Abstract
Genetic recombination relies on a number of biochemical activities that must be present at the right time and place in order for two DNA molecules to be recombined properly. Recent advances in real-time fluorescence microscopy provide us with a glimpse of homologous recombination taking place in living cells. These approaches reveal that homologous recombination is highly choreographed in vivo with its spatio-temporal organization being dependent on both cell cycle phase and the nature of the initiating DNA lesion. In this chapter, we review the cell biology of homologous recombination in mitotic cells with the main focus on the yeast Saccharomyces cerevisiae but also drawing parallels to other eukaryotic organisms.
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References
Alani E, Thresher R, Griffith JD, Kolodner RD (1992) Characterization of DNA-binding and strand-exchange stimulation properties of y-RPA, a yeast single-strand-DNA-binding protein. J Mol Biol 227:54–71
Alpha-Bazin B, Lorphelin A, Nozerand N, Charier G, Marchetti C, Berenguer F, Couprie J, Gilquin B, Zinn-Justin S, Quemeneur E (2005) Boundaries and physical characterization of a new domain shared between mammalian 53BP1 and yeast Rad9 checkpoint proteins. Protein Sci 14:1827–1839
Antunez de Mayolo A, Lisby M, Erdeniz N, Thybo T, Mortensen UH, Rothstein R (2006) Multiple start codons and phosphorylation result in discrete Rad52 protein species. Nucleic Acids Res 34:2587–2597
Aten JA, Stap J, Krawczyk PM, van Oven CH, Hoebe RA, Essers J, Kanaar R (2004) Dynamics of DNA double-strand breaks revealed by clustering of damaged chromosome domains. Science 303:92–95
Baroni E, Viscardi V, Cartagena-Lirola H, Lucchini G, Longhese MP (2004) The functions of budding yeast Sae2 in the DNA damage response require Mec1- and Tel1-dependent phosphorylation. Mol Cell Biol 24:4151–4165
Betts Lindroos H, Strom L, Itoh T, Katou Y, Shirahige K, Sjogren C (2006) Chromosomal association of the Smc5/6 complex reveals that it functions in differently regulated pathways. Mol Cell 22:755–767
Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, Grant PA, Smith MM, Christman MF (2002) Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419:411–415
Blankley RT, Lydall D (2004) A domain of Rad9 specifically required for activation of Chk1 in budding yeast. J Cell Sci 117:601–608
Branzei D, Seki M, Enomoto T (2004) Rad18/Rad5/Mms2-mediated polyubiquitination of PCNA is implicated in replication completion during replication stress. Genes Cells 9:1031–1042
Chiolo I, Carotenuto W, Maffioletti G, Petrini JH, Foiani M, Liberi G (2005) Srs2 and Sgs1 DNA helicases associate with Mre11 in different subcomplexes following checkpoint activation and CDK1-mediated Srs2 phosphorylation. Mol Cell Biol 25:5738–5751
Clever B, Interthal H, Schmuckli-Maurer J, King J, Sigrist M, Heyer WD (1997) Recombinational repair in yeast: functional interactions between Rad51 and Rad54 proteins. EMBO J 16:2535–2544
de Jager M, van Noort J, van Gent DC, Dekker C, Kanaar R, Wyman C (2001) Human Rad50/Mre11 is a flexible complex that can tether DNA ends. Mol Cell 8:1129–1135
De Piccoli G, Cortes-Ledesma F, Ira G, Torres-Rosell J, Uhle S, Farmer S, Hwang JY, Machin F, Ceschia A, McAleenan A, Cordon-Preciado V, Clemente-Blanco A, Vilella-Mitjana F, Ullal P, Jarmuz A, Leitao B, Bressan D, Dotiwala F, Papusha A, Zhao X, Myung K, Haber JE, Aguilera A, Aragon L (2006) Smc5-Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination. Nat Cell Biol 8:1032–1034
Dresser ME, Ewing DJ, Conrad MN, Dominguez AM, Barstead R, Jiang H, Kodadek T (1997) DMC1 functions in a Saccharomyces cerevisiaemeiotic pathway that is largely independent of the RAD51 pathway. Genetics 147:533–544
Dronkert ML, Kanaar R (2001) Repair of DNA interstrand cross-links. Mutat Res 486:217–247
Du LL, Nakamura TM, Russell P (2006) Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks. Genes Dev 20:1583–1596
Essers J, Houtsmuller AB, van Veelen L, Paulusma C, Nigg AL, Pastink A, Vermeulen W, Hoeijmakers JH, Kanaar R (2002) Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage. EMBO J 21:2030–2037
Galli A, Schiestl RH (1996) Hydroxyurea induces recombination in dividing but not in G1 or G2 cell cycle arrested yeast cells. Mutat Res 354:69–75
Gangloff S, McDonald JP, Bendixen C, Arthur L, Rothstein R (1994) The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol 14:8391–8398
Giannattasio M, Lazzaro F, Plevani P, Muzi-Falconi M (2005) The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1. J Biol Chem 280:9879–9886
Gilbert CS, Green CM, Lowndes NF (2001) Budding yeast Rad9 is an ATP-dependent Rad53 activating machine. Mol Cell 8:129–136
Green CM, Erdjument-Bromage H, Tempst P, Lowndes NF (2000) A novel Rad24 checkpoint protein complex closely related to replication factor C. Curr Biol 10:39–42
Harvey AC, Jackson SP, Downs JA (2005) Saccharomyces cerevisiae histone H2A Ser122 facilitates DNA repair. Genetics 170:543–553
Hays SL, Firmenich AA, Berg P (1995) Complex formation in yeast double-strand break repair: participation of Rad51, Rad52, Rad55, and Rad57 proteins. Proc Natl Acad Sci USA 92:6925–6929
Hays SL, Firmenich AA, Massey P, Banerjee R, Berg P (1998) Studies of the interaction between Rad52 protein and the yeast single-stranded DNA binding protein RPA. Mol Cell Biol 18:4400–4406
Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419:135–141
Houston PL, Broach JR (2006) The dynamics of homologous pairing during mating type interconversion in budding yeast. PLoS Genet 2:e98
Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES, Halazonetis TD (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432:406–411
Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W, Liberi G, Bressan D, Wan L, Hollingsworth NM, Haber JE, Foiani M (2004) DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431:1011–1017
Jiang H, Xie Y, Houston P, Stemke-Hale K, Mortensen UH, Rothstein R, Kodadek T (1996) Direct association between the yeast Rad51 and Rad54 recombination proteins. J Biol Chem 271:33181–33186
Johzuka K, Horiuchi T (2002) Replication fork block protein, Fob1, acts as an rDNA region specific recombinator in S. cerevisiae. Genes Cells 7:99–113
Kadyk LC, Hartwell LH (1993) Replication-dependent sister chromatid recombination in rad1 mutants of Saccharomyces cerevisiae. Genetics 133:469–487
Karathanasis E, Wilson TE (2002) Enhancement of Saccharomyces cerevisiae end-joining efficiency by cell growth stage but not by impairment of recombination. Genetics 161:1015–1027
Kaye JA, Melo JA, Cheung SK, Vaze MB, Haber JE, Toczyski DP (2004) DNA breaks promote genomic instability by impeding proper chromosome segregation. Curr Biol 14:2096–2106
Kim HS, Brill SJ (2001) Rfc4 interacts with Rpa1 and is required for both DNA replication and DNA damage checkpoints in Saccharomyces cerevisiae. Mol Cell Biol 21:3725–3737
Kim ST, Lim DS, Canman CE, Kastan MB (1999) Substrate specificities and identification of putative substrates of ATM kinase family members. J Biol Chem 274:37538–37543
Klein HL (1997) RDH54, a RAD54 homologue in Saccharomyces cerevisiae, is required for mitotic diploid-specific recombination and repair and for meiosis. Genetics 147:1533–1543
Kobayashi T, Heck DJ, Nomura M, Horiuchi T (1998) Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev 12:3821–3830
Kobayashi T, Horiuchi T, Tongaonkar P, Vu L, Nomura M (2004) SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell 117:441–453
Krejci L, Damborsky J, Thomsen B, Duno M, Bendixen C (2001) Molecular dissection of interactions between Rad51 and members of the recombination-repair group. Mol Cell Biol 21:966–976
Krogh B, Symington L (2004) Recombination proteins in yeast. Annu Rev Genet 38:233–271
Lee SJ, Duong JK, Stern DF (2004) A Ddc2-Rad53 fusion protein can bypass the requirements for RAD9 and MRC1 in Rad53 activation. Mol Biol Cell 15:5443–5455
Lisby M, Antúnez de Mayolo A, Mortensen UH, Rothstein R (2003a) Cell cycle-regulated centers of DNA double-strand break repair. Cell Cycle 2:479–483
Lisby M, Barlow JH, Burgess RC, Rothstein R (2004) Choreography of the DNA damage response; spatiotemporal relationships among checkpoint and repair proteins. Cell 118:699–713
Lisby M, Mortensen UH, Rothstein R (2003b) Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat Cell Biol 5:572–577
Lisby M, Rothstein R (2005) Localization of checkpoint and repair proteins in eukaryotes. Biochimie 87:579–589
Lisby M, Rothstein R, Mortensen UH (2001) Rad52 forms DNA repair and recombination centers during S phase. Proc Natl Acad Sci USA 98:8276–8282
Llorente B, Symington LS (2004) The Mre11 nuclease is not required for 5′ to 3′ resection at multiple HO-induced double-strand breaks. Mol Cell Biol 24:9682–9694
Lobachev K, Vitriol E, Stemple J, Resnick MA, Bloom K (2004) Chromosome fragmentation after induction of a double-strand break is an active process prevented by the RMX repair complex. Curr Biol 14:2107–2112
Lobachev KS, Gordenin DA, Resnick MA (2002) The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108:183–193
Lopes M, Cotta-Ramusino C, Pellicioli A, Liberi G, Plevani P, Muzi-Falconi M, Newlon CS, Foiani M (2001) The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412:557–561
Lucca C, Vanoli F, Cotta-Ramusino C, Pellicioli A, Liberi G, Haber J, Foiani M (2004) Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing. Oncogene 23:1206–1213
Lukas C, Falck J, Bartkova J, Bartek J, Lukas J (2003) Distinct spatiotemporal dynamics of mammalian checkpoint regulators induced by DNA damage. Nat Cell Biol 5:255–260
Macris MA, Sung P (2005) Multifaceted role of the Saccharomyces cerevisiae Srs2 helicase in homologous recombination regulation. Biochem Soc Trans 33:1447–1450
Majka J, Burgers PM (2003) Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage checkpoint. Proc Natl Acad Sci USA 100:2249–2254
Mallory JC, Bashkirov VI, Trujillo KM, Solinger JA, Dominska M, Sung P, Heyer WD, Petes TD (2003) Amino acid changes in Xrs2p, Dun1p, and Rfa2p that remove the preferred targets of the ATM family of protein kinases do not affect DNA repair or telomere length in Saccharomyces cerevisiae. DNA Repair (Amst) 2:1041–1064
Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM (1999) Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97:621–633
Melo JA, Cohen J, Toczyski DP (2001) Two checkpoint complexes are independently recruited to sites of DNA damage in vivo. Genes Dev 15:2809–2821
Michaelis C, Ciosk R, Nasmyth K (1997) Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell 91:35–45
Miyazaki T, Tsai HF, Bennett JE (2006) Kre29p is a novel nuclear protein involved in DNA repair and mitotic fidelity in Candida glabrata. Curr Genet 50:11–22
Moreau S, Morgan EA, Symington LS (2001) Overlapping functions of the Saccharomyces cerevisiae Mre11, Exo1 and Rad27 nucleases in DNA metabolism. Genetics 159:1423–1433
Nakada D, Hirano Y, Tanaka Y, Sugimoto K (2005) Role of the C terminus of Mec1 checkpoint kinase in its localization to sites of DNA damage. Mol Biol Cell 16:5227–5235
Nakada D, Matsumoto K, Sugimoto K (2003) ATM-related Tel1 associates with double-strand breaks through an Xrs2-dependent mechanism. Genes Dev 17:1957–1962
Nakamura TM, Du LL, Redon C, Russell P (2004) Histone H2A phosphorylation controls Crb2 recruitment at DNA breaks, maintains checkpoint arrest, and influences DNA repair in fission yeast. Mol Cell Biol 24:6215–6230
Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang Y, Struhl K (2002) Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev 16:1518–1527
Osborn AJ, Elledge SJ (2003) Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Genes Dev 17:1755–1767
Paciotti V, Clerici M, Luchinni G, Longhese MP (2000) The checkpoint protein Ddc2, functionally related to S. pombe Rad26, interacts with Mec1 and is regulated by Mec1-dependent phosphorylation in budding yeast. Genes Dev 14:2046–2059
Petukhova G, Sung P, Klein H (2000) Promotion of Rad51-dependent D-loop formation by yeast recombination factor Rdh54/Tid1. Genes Dev 14:2206–2215
Prado F, Cortes-Ledesma F, Huertas P, Aguilera A (2003) Mitotic recombination in Saccharomyces cerevisiae. Curr Genet 42:185–198
Redon C, Pilch DR, Rogakou EP, Orr AH, Lowndes NF, Bonner WM (2003) Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage. EMBO Rep 4:678–684
Reichard P (1988) Interactions between deoxyribonucleotide and DNA synthesis. Annu Rev Biochem 57:379–374
Reid RJ, Rothstein R (2004) Stay close to your sister. Mol Cell 14:418–420
Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146:905–916
Ruskin B, Fink GR (1993) Mutations in POL1 increase the mitotic instability of tandem inverted repeats in Saccharomyces cerevisiae. Genetics 134:43–56
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Lisby, M., Rothstein, R. (2006). The Cell Biology of Mitotic Recombination in Saccharomyces Cerevisiae . In: Aguilera, A., Rothstein, R. (eds) Molecular Genetics of Recombination. Topics in Current Genetics, vol 17. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4735_2006_0212
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DOI: https://doi.org/10.1007/4735_2006_0212
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