456CrossRefGoogle Scholar
Craigie, R. (2002). Retroviral DNA integration. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 613–629CrossRefGoogle Scholar
, , , , and (1999). The topological mechanism of phage lambda integrase. J Mol Biol 289, 747–775CrossRefGoogle ScholarPubMed
, , , and (2000). Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289, 77–85CrossRefGoogle ScholarPubMed
, , and (1994). Hin recombinase bound to DNA: The origin of specificity in major and minor groove interactions. Science 263, 348–355CrossRefGoogle ScholarPubMed
(1986). Copy number amplification of the 2 micron circle plasmid of Saccharomyces cerevisiae. J Theor Biol 119, 197–204CrossRefGoogle ScholarPubMed
Gellert, M. (2002). V(D)J recombination. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 705–729CrossRefGoogle Scholar
, , , and (2000). Structural homology between MarA of the AraC family of transcriptional activators and the integrase family of site-specific recombinases. Mol Microbiol 35, 1582–1583CrossRefGoogle ScholarPubMed
, , and (1998). Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J 17, 4175–4187CrossRefGoogle ScholarPubMed
, and (1999). Structure and mechanism in site-specific recombination. Curr Opin Struct Biol 9, 14–20CrossRefGoogle ScholarPubMed
, , and (2000). Geometry of site alignment during Int family recombination: Antiparallel synapsis by the Flp recombinase. J Mol Biol 298, 749–764CrossRefGoogle ScholarPubMed
, , , , and (2002). Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses. J Mol Biol 320, 515–527CrossRefGoogle ScholarPubMed
Grindley, N. D. F. (2002). The movement of Tn3-like elements: Transposition and cointegrate resolution. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 272–304CrossRefGoogle Scholar
(2000). Two tricks in one bundle: Helix-turn-helix gains enzymatic activity. Nucleic Acids Res 28, 2229–2233CrossRefGoogle ScholarPubMed
, , and (1997). Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389, 40–46CrossRefGoogle Scholar
, , and (1999). Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc Natl Acad Sci U S A 96, 7143–7148CrossRefGoogle ScholarPubMed
, , and (1999). Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: An enzymatic switch in site-specific recombination. Mol Cell 4, 949–959CrossRefGoogle ScholarPubMed
Haniford, D. (2002). Transposon Tn10. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 457–483CrossRefGoogle Scholar
, , , , , , and (2000). Crystal structure of NaeI–An evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J 19, 3110–3118CrossRefGoogle ScholarPubMed
Jayaram, M., Grainge, I., and Tribble, G. D. (2002). Site-specific recombination by the Flp protein of Saccharomyces cerevisiae. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 192–218CrossRefGoogle Scholar
Jayaram, M., Yang, X. M., Mehta, S., Voziyanov, Y., and Velmurugan, S. (2004). The 2 micron plasmid of Saccharomyces cerevisiae. In , ed. The biology of plasmids (Washington, DC, ASM Press), pp. 303–324Google Scholar
Johnson, R. C. (2002). Bacterial site-specific DNA inversion systems. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 230–271CrossRefGoogle Scholar
, , , , , and (1990). Processive recombination by the phage Mu Gin system: Implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62, 353–366CrossRefGoogle ScholarPubMed
, , and (2000). Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: Insights from phosphorothioate stereoselectivity. Cell 101, 295–305CrossRefGoogle ScholarPubMed
, , and (1999). Topological selectivity of a hybrid site-specific recombination system with elements from Tn3 res/resolvase and bacteriophage P1 loxP/Cre. J Mol Biol 289, 1219–1230CrossRefGoogle ScholarPubMed
, and (2000). Catalytic mechanism of DNA topoisomerase Ib. Mol Cell 5, 1035–1041CrossRefGoogle ScholarPubMed
, , and (1990). The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. Genes Dev 4, 525–535CrossRefGoogle ScholarPubMed
(1989). Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem 58, 913–949CrossRefGoogle ScholarPubMed
, and (1995). Role of partner homology in DNA recombination. Complementary base pairing orients the 5′-hydroxyl for strand joining during Flp site-specific recombination. J Biol Chem 270, 4042–4052CrossRefGoogle ScholarPubMed
, , and (1999). Wild-type Flp recombinase cleaves DNA in trans. EMBO J 18, 784–791CrossRefGoogle ScholarPubMed
, , and (1997). Mechanism of active site exclusion in a site-specific recombinase: Role of the DNA substrate in conferring half-of-the-sites activity. Genes Dev 11, 3061–3071CrossRefGoogle Scholar
, and (1995). Ligand-regulated site-specific recombination. Proc Natl Acad Sci U S A. 92, 5940–5944CrossRefGoogle ScholarPubMed
, and (2002). The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu Rev Biochem 71, 71–100CrossRefGoogle ScholarPubMed
(1992a). Polynucleotidyl transfer reactions in transpositional DNA recombination. J Biol Chem 267, 21273–21276Google Scholar
(1992b). Transpositional recombination: Mechanistic insights from studies of Mu and other elements. Annu Rev Biochem 61, 1011–1051CrossRefGoogle Scholar
, and (1991). Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: Evidence for a one-step transesterification mechanism. Cell 66, 129–140CrossRefGoogle ScholarPubMed
, , and (1995). Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr Biol 5, 139–148CrossRefGoogle ScholarPubMed
, , and (1993). Mechanism of cleavage and ligation by FLP recombinase: Classification of mutations in FLP protein by in vitro complementation analysis. Mol Cell Biol 13, 3167–3175CrossRefGoogle ScholarPubMed
, , , and (1988). Step-arrest mutants of FLP recombinase: Implications for the catalytic mechanism of DNA recombination. Mol Cell Biol 8, 3303–3310CrossRefGoogle ScholarPubMed
, , and (2002). Path of DNA within the Mu transpososome. Transposase interactions bridging two Mu ends and the enhancer trap five DNA supercoils. Cell 109, 425–436CrossRefGoogle ScholarPubMed
(1998). Protein splicing of inteins and hedgehog autoproteolysis: Structure, function, and evolution. Cell 92, 1–4CrossRefGoogle ScholarPubMed
(1993). Ribozymes: A distinct class of metalloenzymes. Science 261, 709–714CrossRefGoogle ScholarPubMed
Recchia, G. D., and Sherratt, D. J. (2002). Gene acquisition in bacteria by integron mediated site-specific recombination. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 162–176CrossRefGoogle Scholar
, , , , and (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279, 1504–1513CrossRefGoogle ScholarPubMed
Reznikoff, W. (2002). Tn5 transposition. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 403–422CrossRefGoogle Scholar
Rice, P. A. (2002). Theme and variation in tyrosine recombinases: Structure of a Flp-DNA complex. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 219–229CrossRefGoogle Scholar
, and (1994a). Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. EMBO J 13, 1514–1524Google Scholar
, and (1994b). Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure 2, 371–384CrossRefGoogle Scholar
, and (2002). Non-contact positions impose site selectivity on Cre recombinase. Nucleic Acids Res 30, 2764–2771CrossRefGoogle ScholarPubMed
, , , , , , and (1990). The crystal structure of the catalytic domain of the site-specific recombination enzyme gamma delta resolvase at 2.7 Åresolution. Cell 63, 1323–1329CrossRefGoogle Scholar
, and (2002). Directed evolution of the site specificity of Cre recombinase. Proc Natl Acad Sci U S A 99, 4185–4190CrossRefGoogle ScholarPubMed
, , , , , and (2001). Biochemical and kinetic analysis of the RNase active sites of the integrase/tyrosine family site-specific DNA recombinases. J Biol Chem 276, 46612–46623CrossRefGoogle ScholarPubMed
Sauer, B. (2002). Chromosome manipulation by Cre-lox recombination. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp 38–58CrossRefGoogle Scholar
, and (1997). Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I. Mol Cell 1, 89–97CrossRefGoogle ScholarPubMed
, and (1998). Conserved themes but novel activities in recombinases and topoisomerases. Cell 93, 149–152CrossRefGoogle ScholarPubMed
, , and (1989). Site-specific recombination by Tn3 resolvase: Topological changes in the forward and reverse reactions. Cell 58, 779–790CrossRefGoogle ScholarPubMed
, and (1993). A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci U S A 90, 6498–6502CrossRefGoogle ScholarPubMed
, , , , and (1998). A model for the mechanism of human topoisomerase I. Science 279, 1534–1541CrossRefGoogle ScholarPubMed
, , , , and (2000). Stereochemical outcome and kinetic effects of Rp- and Sp-phosphorothioate substitutions at the cleavage site of vaccinia type I DNA topoisomerase. Biochemistry 39, 5561–5572CrossRefGoogle ScholarPubMed
, , , and (1995). Analysis of the mechanism of DNA recombination using tangles. Q Rev Biophys 28, 253–313CrossRefGoogle ScholarPubMed
Van Duyne, G. (2002). A structural view of tyrosine recombinase site-specific recombination. In , , , and , eds. Mobile DNA II (Washington, DC, ASM Press), pp. 93–117CrossRefGoogle Scholar
, , and (1999). A general model for site-specific recombination by the integrase family recombinases. Nucleic Acids Res 27, 930–941CrossRefGoogle ScholarPubMed
, , and (2002). A dual reporter screening system identifies the amino acid at position 82 in Flp site-specific recombinase as a determinant for target specificity. Nucleic Acids Res 30, 1656–1663CrossRefGoogle ScholarPubMed
(2002). Cellular roles of DNA topoisomerases: A molecular perspective. Nat Rev Mol Cell Biol 3, 430–440CrossRefGoogle ScholarPubMed
, and (1986). Biochemical topology: Applications to DNA recombination and replication. Science 232, 951–960CrossRefGoogle Scholar
, , and (1998). Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease. Nucleic Acids Res 26, 490–496CrossRefGoogle ScholarPubMed
, , , , and (1998). Unveiling two distinct ribonuclease activities and a topoisomerase activity in a site-specific DNA recombinase. Mol Cell 1, 729–739CrossRefGoogle Scholar
, and (1995). Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site. Cell 82, 193–207CrossRefGoogle ScholarPubMed
- 4
- Cited by