A Polar and Nucleotide-Dependent Mechanism of Action for RAD51 Paralogs in RAD51 Filament Remodeling

. 2016 Dec 01 ; 64 (5) : 926-939. [epub] 20161117

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid27867009

Grantová podpora
FC0010048 Medical Research Council - United Kingdom
110014/Z/15/Z Wellcome Trust - United Kingdom
R35 GM118026 NIGMS NIH HHS - United States
FC0010048 Cancer Research UK - United Kingdom
FC0010048 Wellcome Trust - United Kingdom
11581 Cancer Research UK - United Kingdom

Odkazy

PubMed 27867009
PubMed Central PMC5145814
DOI 10.1016/j.molcel.2016.10.020
PII: S1097-2765(16)30665-7
Knihovny.cz E-zdroje

Central to homologous recombination in eukaryotes is the RAD51 recombinase, which forms helical nucleoprotein filaments on single-stranded DNA (ssDNA) and catalyzes strand invasion with homologous duplex DNA. Various regulatory proteins assist this reaction including the RAD51 paralogs. We recently discovered that a RAD51 paralog complex from C. elegans, RFS-1/RIP-1, functions predominantly downstream of filament assembly by binding and remodeling RAD-51-ssDNA filaments to a conformation more proficient for strand exchange. Here, we demonstrate that RFS-1/RIP-1 acts by shutting down RAD-51 dissociation from ssDNA. Using stopped-flow experiments, we show that RFS-1/RIP-1 confers this dramatic stabilization by capping the 5' end of RAD-51-ssDNA filaments. Filament end capping propagates a stabilizing effect with a 5'→3' polarity approximately 40 nucleotides along individual filaments. Finally, we discover that filament capping and stabilization are dependent on nucleotide binding, but not hydrolysis by RFS-1/RIP-1. These data define the mechanism of RAD51 filament remodeling by RAD51 paralogs.

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Antony E., Tomko E.J., Xiao Q., Krejci L., Lohman T.M., Ellenberger T. Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA. Mol. Cell. 2009;35:105–115. PubMed PMC

Chapman J.R., Taylor M.R.G., Boulton S.J. Playing the end game: DNA double-strand break repair pathway choice. Mol. Cell. 2012;47:497–510. PubMed

Chen Z., Yang H., Pavletich N.P. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature. 2008;453:489–494. PubMed

Chun J., Buechelmaier E.S., Powell S.N. Rad51 paralog complexes BCDX2 and CX3 act at different stages in the BRCA1-BRCA2-dependent homologous recombination pathway. Mol. Cell. Biol. 2013;33:387–395. PubMed PMC

Conway A.B., Lynch T.W., Zhang Y., Fortin G.S., Fung C.W., Symington L.S., Rice P.A. Crystal structure of a Rad51 filament. Nat. Struct. Mol. Biol. 2004;11:791–796. PubMed

French C.A., Masson J.-Y., Griffin C.S., O’Regan P., West S.C., Thacker J. Role of mammalian RAD51L2 (RAD51C) in recombination and genetic stability. J. Biol. Chem. 2002;277:19322–19330. PubMed

Gaines W.A., Godin S.K., Kabbinavar F.F., Rao T., VanDemark A.P., Sung P., Bernstein K.A. Promotion of presynaptic filament assembly by the ensemble of S. cerevisiae Rad51 paralogues with Rad52. Nat. Commun. 2015;6:7834. PubMed PMC

Genois M.M., Plourde M., Éthier C., Roy G., Poirier G.G., Ouellette M., Masson J.Y. Roles of Rad51 paralogs for promoting homologous recombination in Leishmania infantum. Nucleic Acids Res. 2015;43:2701–2715. PubMed PMC

Gibb B., Ye L.F., Gergoudis S.C., Kwon Y., Niu H., Sung P., Greene E.C. Concentration-dependent exchange of replication protein A on single-stranded DNA revealed by single-molecule imaging. PLoS ONE. 2014;9:e87922. PubMed PMC

Gibb B., Ye L.F., Kwon Y., Niu H., Sung P., Greene E.C. Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules. Nat. Struct. Mol. Biol. 2014;21:893–900. PubMed PMC

Godin S.K., Meslin C., Kabbinavar F., Bratton-Palmer D.S., Hornack C., Mihalevic M.J., Yoshida K., Sullivan M., Clark N.L., Bernstein K.A. Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. Genetics. 2015;199:1023–1033. PubMed PMC

Herrera J.E., Chaires J.B. Characterization of preferred deoxyribonuclease I cleavage sites. J. Mol. Biol. 1994;236:405–411. PubMed

Hwang H., Myong S. Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions. Chem. Soc. Rev. 2014;43:1221–1229. PubMed PMC

Hwang H., Kim H., Myong S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. Proc. Natl. Acad. Sci. USA. 2011;108:7414–7418. PubMed PMC

Jensen R.B., Carreira A., Kowalczykowski S.C. Purified human BRCA2 stimulates RAD51-mediated recombination. Nature. 2010;467:678–683. PubMed PMC

Johnson R.D., Jasin M. Double-strand-break-induced homologous recombination in mammalian cells. Biochem. Soc. Trans. 2001;29:196–201. PubMed

Johnson R.D., Liu N., Jasin M. Mammalian XRCC2 promotes the repair of DNA double-strand breaks by homologous recombination. Nature. 1999;401:397–399. PubMed

Krejci L., Altmannova V., Spirek M., Zhao X. Homologous recombination and its regulation. Nucleic Acids Res. 2012;40:5795–5818. PubMed PMC

Liu J., Doty T., Gibson B., Heyer W.-D. Human BRCA2 protein promotes RAD51 filament formation on RPA-covered single-stranded DNA. Nat. Struct. Mol. Biol. 2010;17:1260–1262. PubMed PMC

Liu T., Wan L., Wu Y., Chen J., Huang J. hSWS1·SWSAP1 is an evolutionarily conserved complex required for efficient homologous recombination repair. J. Biol. Chem. 2011;286:41758–41766. PubMed PMC

Manglik A., Kim T.H., Masureel M., Altenbach C., Yang Z., Hilger D., Lerch M.T., Kobilka T.S., Thian F.S., Hubbell W.L. Structural insights into the dynamic process of β2-adrenergic receptor signaling. Cell. 2015;161:1101–1111. PubMed PMC

Martín V., Chahwan C., Gao H., Blais V., Wohlschlegel J., Yates J.R., 3rd, McGowan C.H., Russell P. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells. EMBO J. 2006;25:2564–2574. PubMed PMC

McClendon T.B., Sullivan M.R., Bernstein K.A., Yanowitz J.L. Promotion of homologous recombination by SWS-1 in complex with RAD-51 paralogs in Caenorhabditis elegans. Genetics. 2016;203:133–145. PubMed PMC

Pellegrini L., Yu D.S., Lo T., Anand S., Lee M., Blundell T.L., Venkitaraman A.R. Insights into DNA recombination from the structure of a RAD51-BRCA2 complex. Nature. 2002;420:287–293. PubMed

Pierce A.J., Johnson R.D., Thompson L.H., Jasin M. XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev. 1999;13:2633–2638. PubMed PMC

Qi Z., Redding S., Lee J.Y., Gibb B., Kwon Y., Niu H., Gaines W.A., Sung P., Greene E.C. DNA sequence alignment by microhomology sampling during homologous recombination. Cell. 2015;160:856–869. PubMed PMC

Qiu Y., Antony E., Doganay S., Koh H.R., Lohman T.M., Myong S. Srs2 prevents Rad51 filament formation by repetitive motion on DNA. Nat. Commun. 2013;4:2281. PubMed PMC

Rattray A.J., Symington L.S. Multiple pathways for homologous recombination in Saccharomyces cerevisiae. Genetics. 1995;139:45–56. PubMed PMC

San Filippo J., Sung P., Klein H. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 2008;77:229–257. PubMed

Sasanuma H., Tawaramoto M.S., Lao J.P., Hosaka H., Sanda E., Suzuki M., Yamashita E., Hunter N., Shinohara M., Nakagawa A., Shinohara A. A new protein complex promoting the assembly of Rad51 filaments. Nat. Commun. 2013;4:1676. PubMed PMC

Shahid T., Soroka J., Kong E.H., Malivert L., McIlwraith M.J., Pape T., West S.C., Zhang X. Structure and mechanism of action of the BRCA2 breast cancer tumor suppressor. Nat. Struct. Mol. Biol. 2014;21:962–968. PubMed PMC

She Z., Gao Z.Q., Liu Y., Wang W.J., Liu G.F., Shtykova E.V., Xu J.H., Dong Y.H. Structural and SAXS analysis of the budding yeast SHU-complex proteins. FEBS Lett. 2012;586:2306–2312. PubMed

Sigurdsson S., Van Komen S., Bussen W., Schild D., Albala J.S., Sung P. Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange. Genes Dev. 2001;15:3308–3318. PubMed PMC

Solinger J.A., Kiianitsa K., Heyer W.D. Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments. Mol. Cell. 2002;10:1175–1188. PubMed

Sounier R., Mas C., Steyaert J., Laeremans T., Manglik A., Huang W., Kobilka B.K., Déméné H., Granier S. Propagation of conformational changes during μ-opioid receptor activation. Nature. 2015;524:375–378. PubMed PMC

Stennett E.M., Ciuba M.A., Lin S., Levitus M. Demystifying PIFE: The photophysics behind the protein-induced fluorescence enhancement phenomenon in Cy3. J. Phys. Chem. Lett. 2015;6:1819–1823. PubMed

Sung P. Yeast Rad55 and Rad57 proteins form a heterodimer that functions with replication protein A to promote DNA strand exchange by Rad51 recombinase. Genes Dev. 1997;11:1111–1121. PubMed

Takata M., Sasaki M.S., Tachiiri S., Fukushima T., Sonoda E., Schild D., Thompson L.H., Takeda S. Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs. Mol. Cell. Biol. 2001;21:2858–2866. PubMed PMC

Tao Y., Li X., Liu Y., Ruan J., Qi S., Niu L., Teng M. Structural analysis of Shu proteins reveals a DNA binding role essential for resisting damage. J. Biol. Chem. 2012;287:20231–20239. PubMed PMC

Taylor M.R., Špírek M., Chaurasiya K.R., Ward J.D., Carzaniga R., Yu X., Egelman E.H., Collinson L.M., Rueda D., Krejci L., Boulton S.J. Rad51 paralogs remodel pre-synaptic Rad51 filaments to stimulate homologous recombination. Cell. 2015;162:271–286. PubMed PMC

Thorslund T., McIlwraith M.J., Compton S.A., Lekomtsev S., Petronczki M., Griffith J.D., West S.C. The breast cancer tumor suppressor BRCA2 promotes the specific targeting of RAD51 to single-stranded DNA. Nat. Struct. Mol. Biol. 2010;17:1263–1265. PubMed PMC

Walker J.E., Saraste M., Runswick M.J., Gay N.J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1:945–951. PubMed PMC

Ward J.D., Barber L.J., Petalcorin M.I., Yanowitz J., Boulton S.J. Replication blocking lesions present a unique substrate for homologous recombination. EMBO J. 2007;26:3384–3396. PubMed PMC

Wold M.S. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 1997;66:61–92. PubMed

Yu X., Jacobs S.A., West S.C., Ogawa T., Egelman E.H. Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proc. Natl. Acad. Sci. USA. 2001;98:8419–8424. PubMed PMC

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