Single-molecule visualization of human RECQ5 interactions with single-stranded DNA recombination intermediates
Jazyk angličtina Země Anglie, Velká Británie Médium print
Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem
Grantová podpora
206292/Z/17/Z
Wellcome Trust - United Kingdom
R01 CA236606
NCI NIH HHS - United States
P01 CA092584
NCI NIH HHS - United States
Wellcome Trust - United Kingdom
F31 CA210663
NCI NIH HHS - United States
R35 CA241801
NCI NIH HHS - United States
PubMed
33332547
PubMed Central
PMC7797033
DOI
10.1093/nar/gkaa1184
PII: 6041011
Knihovny.cz E-zdroje
- MeSH
- adenosintrifosfát metabolismus MeSH
- bodová mutace MeSH
- helikasy RecQ genetika metabolismus ultrastruktura MeSH
- homologní rekombinace * MeSH
- hydrolýza MeSH
- jednovláknová DNA metabolismus ultrastruktura MeSH
- kinetika MeSH
- lidé MeSH
- mikroskopie atomárních sil MeSH
- missense mutace MeSH
- molekulární motory metabolismus ultrastruktura MeSH
- rekombinantní fúzní proteiny metabolismus MeSH
- rekombinantní proteiny metabolismus MeSH
- rekombinasa Rad51 genetika metabolismus MeSH
- replikační protein A metabolismus MeSH
- substrátová specifita MeSH
- zobrazení jednotlivé molekuly * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- adenosintrifosfát MeSH
- helikasy RecQ MeSH
- jednovláknová DNA MeSH
- molekulární motory MeSH
- RAD51 protein, human MeSH Prohlížeč
- RECQL5 protein, human MeSH Prohlížeč
- rekombinantní fúzní proteiny MeSH
- rekombinantní proteiny MeSH
- rekombinasa Rad51 MeSH
- replikační protein A MeSH
- RPA1 protein, human MeSH Prohlížeč
RECQ5 is one of five RecQ helicases found in humans and is thought to participate in homologous DNA recombination by acting as a negative regulator of the recombinase protein RAD51. Here, we use kinetic and single molecule imaging methods to monitor RECQ5 behavior on various nucleoprotein complexes. Our data demonstrate that RECQ5 can act as an ATP-dependent single-stranded DNA (ssDNA) motor protein and can translocate on ssDNA that is bound by replication protein A (RPA). RECQ5 can also translocate on RAD51-coated ssDNA and readily dismantles RAD51-ssDNA filaments. RECQ5 interacts with RAD51 through protein-protein contacts, and disruption of this interface through a RECQ5-F666A mutation reduces translocation velocity by ∼50%. However, RECQ5 readily removes the ATP hydrolysis-deficient mutant RAD51-K133R from ssDNA, suggesting that filament disruption is not coupled to the RAD51 ATP hydrolysis cycle. RECQ5 also readily removes RAD51-I287T, a RAD51 mutant with enhanced ssDNA-binding activity, from ssDNA. Surprisingly, RECQ5 can bind to double-stranded DNA (dsDNA), but it is unable to translocate. Similarly, RECQ5 cannot dismantle RAD51-bound heteroduplex joint molecules. Our results suggest that the roles of RECQ5 in genome maintenance may be regulated in part at the level of substrate specificity.
Department of Biochemistry and Molecular Biophysics Columbia University New York NY 10032 USA
Department of Biology Masaryk University Brno 62500 Czech Republic
DSB Repair Metabolism Lab The Francis Crick Institute Midland Road London NW1 1AT UK
International Clinical Research Center St Anne's University Hospital Brno Brno 65691 Czech Republic
National Centre for Biomolecular Research Masaryk Brno 62500 Czech Republic
Zobrazit více v PubMed
Bernstein K.A., Gangloff S., Rothstein R.. The RecQ DNA helicases in DNA repair. Annu. Rev. Genet. 2010; 44:393–417. PubMed PMC
Branzei D., Foiani M.. RecQ helicases queuing with Srs2 to disrupt Rad51 filaments and suppress recombination. Genes Dev. 2007; 21:3019–3026. PubMed
Branzei D., Szakal B.. Building up and breaking down: mechanisms controlling recombination during replication. Crit Rev Biochem. 2017; 52:381–394. PubMed
Croteau D.L., Popuri V., Opresko P.L., Bohr V.A.. Human RecQ helicases in DNA repair, recombination, and replication. Annu. Rev. Biochem. 2014; 83:519–552. PubMed PMC
Chu W.K., Hickson I.D.. RecQ helicases: multifunctional genome caretakers. Nat. Rev. Cancer. 2009; 9:644–654. PubMed
Larsen N.B., Hickson I.D.. RecQ Helicases: conserved guardians of genomic integrity. Adv. Exp. Med. Biol. 2013; 767:161–184. PubMed
Brosh R.M., Jr DNA helicases involved in DNA repair and their roles in cancer. Nat. Rev. Cancer. 2013; 13:542–558. PubMed PMC
Krejci L., Altmannova V., Spirek M., Zhao X.. Homologous recombination and its regulation. Nucleic Acids Res. 2012; 40:5795–5818. PubMed PMC
Kowalczykowski S.C. An overview of the molecular mechanisms of recombinational DNA repair. Cold Spring Harb. Perspect. Biol. 2015; 7:a016410. PubMed PMC
Arora H., Chacon A.H., Choudhary S., McLeod M.P., Meshkov L., Nouri K., Izakovic J.. Bloom syndrome. Int. J. Dermatol. 2014; 53:798–802. PubMed
Campbell M.B., Campbell W.C., Rogers J., Rogers N., Rogers Z., van den Hurk A.M., Webb A., Webb T., Zaslaw P.. Bloom syndrome: research and data priorities for the development of precision medicine as identified by some affected families. Cold Spring Harb Mol Case Stud. 2018; 4:a002816. PubMed PMC
Ellis N.A., Groden J., Ye T.Z., Straughen J., Lennon D.J., Ciocci S., Proytcheva M., German J.. The Bloom's syndrome gene product is homologous to RecQ helicases. Cell. 1995; 83:655–666. PubMed
German J. Bloom's syndrome. XX. The first 100 cancers. Cancer Genet. Cytogenet. 1997; 93:100–106. PubMed
Kowalczykowski S.C. An overview of the molecular mechanisms of recombinational DNA repair. Cold Spring Harb. Perspect. Biol. 2015; 7:a016410. PubMed PMC
San Filippo J., Sung P., Klein H.. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 2008; 77:229–257. PubMed
Heyer W.D., Ehmsen K.T., Liu J.. Regulation of homologous recombination in eukaryotes. Annu. Rev. Genet. 2010; 44:113–139. PubMed PMC
Tavera-Tapia A., de la Hoya M., Calvete O., Martin-Gimeno P., Fernandez V., Macias J.A., Alonso B., Pombo L., de Diego C., Alonso R. et al. .. RECQL5: Another DNA helicase potentially involved in hereditary breast cancer susceptibility. Hum Mutat. 2019; 40:566–577. PubMed
Peng J., Tang L., Cai M., Chen H., Wong J., Zhang P.. RECQL5 plays an essential role in maintaining genome stability and viability of triple-negative breast cancer cells. Cancer Med. 2019; 8:4743–4752. PubMed PMC
Fu W., Ligabue A., Rogers K.J., Akey J.M., Monnat R.J. Jr. Human RECQ helicase pathogenic variants, population variation and “Missing” diseases. Hum. Mutat. 2017; 38:193–203. PubMed PMC
Saponaro M., Kantidakis T., Mitter R., Kelly G.P., Heron M., Williams H., Soding J., Stewart A., Svejstrup J.Q.. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell. 2014; 157:1037–1049. PubMed PMC
Hu Y., Raynard S., Sehorn M.G., Lu X., Bussen W., Zheng L., Stark J.M., Barnes E.L., Chi P., Janscak P. et al. .. RECQL5/Recql5 helicase regulates homologous recombination and suppresses tumor formation via disruption of Rad51 presynaptic filaments. Genes Dev. 2007; 21:3073–3084. PubMed PMC
Popuri V., Huang J., Ramamoorthy M., Tadokoro T., Croteau D.L., Bohr V.A.. RECQL5 plays co-operative and complementary roles with WRN syndrome helicase. Nucleic Acids Res. 2013; 41:881–899. PubMed PMC
Olson H.C., Davis L., Kiianitsa K., Khoo K.J., Liu Y., Knijnenburg T.A., Maizels N.. Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways. Nucleic Acids Res. 2018; 46:9496–9509. PubMed PMC
Paliwal S., Kanagaraj R., Sturzenegger A., Burdova K., Janscak P.. Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing. Nucleic Acids Res. 2014; 42:2380–2390. PubMed PMC
Schwendener S., Raynard S., Paliwal S., Cheng A., Kanagaraj R., Shevelev I., Stark J.M., Sung P., Janscak P.. Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity. J. Biol. Chem. 2010; 285:15739–15745. PubMed PMC
Aygun O., Svejstrup J.Q.. RECQL5 helicase: connections to DNA recombination and RNA polymerase II transcription. DNA Repair (Amst.). 2010; 9:345–353. PubMed
Aygun O., Svejstrup J., Liu Y.. A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin. Proc. Natl. Acad. Sci. U.S.A. 2008; 105:8580–8584. PubMed PMC
Kanagaraj R., Huehn D., MacKellar A., Menigatti M., Zheng L., Urban V., Shevelev I., Greenleaf A.L., Janscak P.. RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription. Nucleic Acids Res. 2010; 38:8131–8140. PubMed PMC
Urban V., Dobrovolna J., Huhn D., Fryzelkova J., Bartek J., Janscak P.. RECQ5 helicase promotes resolution of conflicts between replication and transcription in human cells. J. Cell Biol. 2016; 214:401–415. PubMed PMC
Di Marco S., Hasanova Z., Kanagaraj R., Chappidi N., Altmannova V., Menon S., Sedlackova H., Langhoff J., Surendranath K., Huhn D. et al. .. RECQ5 helicase cooperates with MUS81 endonuclease in processing stalled replication forks at common fragile sites during mitosis. Mol. Cell. 2017; 66:658–671. PubMed
Kitano K. Structural mechanisms of human RecQ helicases WRN and BLM. Front Genet. 2014; 5:366. PubMed PMC
Bennett R.J., Sharp J.A., Wang J.C.. Purification and characterization of the Sgs1 DNA helicase activity of Saccharomyces cerevisiae. J. Biol. Chem. 1998; 273:9644–9650. PubMed
Bernstein D.A., Keck J.L.. Domain mapping of Escherichia coli RecQ defines the roles of conserved N- and C-terminal regions in the RecQ family. Nucleic Acids Res. 2003; 31:2778–2785. PubMed PMC
Bugreev D.V., Yu X., Egelman E.H., Mazin A.V.. Novel pro- and anti-recombination activities of the Bloom's syndrome helicase. Genes Dev. 2007; 21:3085–3094. PubMed PMC
Xue C., Daley J.M., Xue X., Steinfeld J., Kwon Y., Sung P., Greene E.C.. Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates. Nucleic Acids Res. 2019; 41:11225–11237. PubMed PMC
Spirek M., Mlcouskova J., Belan O., Gyimesi M., Harami G.M., Molnar E., Novacek J., Kovacs M., Krejci L.. Human RAD51 rapidly forms intrinsically dynamic nucleoprotein filaments modulated by nucleotide binding state. Nucleic Acids Res. 2018; 46:3967–3980. PubMed PMC
Kinebuchi T., Kagawa W., Enomoto R., Tanaka K., Miyagawa K., Shibata T., Kurumizaka H., Yokoyama S.. Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1. Mol. Cell. 2004; 14:363–374. PubMed
Chi P., Van Komen S., Sehorn M.G., Sigurdsson S., Sung P.. Roles of ATP binding and ATP hydrolysis in human Rad51 recombinase function. DNA Repair (Amst.). 2006; 5:381–391. PubMed
Ma C.J., Steinfeld J.B., Greene E.C.. Single-Stranded DNA curtains for studying homologous recombination. Meth Enzymol. 2017; 582:193–219. PubMed PMC
De Tullio L., Kaniecki K., Greene E.C.. Single-Stranded DNA curtains for studying the Srs2 helicase using total internal reflection fluorescence microscopy. Meth Enzymol. 2018; 600:407–437. PubMed PMC
Crickard J.B., Kaniecki K., Kwon Y., Sung P., Greene E.C.. Meiosis-specific recombinase Dmc1 is a potent inhibitor of the Srs2 antirecombinase. Proc. Natl. Acad. Sci. U.S.A. 2018; 115:E10041–E10048. PubMed PMC
Kaniecki K., De Tullio L., Gibb B., Kwon Y., Sung P., Greene E.C.. Dissociation of Rad51 presynaptic complexes and heteroduplex DNA joints by tandem assemblies of Srs2. Cell Rep. 2017; 21:3166–3177. PubMed PMC
Binz S.K., Sheehan A.M., Wold M.S.. Replication protein A phosphorylation and the cellular response to DNA damage. DNA Repair (Amst.). 2004; 3:1015–1024. PubMed
Chen R., Wold M.S.. Replication protein A: single-stranded DNA’s first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays. 2014; 36:1156–1161. 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
Bugreev D.V., Mazin A.V.. Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity. Proc. Natl. Acad. Sci. U.S.A. 2004; 101:9988–9993. PubMed PMC
Ma C.J., Gibb B., Kwon Y., Sung P., Greene E.C.. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res. 2017; 45:749–761. PubMed PMC
Concepcion J., Witte K., Wartchow C., Choo S., Yao D., Persson H., Wei J., Li P., Heidecker B., Ma W. et al. .. Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization. Comb. Chem. High Throughput Screen. 2009; 12:791–800. PubMed
Davies A.A., Masson J.Y., McIlwraith M.J., Stasiak A.Z., Stasiak A., Venkitaraman A.R., West S.C.. Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Mol. Cell. 2001; 7:273–282. PubMed
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
Chen Z., Yang H., Pavletich N.P.. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature. 2008; 453:489–484. PubMed
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
Fung C.W., Fortin G.S., Peterson S.E., Symington L.S.. The rad51-K191R ATPase-defective mutant is impaired for presynaptic filament formation. Mol. Cell. Biol. 2006; 26:9544–9554. PubMed PMC
Morgan E.A., Shah N., Symington L.S.. The requirement for ATP hydrolysis by Saccharomyces cerevisiae Rad51 is bypassed by mating-type heterozygosity or RAD54 in high copy. Mol. Cell. Biol. 2002; 22:6336–6343. PubMed PMC
Fortin G.S., Symington L.S.. Mutations in yeast Rad51 that partially bypass the requirement for Rad55 and Rad57 in DNA repair by increasing the stability of Rad51-DNA complexes. EMBO J. 2002; 21:3160–3170. PubMed PMC
Davies O.R., Pellegrini L.. Interaction with the BRCA2 C terminus protects RAD51-DNA filaments from disassembly by BRC repeats. Nat. Struct. Mol. Biol. 2007; 14:475–483. PubMed PMC
Brown M.S., Bishop D.K.. DNA strand exchange and RecA homologs in meiosis. Cold Spring Harb. Perspect. Biol. 2014; 7:a016659. PubMed PMC
Neale M.J., Keeney S.. Clarifying the mechanics of DNA strand exchange in meiotic recombination. Nature. 2006; 442:153–158. PubMed PMC
Sasanuma H., Furihata Y., Shinohara M., Shinohara A.. Remodeling of the Rad51 DNA strand-exchange protein by the Srs2 helicase. Genetics. 2013; 194:859–872. PubMed PMC
Crickard J.B., Xue C., Wang W., Kwon Y., Sung P., Greene E.C.. The RecQ helicase Sgs1 drives ATP-dependent disruption of Rad51 filaments. Nucleic Acids Res. 2019; 47:4694–4706. PubMed PMC
Greene E.C., Wind S., Fazio T., Gorman J., Visnapuu M.L.. DNA curtains for high-throughput single-molecule optical imaging. Meth Enzymol. 2010; 472:293–315. PubMed PMC
Crickard J.B., Xue C., Wang W., Kwon Y., Sung P., Greene E.C.. The RecQ helicase Sgs1 drives ATP-dependent disruption of Rad51 filaments. Nucleic Acids Res. 2019; 47:4694–4706. PubMed PMC
Garcia P.L., Liu Y., Jiricny J., West S.C., Janscak P.. Human RECQ5beta, a protein with DNA helicase and strand-annealing activities in a single polypeptide. EMBO J. 2004; 23:2882–2891. PubMed PMC
Xue C., Wang W., Crickard J.B., Moevus C.J., Kwon Y., Sung P., Greene E.C.. Regulatory control of Sgs1 and Dna2 during eukaryotic DNA end resection. Proc. Natl. Acad. Sci. U.S.A. 2019; 116:6091–6100. PubMed PMC
Lee J.Y., Terakawa T., Qi Z., Steinfeld J.B., Redding S., Kwon Y., Gaines W.A., Zhao W., Sung P., Greene E.C.. Base triplet stepping by the Rad51/RecA family of recombinases. Science. 2015; 349:977–981. PubMed PMC
Krejci L., Van Komen S., Li Y., Villemain J., Reddy M.S., Klein H., Ellenberger T., Sung P.. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature. 2003; 423:305–309. PubMed
Veaute X., Jeusset J., Soustelle C., Kowalczykowski S.C., Le Cam E., Fabre F.. The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments. Nature. 2003; 423:309–312. PubMed
De Tullio L., Kaniecki K., Kwon Y., Crickard J.B., Sung P., Greene E.C.. Yeast Srs2 helicase promotes redistribution of Single-Stranded DNA-Bound RPA and Rad52 in homologous recombination regulation. Cell Rep. 2017; 21:570–577. PubMed PMC
Malik P.S., Symington L.S.. Rad51 gain-of-function mutants that exhibit high affinity DNA binding cause DNA damage sensitivity in the absence of Srs2. Nucleic Acids Res. 2008; 36:6504–6510. PubMed PMC
Nimonkar A.V., Genschel J., Kinoshita E., Polaczek P., Campbell J.L., Wyman C., Modrich P., Kowalczykowski S.C.. BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev. 2011; 25:350–362. PubMed PMC
Daley J.M., Chiba T., Xue X., Niu H., Sung P.. Multifaceted role of the Topo IIIalpha-RMI1-RMI2 complex and DNA2 in the BLM-dependent pathway of DNA break end resection. Nucleic Acids Res. 2014; 42:11083–11091. PubMed PMC
Shimamoto A., Nishikawa K., Kitao S., Furuichi Y.. Human RecQ5beta, a large isomer of RecQ5 DNA helicase, localizes in the nucleoplasm and interacts with topoisomerases 3alpha and 3beta. Nucleic Acids Res. 2000; 28:1647–1655. PubMed PMC
Patel D.S., Misenko S.M., Her J., Bunting S.F.. BLM helicase regulates DNA repair by counteracting RAD51 loading at DNA double-strand break sites. J. Cell Biol. 2017; 216:3521–3534. PubMed PMC
Brouwer I., Moschetti T., Candelli A., Garcin E.B., Modesti M., Pellegrini L., Wuite G.J., Peterman E.J.. Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA. EMBO J. 2018; 37:e98162. PubMed PMC
Karmakar P., Seki M., Kanamori M., Hashiguchi K., Ohtsuki M., Murata E., Inoue E., Tada S., Lan L., Yasui A. et al. .. BLM is an early responder to DNA double-strand breaks. Biochem. Biophys. Res. Commun. 2006; 348:62–69. PubMed
Lan L., Nakajima S., Komatsu K., Nussenzweig A., Shimamoto A., Oshima J., Yasui A.. Accumulation of Werner protein at DNA double-strand breaks in human cells. J. Cell Sci. 2005; 118:4153–4162. PubMed
Liu Z., Macias M.J., Bottomley M.J., Stier G., Linge J.P., Nilges M., Bork P., Sattler M.. The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Structure. 1999; 7:1557–1566. PubMed
Samanta S., Karmakar P.. Recruitment of HRDC domain of WRN and BLM to the sites of DNA damage induced by mitomycin C and methyl methanesulfonate. Cell Biol. Int. 2012; 36:873–881. PubMed