Nucleotide proofreading functions by nematode RAD51 paralogs facilitate optimal RAD51 filament function
Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
206292/Z/17/Z
Wellcome Trust - United Kingdom
110014/Z/15/Z
Wellcome Trust - United Kingdom
206292/E/17/Z
Wellcome Trust - United Kingdom
PubMed
34545070
PubMed Central
PMC8452638
DOI
10.1038/s41467-021-25830-x
PII: 10.1038/s41467-021-25830-x
Knihovny.cz E-zdroje
- MeSH
- adenosindifosfát farmakologie MeSH
- adenosintrifosfát farmakologie MeSH
- Caenorhabditis elegans metabolismus MeSH
- druhová specificita MeSH
- fluorescence MeSH
- interferometrie MeSH
- jednovláknová DNA metabolismus MeSH
- nukleotidy metabolismus MeSH
- proteiny Caenorhabditis elegans metabolismus MeSH
- rekombinasa Rad51 chemie metabolismus MeSH
- sekvenční homologie aminokyselin * MeSH
- stabilita proteinů účinky léků MeSH
- vazba proteinů účinky léků MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adenosindifosfát MeSH
- adenosintrifosfát MeSH
- jednovláknová DNA MeSH
- nukleotidy MeSH
- proteiny Caenorhabditis elegans MeSH
- rekombinasa Rad51 MeSH
The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Here, we define unappreciated mechanisms by which the RAD51 paralog complex RFS-1/RIP-1 limits the accumulation of RAD-51-ssDNA complexes with unfavorable nucleotide content. We find RAD51 paralogs promote the turnover of ADP-bound RAD-51 from ssDNA, in striking contrast to their ability to stabilize productive ATP-bound RAD-51 nucleoprotein filaments. In addition, RFS-1/RIP-1 inhibits binding of nucleotide-free RAD-51 to ssDNA. We propose that 'nucleotide proofreading' activities of RAD51 paralogs co-operate to ensure the enrichment of active, ATP-bound RAD-51 filaments on ssDNA to promote HR.
Department of Biology Masaryk University 62500 Brno Czech Republic
National Centre for Biomolecular Research Masaryk University 62500 Brno Czech Republic
The Francis Crick Institute 1 Midland Road London NW1 1AT UK
Zobrazit více v PubMed
Chapman JR, Taylor MR, Boulton SJ. Playing the end game: DNA double-strand break repair pathway choice. Mol. Cell. 2012;47:497–510. doi: 10.1016/j.molcel.2012.07.029. PubMed DOI
Jensen RB, Carreira A, Kowalczykowski SC. Purified human BRCA2 stimulates RAD51-mediated recombination. Nature. 2010;467:678–683. doi: 10.1038/nature09399. PubMed DOI PMC
Thorslund T, et al. The breast cancer tumor suppressor BRCA2 promotes the specific targeting of RAD51 to single-stranded DNA. Nat. Struct. Mol. Biol. 2010;17:1263–1265. doi: 10.1038/nsmb.1905. PubMed DOI PMC
Liu J, Doty T, Gibson B, Heyer WD. Human BRCA2 protein promotes RAD51 filament formation on RPA-covered single-stranded DNA. Nat. Struct. Mol. Biol. 2010;17:1260–1262. doi: 10.1038/nsmb.1904. PubMed DOI PMC
New JH, Sugiyama T, Zaitseva E, Kowalczykowski SC. Rad52 protein stimulates DNA strand exchange by Rad51 and replication protein A. Nature. 1998;391:407–410. doi: 10.1038/34950. PubMed DOI
Taylor MRG, et al. Rad51 Paralogs Remodel Pre-synaptic Rad51 Filaments to Stimulate Homologous Recombination. Cell. 2015;162:271–286. doi: 10.1016/j.cell.2015.06.015. PubMed DOI PMC
Taylor MRG, et al. A Polar and Nucleotide-Dependent Mechanism of Action for RAD51 Paralogs in RAD51 Filament Remodeling. Mol. Cell. 2016;64:926–939. doi: 10.1016/j.molcel.2016.10.020. PubMed DOI PMC
Amunugama R, et al. RAD51 protein ATP cap regulates nucleoprotein filament stability. J. Biol. Chem. 2012;287:8724–8736. doi: 10.1074/jbc.M111.239426. PubMed DOI PMC
Sung P. Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein. Science. 1994;265:1241–1243. doi: 10.1126/science.8066464. PubMed DOI
Baumann P, Benson FE, West SC. Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell. 1996;87:757–766. doi: 10.1016/S0092-8674(00)81394-X. PubMed DOI
Tombline G, Fishel R. Biochemical characterization of the human RAD51 protein. I. ATP hydrolysis. J. Biol. Chem. 2002;277:14417–14425. doi: 10.1074/jbc.M109915200. PubMed DOI
Zellweger R, et al. Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J. Cell Biol. 2015;208:563–579. doi: 10.1083/jcb.201406099. PubMed DOI PMC
Hashimoto Y, Ray Chaudhuri A, Lopes M, Costanzo V. Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat. Struct. Mol. Biol. 2010;17:1305–1311. doi: 10.1038/nsmb.1927. PubMed DOI PMC
Schlacher K, et al. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell. 2011;145:529–542. doi: 10.1016/j.cell.2011.03.041. PubMed DOI PMC
Petermann E, Orta ML, Issaeva N, Schultz N, Helleday T. Hydroxyurea-stalled replication forks become progressively inactivated and require two different RAD51-mediated pathways for restart and repair. Mol. Cell. 2010;37:492–502. doi: 10.1016/j.molcel.2010.01.021. PubMed DOI PMC
Mason JM, Chan YL, Weichselbaum RW, Bishop DK. Non-enzymatic roles of human RAD51 at stalled replication forks. Nat. Commun. 2019;10:4410. doi: 10.1038/s41467-019-12297-0. PubMed DOI PMC
Kim TM, et al. RAD51 mutants cause replication defects and chromosomal instability. Mol. Cell Biol. 2012;32:3663–3680. doi: 10.1128/MCB.00406-12. PubMed DOI PMC
Belan O, et al. Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins. Mol. Cell. 2021;81:1058–1073.e7. doi: 10.1016/j.molcel.2020.12.020. PubMed DOI PMC
Concepcion J, et al. Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization. Comb. Chem. High. Throughput Screen. 2009;12:791–800. doi: 10.2174/138620709789104915. PubMed DOI
Petalcorin MI, Galkin VE, Yu X, Egelman EH, Boulton SJ. Stabilization of RAD-51-DNA filaments via an interaction domain in Caenorhabditis elegans BRCA2. Proc. Natl Acad. Sci. USA. 2007;104:8299–8304. doi: 10.1073/pnas.0702805104. PubMed DOI PMC
Galkin VE, et al. The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity. Structure. 2006;14:983–992. doi: 10.1016/j.str.2006.04.001. PubMed DOI
Menge KL, Bryant FR. Effect of nucleotide cofactor structure on recA protein-promoted DNA pairing. 2. DNA renaturation reaction. Biochemistry. 1992;31:5158–5165. doi: 10.1021/bi00137a010. PubMed DOI
Yonesaki T. Recombination apparatus of T4 phage. Adv. Biophys. 1995;31:3–22. doi: 10.1016/0065-227X(95)99380-8. PubMed DOI
Krejci L, Altmannova V, Spirek M, Zhao X. Homologous recombination and its regulation. Nucleic Acids Res. 2012;40:5795–5818. doi: 10.1093/nar/gks270. PubMed DOI PMC
Carreira A, et al. The BRC repeats of BRCA2 modulate the DNA-binding selectivity of RAD51. Cell. 2009;136:1032–1043. doi: 10.1016/j.cell.2009.02.019. PubMed DOI PMC
Masson JY, et al. Identification and purification of two distinct complexes containing the five RAD51 paralogs. Genes Dev. 2001;15:3296–3307. doi: 10.1101/gad.947001. PubMed DOI PMC
Kurumizaka H, et al. Homologous-pairing activity of the human DNA-repair proteins Xrcc3.Rad51C. Proc. Natl Acad. Sci. USA. 2001;98:5538–5543. doi: 10.1073/pnas.091603098. PubMed DOI PMC
Kurumizaka H, et al. Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex. J. Biol. Chem. 2002;277:14315–14320. doi: 10.1074/jbc.M105719200. PubMed DOI
Sigurdsson S, et al. Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange. Genes Dev. 2001;15:3308–3318. doi: 10.1101/gad.935501. PubMed DOI PMC
Špírek M, et al. Human RAD51 rapidly forms intrinsically dynamic nucleoprotein filaments modulated by nucleotide binding state. Nucleic Acids Res. 2018;46:3967–3980. doi: 10.1093/nar/gky111. PubMed DOI PMC
Bugreev DV, Mazin AV. Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity. Proc. Natl Acad. Sci. USA. 2004;101:9988–9993. doi: 10.1073/pnas.0402105101. PubMed DOI PMC
Brouwer, I. et al. Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA. EMBO J. 37, e98162 (2018). PubMed PMC
Bugreev DV, et al. HOP2-MND1 modulates RAD51 binding to nucleotides and DNA. Nat. Commun. 2014;5:4198. doi: 10.1038/ncomms5198. PubMed DOI PMC
van Mameren J, et al. Counting RAD51 proteins disassembling from nucleoprotein filaments under tension. Nature. 2009;457:745–748. doi: 10.1038/nature07581. PubMed DOI PMC
Su GC, et al. Enhancement of ADP release from the RAD51 presynaptic filament by the SWI5-SFR1 complex. Nucleic Acids Res. 2014;42:349–358. doi: 10.1093/nar/gkt879. PubMed DOI PMC
Shim KS, Schmutte C, Tombline G, Heinen CD, Fishel R. hXRCC2 enhances ADP/ATP processing and strand exchange by hRAD51. J. Biol. Chem. 2004;279:30385–30394. doi: 10.1074/jbc.M306066200. PubMed DOI
Krejci L, et al. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature. 2003;423:305–309. doi: 10.1038/nature01577. PubMed DOI
Veaute X, et al. The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments. Nature. 2003;423:309–312. doi: 10.1038/nature01585. PubMed DOI
Hu Y, et al. RECQL5/Recql5 helicase regulates homologous recombination and suppresses tumor formation via disruption of Rad51 presynaptic filaments. Genes Dev. 2007;21:3073–3084. doi: 10.1101/gad.1609107. PubMed DOI PMC
Antony E, et al. Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA. Mol. Cell. 2009;35:105–115. doi: 10.1016/j.molcel.2009.05.026. PubMed DOI PMC
Kim C, Snyder RO, Wold MS. Binding properties of replication protein A from human and yeast cells. Mol. Cell Biol. 1992;12:3050–3059. PubMed PMC
Zhao W, et al. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry. Mol. Cell. 2015;59:176–187. doi: 10.1016/j.molcel.2015.05.032. PubMed DOI PMC
San Filippo J, et al. Recombination mediator and Rad51 targeting activities of a human BRCA2 polypeptide. J. Biol. Chem. 2006;281:11649–11657. doi: 10.1074/jbc.M601249200. PubMed DOI PMC
Ward JD, Barber LJ, Petalcorin MI, Yanowitz J, Boulton SJ. Replication blocking lesions present a unique substrate for homologous recombination. EMBO J. 2007;26:3384–3396. doi: 10.1038/sj.emboj.7601766. PubMed DOI PMC
Taylor MRG, Yeeles JTP. The Initial Response of a Eukaryotic Replisome to DNA Damage. Mol. Cell. 2018;70:1067–1080.e12. doi: 10.1016/j.molcel.2018.04.022. PubMed DOI PMC
Short JM, et al. High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Res. 2016;44:9017–9030. PubMed PMC
Shahid T, et al. Structure and mechanism of action of the BRCA2 breast cancer tumor suppressor. Nat. Struct. Mol. Biol. 2014;21:962–968. doi: 10.1038/nsmb.2899. PubMed DOI PMC
Bhat KP, Cortez D. RPA and RAD51: fork reversal, fork protection, and genome stability. Nat. Struct. Mol. Biol. 2018;25:446–453. doi: 10.1038/s41594-018-0075-z. PubMed DOI PMC
Schlacher K, Wu H, Jasin M. A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. Cancer Cell. 2012;22:106–116. doi: 10.1016/j.ccr.2012.05.015. PubMed DOI PMC
Zadorozhny K, et al. Fanconi-Anemia-Associated Mutations Destabilize RAD51 Filaments and Impair Replication Fork Protection. Cell Rep. 2017;21:333–340. doi: 10.1016/j.celrep.2017.09.062. PubMed DOI
Berti M, et al. Sequential role of RAD51 paralog complexes in replication fork remodeling and restart. Nat. Commun. 2020;11:3531. doi: 10.1038/s41467-020-17324-z. PubMed DOI PMC
Li X, Heyer WD. RAD54 controls access to the invading 3’-OH end after RAD51-mediated DNA strand invasion in homologous recombination in Saccharomyces cerevisiae. Nucleic Acids Res. 2009;37:638–646. doi: 10.1093/nar/gkn980. PubMed DOI PMC
Ward JD, et al. Overlapping mechanisms promote postsynaptic RAD-51 filament disassembly during meiotic double-strand break repair. Mol. Cell. 2010;37:259–272. doi: 10.1016/j.molcel.2009.12.026. PubMed DOI
Vaz F, et al. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Nat. Genet. 2010;42:406–409. doi: 10.1038/ng.570. PubMed DOI
Somyajit K, Subramanya S, Nagaraju G. RAD51C: a novel cancer susceptibility gene is linked to Fanconi anemia and breast cancer. Carcinogenesis. 2010;31:2031–2038. doi: 10.1093/carcin/bgq210. PubMed DOI PMC
Mechanism of BCDX2-mediated RAD51 nucleation on short ssDNA stretches and fork DNA