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Recombination: Mechanisms, Pathways, and Applications

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Synopsis

Recombination is a process that brings about reassortment of genetic information in and among chromosomes. Recombination serves several functions in organisms, including DNA repair in bacteria and eukaryotes, and ensures the correct alignment and segregation of chromosomes during meiosis in eukaryotes. Recombination is thought to be important for evolution since it provides new combinations of genes that may give rise to beneficial traits in an organism. Recombination enzymes and pathways are also used in some specialized cellular functions such as the diversification of genes that encode antibody proteins in vertebrates (V(D)J recombination) and telomere maintenance in tumor cells. Homologous recombination relies on complementary DNA sequences to transfer genetic information between identical and nearly identical (homologous) chromosomes. Genetic rearrangements can also occur through site-specific recombination and transposition reactions that are directed by protein-DNA...

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References

  • Adhya SL, Shapiro JA (1969) The galactose operon of E. coli K-12. I. Structural and pleiotropic mutations of the operon. Genetics 62:231–247

    CAS  PubMed  PubMed Central  Google Scholar 

  • Amundsen SK, Taylor AF, Chaudhury AM, Smith GR (1986) recD: the gene for an essential third subunit of exonuclease V. Proc Natl Acad Sci U S A 83:5558–5562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babatz TD, Burns KH (2013) Functional impact of the human mobilome. Curr Opin Genet Dev 23:264–270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barbour SD, Nagaishi H, Templin A, Clark AJ (1970) Biochemical and genetic studies of recombination proficiency in Escherichia coli. II. Rec+ revertants caused by indirect suppression of rec- mutations. Proc Natl Acad Sci U S A 67:128–135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Batey MA, Zhao Y, Kyle S, Richardson C, Slade A, Martin NM, Lau A, Newell DR, Curtin NJ (2013) Preclinical evaluation of a novel ATM inhibitor, KU59403, in vitro and in vivo in p53 functional and dysfunctional models of human cancer. Mol Cancer Ther 12:959–967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berg P, Mertz JE (2010) Personal reflections on the origins and emergence of recombinant DNA technology. Genetics 184:9–17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bishop DK, Park D, Xu L, Kleckner N (1992) DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 69:439–456

    Article  CAS  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  PubMed Central  Google Scholar 

  • Boeke JD, Garfinkel DJ, Styles CA, Fink GR (1985) Ty elements transpose through an RNA intermediate. Cell 40:491–500

    Article  CAS  PubMed  Google Scholar 

  • Calef E, Licciardello G (1960) Recombination experiments on prophage host relationships. Virology 12:81–103

    Article  Google Scholar 

  • Campbell A (1961) Episomes. Adv Genet 11:101–145

    Google Scholar 

  • Chang CJ, Bouhassira EE (2012) Zinc-finger nuclease-mediated correction of alpha-thalassemia in iPS cells. Blood 120:3906–3914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chaudhury AM, Smith GR (1984) A new class of Escherichia coli recBC mutants: implications for the role of RecBC enzyme in homologous recombination. Proc Natl Acad Sci U S A 81:7850–7854

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Z, Yang H, Pavletich NP (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature 453:489–484

    Article  CAS  PubMed  Google Scholar 

  • Clark AJ (1973) Recombination deficient mutants of E. coli and other bacteria. Annu Rev Genet 7:67–86

    Article  CAS  PubMed  Google Scholar 

  • Clark AJ, Margulies AD (1965) Isolation and characterization of recombination-deficient mutants of Escherichia Coli K12. Proc Natl Acad Sci U S A 53:451–459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cohen SN (2013) DNA cloning: a personal view after 40 years. Proc Natl Acad Sci U S A 110:15521–15529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Courcelle J, Ganesan AK, Hanawalt PC (2001) Therefore, what are recombination proteins there for? BioEssays 23:463–470

    Article  CAS  PubMed  Google Scholar 

  • Cox MM (2007) Regulation of bacterial RecA protein function. Crit Rev Biochem Mol Biol 42:41–63

    Article  CAS  PubMed  Google Scholar 

  • Cox MM, Goodman MF, Kreuzer KN, Sherratt DJ, Sandler SJ, Marians KJ (2000) The importance of repairing stalled replication forks. Nature 404:37–41

    Article  CAS  PubMed  Google Scholar 

  • Curcio MJ, Derbyshire KM (2003) The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol 4:865–877

    Article  CAS  PubMed  Google Scholar 

  • Dillingham MS, Kowalczykowski SC (2008) RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev 72:642–671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dupuy A, Valton J, Leduc S, Armier J, Galetto R, Gouble A, Lebuhotel C, Stary A, Paques F, Duchateau P et al (2013) Targeted gene therapy of xeroderma pigmentosum cells using meganuclease and TALEN. PLoS One 8:e78678

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Evers B, Helleday T, Jonkers J (2010) Targeting homologous recombination repair defects in cancer. Trends Pharmacol Sci 31:372–380

    Article  CAS  PubMed  Google Scholar 

  • Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Game JC, Zamb TJ, Braun RJ, Resnick M, Roth RM (1980) The role of radiation (rad) genes in meiotic recombination in yeast. Genetics 94:51–68

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ghosh K, Guo F, Van Duyne GD (2007) Synapsis of loxP sites by Cre recombinase. J Biol Chem 282:24004–24016

    Article  CAS  PubMed  Google Scholar 

  • Grindley ND, Whiteson KL, Rice PA (2006) Mechanisms of site-specific recombination. Annu Rev Biochem 75:567–605

    Article  CAS  PubMed  Google Scholar 

  • Hedges RW, Jacob AE (1974) Transposition of ampicillin resistance from RP4 to other replicons. Mol Gen Genet 132:31–40

    Article  CAS  PubMed  Google Scholar 

  • Heller RC, Marians KJ (2006) Replisome assembly and the direct restart of stalled replication forks. Nat Rev Mol Cell Biol 7:932–943

    Article  CAS  PubMed  Google Scholar 

  • Holliday R (1964) A mechanism for gene conversion in fungi. Genet Res 5:282–304

    Article  Google Scholar 

  • Holloman WK (2011) Unraveling the mechanism of BRCA2 in homologous recombination. Nat Struct Mol Biol 18:748–754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holloman WK, Wiegand R, Hoessli C, Radding CM (1975) Uptake of homologous single-stranded fragments by superhelical DNA: a possible mechanism for initiation of genetic recombination. Proc Natl Acad Sci U S A 72:2394–2398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • https://www.sheffield.ac.uk/mbb/ruva. Accessed 24 May 2017

  • Jackson DA, Symons RH, Berg P (1972) Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc Natl Acad Sci U S A 69:2904–2909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jasin M, Rothstein R (2013) Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol 5:a012740

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jekimovs C, Bolderson E, Suraweera A, Adams M, O'Byrne KJ, Richard DJ (2014) Chemotherapeutic compounds targeting the DNA double-strand break repair pathways: the good, the bad, and the promising. Front Oncol 4:86

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones RN (2005) McClintock’s controlling elements: the full story. Cytogenet Genome Res 109:90–103

    Article  CAS  PubMed  Google Scholar 

  • Keller EF (1983) A feeling for the organism. W. H. Freeman and Co., New York

    Google Scholar 

  • Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58:401–465

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lam ST, Stahl MM, McMilin KD, Stahl FW (1974) Rec-mediated recombinational hot spot activity in bacteriophage lambda. II A mutation which causes hot spot activity. Genetics 77:425–433

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee AM, Xiao J, Singleton SF (2006) Origins of sequence selectivity in homologous genetic recombination: insights from rapid kinetic probing of RecA-mediated DNA strand exchange. J Mol Biol 360:343–359

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Ehmsen KT, Heyer WD, Morrical SW (2011) Presynaptic filament dynamics in homologous recombination and DNA repair. Crit Rev Biochem Mol Biol 46:240–270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lwoff A (1953) Lysogeny. Bacteriol Rev 17:269–337

    CAS  PubMed  PubMed Central  Google Scholar 

  • Maniatis T, Kee SG, Efstratiadis A, Kafatos FC (1976) Amplification and characterization of a beta-globin gene synthesized in vitro. Cell 8:163–182

    Article  CAS  PubMed  Google Scholar 

  • Mazina OM, Rossi MJ, Deakyne JS, Huang F, Mazin AV (2012) Polarity and bypass of DNA heterology during branch migration of Holliday junctions by human RAD54, BLM, and RECQ1 proteins. J Biol Chem 287:11820–11832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A 36:344–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McClintock B (1951) Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 16:13–47

    Article  CAS  PubMed  Google Scholar 

  • McReynolds LA, Monahan JJ, Bendure DW, Woo SL, Paddock GV, Salser W, Dorson J, Moses RE, O'Malley BW (1977) The ovalbumin gene. Insertion of ovalbumin gene sequences in chimeric bacterial plasmids. J Biol Chem 252:1840–1843

    CAS  PubMed  Google Scholar 

  • Meselson MS, Radding CM (1975) A general model for genetic recombination. Proc Natl Acad Sci U S A 72:358–361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Michel B, Boubakri H, Baharoglu Z, LeMasson M, Lestini R (2007) Recombination proteins and rescue of arrested replication forks. DNA Repair (Amst) 6:967–980

    Article  CAS  Google Scholar 

  • Montano SP, Rice PA (2011) Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol 21:370–378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morimatsu K, Wu Y, Kowalczykowski SC (2012) RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5′ terminus: implication for repair of stalled replication forks. J Biol Chem 287:35621–35630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orr-Weaver TL, Szostak JW (1985) Fungal recombination. Microbiol Rev 49:33–58

    CAS  PubMed  PubMed Central  Google Scholar 

  • Parsons CA, Stasiak A, Bennett RJ, West SC (1995) Structure of a multisubunit complex that promotes DNA branch migration. Nature 374:375–378

    Article  CAS  PubMed  Google Scholar 

  • Ponticelli AS, Schultz DW, Taylor AF, Smith GR (1985) Chi-dependent DNA strand cleavage by RecBC enzyme. Cell 41:145–151

    Article  CAS  PubMed  Google Scholar 

  • Potter H, Dressler D (1976) On the mechanism of genetic recombination: electron microscopic observation of recombination intermediates. Proc Natl Acad Sci U S A 73:3000–3004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ragunathan K, Joo C, Ha T (2011) Real-time observation of strand exchange reaction with high spatiotemporal resolution. Structure 19:1064–1073

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rosen EM, Pishvaian MJ (2014) Targeting the BRCA1/2 tumor suppressors. Curr Drug Targets 15:17–31

    Article  CAS  PubMed  Google Scholar 

  • Saedler H, Starlinger P (1967) 0 degree mutations in the galactose operon in E. coli. I. Genetic characterization. Mol Gen Genet 100:178–189

    Article  CAS  PubMed  Google Scholar 

  • Sakai A, Cox MM (2009) RecFOR and RecOR as distinct RecA loading pathways. J Biol Chem 284:3264–3272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Schwank G, Koo BK, Sasselli V, Dekkers JF, Heo I, Demircan T, Sasaki N, Boymans S, Cuppen E, van der Ent CK et al (2013) Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 13:653–658

    Article  CAS  PubMed  Google Scholar 

  • Sharan SK, Thomason LC, Kuznetsov SG, Court DL (2009) Recombineering: a homologous recombination-based method of genetic engineering. Nat Protoc 4:206–223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shibata T, DasGupta C, Cunningham RP, Radding CM (1979) Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci U S A 76:1638–1642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shinohara A, Ogawa H, Ogawa T (1992) Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69:457–470

    Article  CAS  PubMed  Google Scholar 

  • Singleton MR, Scaife S, Wigley DB (2001) Structural analysis of DNA replication fork reversal by RecG. Cell 107:79–89

    Article  CAS  PubMed  Google Scholar 

  • Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB (2004) Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432:187–193

    Article  CAS  PubMed  Google Scholar 

  • Smith GR (2012) How RecBCD enzyme and Chi promote DNA break repair and recombination: a molecular biologist’s view. Microbiol Mol Biol Rev 76:217–228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stahl FW (1979) Genetic recombination. Thinking about it in phage and fungi. W. H. Freeman and Co., San Francisco

    Google Scholar 

  • Starlinger P (1977) DNA rearrangements in prokaryotes. Annu Rev Genet 11:103–126

    Article  CAS  PubMed  Google Scholar 

  • Story RM, Steitz TA (1992) Structure of the recA protein-ADP complex. Nature 355:374–376

    Article  CAS  PubMed  Google Scholar 

  • Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW (1983) The double-strand-break repair model for recombination. Cell 33:25–35

    Article  CAS  PubMed  Google Scholar 

  • Taylor AL (1963) Bacteriophage-induced mutation in Escherichia Coli. Proc Natl Acad Sci U S A 50:1043–1051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Temin HM (1980) Origin of retroviruses from cellular moveable genetic elements. Cell 21:599–600

    Article  CAS  PubMed  Google Scholar 

  • Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, van den Heuvel S, Vidal M (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328:575–592

    Article  CAS  PubMed  Google Scholar 

  • Wigley DB (2013) Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 11:9–13

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Douglas A. Julin .

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Julin, D.A. (2018). Recombination: Mechanisms, Pathways, and Applications. In: Wells, R.D., Bond, J.S., Klinman, J., Masters, B.S.S. (eds) Molecular Life Sciences. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1531-2_366

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