Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains
Language English Country Great Britain, England Media print-electronic
Document type Journal Article
PubMed
27694623
PubMed Central
PMC5224511
DOI
10.1093/nar/gkw882
PII: gkw882
Knihovny.cz E-resources
- MeSH
- Chromatids chemistry metabolism MeSH
- DNA, Fungal genetics metabolism MeSH
- DNA-Binding Proteins chemistry genetics metabolism MeSH
- Endonucleases chemistry genetics metabolism MeSH
- Escherichia coli genetics metabolism MeSH
- Nuclear Proteins chemistry genetics metabolism MeSH
- Cloning, Molecular MeSH
- DNA, Cruciform chemistry metabolism MeSH
- Small Ubiquitin-Related Modifier Proteins chemistry genetics metabolism MeSH
- Genomic Instability MeSH
- DNA Damage MeSH
- Protein Domains MeSH
- Cell Cycle Proteins MeSH
- Gene Expression Regulation, Fungal * MeSH
- Recombinant Proteins chemistry genetics metabolism MeSH
- DNA Replication MeSH
- Saccharomyces cerevisiae Proteins chemistry genetics metabolism MeSH
- Saccharomyces cerevisiae genetics metabolism MeSH
- Protein Binding MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DNA, Fungal MeSH
- DNA-Binding Proteins MeSH
- Endonucleases MeSH
- Esc2 protein, S cerevisiae MeSH Browser
- Nuclear Proteins MeSH
- DNA, Cruciform MeSH
- Small Ubiquitin-Related Modifier Proteins MeSH
- MUS81 protein, S cerevisiae MeSH Browser
- Cell Cycle Proteins MeSH
- Recombinant Proteins MeSH
- Saccharomyces cerevisiae Proteins MeSH
Replication across damaged DNA templates is accompanied by transient formation of sister chromatid junctions (SCJs). Cells lacking Esc2, an adaptor protein containing no known enzymatic domains, are defective in the metabolism of these SCJs. However, how Esc2 is involved in the metabolism of SCJs remains elusive. Here we show interaction between Esc2 and a structure-specific endonuclease Mus81-Mms4 (the Mus81 complex), their involvement in the metabolism of SCJs, and the effects Esc2 has on the enzymatic activity of the Mus81 complex. We found that Esc2 specifically interacts with the Mus81 complex via its SUMO-like domains, stimulates enzymatic activity of the Mus81 complex in vitro, and is involved in the Mus81 complex-dependent resolution of SCJs in vivo Collectively, our data point to the possibility that the involvement of Esc2 in the metabolism of SCJs is, in part, via modulation of the activity of the Mus81 complex.
Department of Biology Masaryk University Kamenice 5 A7 CZ 62500 Brno Czech Republic
Department of Biology University of Copenhagen DK 2200 Copenhagen Denmark
IFOM the FIRC Institute of Molecular Oncology Via Adamello 16 IT 20139 Milan Italy
See more in PubMed
Jackson S.P., Bartek J. The DNA-damage response in human biology and disease. Nature. 2009;461:1071–1078. PubMed PMC
Branzei D. Ubiquitin family modifications and template switching. FEBS Lett. 2011;585:2810–2817. PubMed
Ulrich H.D. Timing and spacing of ubiquitin-dependent DNA damage bypass. FEBS Lett. 2011;585:2861–2867. PubMed
Zhang H., Lawrence C.W. The error-free component of the RAD6/RAD18 DNA damage tolerance pathway of budding yeast employs sister-strand recombination. Proc. Natl. Acad. Sci. U.S.A. 2005;102:15954–15959. PubMed PMC
Branzei D., Vanoli F., Foiani M. SUMOylation regulates Rad18-mediated template switch. Nature. 2008;456:915–920. PubMed
Minca E.C., Kowalski D. Multiple Rad5 activities mediate sister chromatid recombination to bypass DNA damage at stalled replication forks. Mol. Cell. 2010;38:649–661. PubMed PMC
Vanoli F., Fumasoni M., Szakal B., Maloisel L., Branzei D. Replication and recombination factors contributing to recombination-dependent bypass of DNA lesions by template switch. PLoS Genet. 2010;6:e1001205. PubMed PMC
Karras G.I., Fumasoni M., Sienski G., Vanoli F., Branzei D., Jentsch S. Noncanonical role of the 9-1-1 clamp in the error-free DNA damage tolerance pathway. Mol. Cell. 2012 doi:10.1016/j.molcel.2012.11.016. PubMed
Szakal B., Branzei D. Premature Cdk1/Cdc5/Mus81 pathway activation induces aberrant replication and deleterious crossover. EMBO J. 2013;32:1155–1167. PubMed PMC
Ashton T.M., Mankouri H.W., Heidenblut A., McHugh P.J., Hickson I.D. Pathways for Holliday junction processing during homologous recombination in Saccharomyces cerevisiae. Mol. Cell. Biol. 2011;31:1921–1933. PubMed PMC
Ciccia A., Constantinou A., West SC. Identification and characterization of the human Mus81-Eme1 endonuclease. J. Biol. Chem. 2003;278:25172–25178. PubMed
Whitby M.C., Osman F., Dixon J. Cleavage of model replication forks by fission yeast Mus81-Eme1 and budding yeast Mus81-Mms4. J. Biol. Chem. 2003;278:6928–6935. PubMed
Ogrunc M., Sancar A. Identification and characterization of human MUS81-MMS4 structure-specific endonuclease. J. Biol. Chem. 2003;278:21715–21720. PubMed
Fricke W.M., Bastin-Shanower S.A., Brill S.J. Substrate specificity of the Saccharomyces cerevisiae Mus81–Mms4 endonuclease. DNA Repair (Amst.) 2005;4:243–251. PubMed
Ehmsen K.T., Heyer W.D. Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease. Nucleic Acids Res. 2008;36:2182–2195. PubMed PMC
Interthal H., Heyer W.D. MUS81 encodes a novel Helix-hairpin-Helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae. Mol. Gen. Genet. MGG. 2000;263:812–827. PubMed
Osman F., Whitby M. Exploring the roles of Mus81-Eme1/Mms4 at perturbed replication forks. DNA Repair (Amst.) 2007;6:1004–1017. PubMed
Regairaz M., Zhang Y.-W., Fu H., Agama K.K., Tata N., Agrawal S., Aladjem M.I., Pommier Y. Mus81-mediated DNA cleavage resolves replication forks stalled by topoisomerase I–DNA complexes. J. Cell Biol. 2011;195:739–749. PubMed PMC
Mayle R., Campbell I.M., Beck C.R., Yu Y., Wilson M., Shaw C.A., Bjergbaek L., Lupski J.R., Ira G. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015;349:742–747. PubMed PMC
Oh S.D., Lao J.P., Hwang P.Y.-H., Taylor A.F., Smith G.R., Hunter N. BLM ortholog, Sgs1, prevents aberrant crossing-over by suppressing formation of multichromatid joint molecules. Cell. 2008;130:259–272. PubMed PMC
Jessop L., Lichten M. Mus81/Mms4 endonuclease and Sgs1 helicase collaborate to ensure proper recombination intermediate metabolism during meiosis. Mol. Cell. 2008;31:313–323. PubMed PMC
Ying S., Minocherhomji S., Chan K.L., Palmai-Pallag T., Chu W., Wass T., Mankouri H.W., Liu Y., Hickson I.D. MUS81 promotes common fragile site expression. Nat. Cell Biol. 2013;15:1001–1007. PubMed
Naim V., Wilhelm T., Debatisse M., Rosselli F. ERCC1 and MUS81–EME1 promote sister chromatid separation by processing late replication intermediates at common fragile sites during mitosis. Nat. Cell Biol. 2013;15:1008–1015. PubMed
Minocherhomji S., Ying S., Bjerregaard V.A., Bursomanno S., Aleliunaite A., Wu W., Mankouri H.W., Shen H., Liu Y., Hickson I.D. Replication stress activates DNA repair synthesis in mitosis. Nature. 2015;528:286–290. PubMed
Matos J., Blanco M.G., Maslen S., Skehel J.M., West S.C. Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell. 2011;147:158–172. PubMed PMC
Gallo-Fernández M., Saugar I., Ortiz-Bazán M.Á., Vázquez M.V., Tercero J.A. Cell cycle-dependent regulation of the nuclease activity of Mus81–Eme1/Mms4. Nucleic Acids Res. 2012;40:8325–8335. PubMed PMC
Gritenaite D., Princz L.N., Szakal B., Bantele S.C.S., Wendeler L., Schilbach S., Habermann B.H., Matos J., Lisby M., Branzei D., et al. A cell cycle-regulated Slx4–Dpb11 complex promotes the resolution of DNA repair intermediates linked to stalled replication. Genes Dev. 2014;28:1604–1619. PubMed PMC
Dhillon N., Kamakaka R.T. A Histone Variant, Htz1p, and a Sir1p-like Protein, Esc2p, Mediate Silencing at HMR. Mol. Cell. 2000;6:769–780. PubMed
Novatchkova M., Bachmair A., Eisenhaber B., Eisenhaber F. Proteins with two SUMO/like domains in chromatin/associated complexes: The RENi (Rad60/Esc2/NIP45) family. BMC Bioinformatics. 2005;6:22. PubMed PMC
Sollier J., Driscoll R., Castellucci F., Foiani M., Jackson S.P., Branzei D. The Saccharomyces cerevisiae Esc2 and Smc5-6 Proteins Promote Sister Chromatid Junction-mediated Intra-S Repair. Mol. Biol. Cell. 2009;20:1671–1682. PubMed PMC
Mankouri H.W., Ngo H.-P., Hickson I.D. Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae. Mol. Biol. Cell. 2009;20:1683–1694. PubMed PMC
Urulangodi M., Sebesta M., Menolfi D., Szakal B., Sollier J., Sisakova A., Krejci L., Branzei D. Local regulation of the Srs2 helicase by the SUMO-like domain protein Esc2 promotes recombination at sites of stalled replication. Genes Dev. 2015;29:2067–2080. PubMed PMC
Thomas B.J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 1989;56:619–630. PubMed
Matulova P., Marini V., Burgess R.C., Sisakova A., Kwon Y., Rothstein R., Sung P., Krejci L. Cooperativity of Mus81·Mms4 with Rad54 in the resolution of recombination and replication intermediates. J. Biol. Chem. 2009;284:7733–7745. PubMed PMC
Silva S., Gallina I., Eckert-Boulet N., Lisby M. Live cell microscopy of DNA damage response in Saccharomyces cerevisiae. Methods Mol Biol. 2012;920:433–443. PubMed
Orm M., Cubitt A.B., Kallio K., Gross L.A., Tsien R.Y., Remington S.J. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996;273:1392–1395. PubMed
Goedhart J., von Stetten D., Noirclerc-Savoye M., Lelimousin M., Joosen L., Hink M.A., van Weeren L., Gadella T.W.J., Royant A. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93% Nat. Commun. 2012;3:751. PubMed PMC
Bartosova Z., Krejci L. Nucleases in homologous recombination as targets for cancer therapy. FEBS Lett. 2014;588:2446–2456. PubMed
Ayyagari R., Gomes X.V., Gordenin D.A., Burgers P.M.J. Okazaki fragment maturation in yeast: I. Distribution of functions between FEN1 and DNA2. J. Biol. Chem. 2003;278:1618–1625. PubMed
Kao H.I., Henricksen L.A., Liu Y., Bambara R.A. Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate. J. Biol. Chem. 2002;277:14379–14389. PubMed
Tomkinson A.E., Bardwell A.J., Bardwell L., Tappe N.J., Friedberg E.C. Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature. 1993;362:860–862. PubMed
Chen X.-B., Melchionna R., Denis C.-M., Gaillard P.-H.L., Blasina A., Van de Weyer I., Boddy M.N., Russell P., Vialard J., McGowan C.H. Human Mus81-associated endonuclease cleaves Holliday junctions in vitro. Mol. Cell. 2001;8:1117–1127. PubMed
Boddy M.N., Gaillard P.-H.L., McDonald W.H., Shanahan P., Yates J.R., Russell P. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell. 2001;107:537–548. PubMed
Ip S.C.Y., Rass U., Blanco M.G., Flynn H.R., Skehel J.M., West S.C. Identification of Holliday junction resolvases from humans and yeast. Nature. 2008;456:357–361. PubMed
Ho C.K., Mazón G., Lam A.F., Symington L.S. Mus81 and Yen1 promote reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. Mol. Cell. 2010;40:988–1000. PubMed PMC
Blanco M.G., Matos J., Rass U., Ip S.C.Y., West S.C. Functional overlap between the structure-specific nucleases Yen1 and Mus81-Mms4 for DNA-damage repair in S. cerevisiae. DNA Repair (Amst.) 2010;9:394–402. PubMed
Giannattasio M., Zwicky K., Follonier C., Foiani M., Lopes M., Branzei D. Visualization of recombination-mediated damage bypass by template switching. Nat. Struct. Mol. Biol. 2014 doi:10.1038/nsmb.2888. PubMed PMC
Gangloff S., Fabre F., Soustelle C. Homologous recombination is responsible for cell death in the absence of the Sgs1 and Srs2 helicases. Nat. Genet. 2000;25:192–194. PubMed
Krejci L., Altmannova V., Spirek M., Zhao X. Homologous recombination and its regulation. Nucleic Acids Res. 2012;40:5795–5818. PubMed PMC
Branzei D., Foiani M. Maintaining genome stability at the replication fork. Nat Rev Mol Cell Biol. 2010;11:208–219. PubMed
Hicks J.M., Hsu V.L. The extended left-handed helix: a simple nucleic acid-binding motif. Proteins. 2004;55:330–338. PubMed
Siligardi G., Drake A.F. The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides. Biopolymers. 1995;37:281–292. PubMed
Chen C.-F., Brill S.J. Binding and activation of DNA topoisomerase III by the Rmi1 subunit. J. Biol. Chem. 2007;282:28971–28979. PubMed PMC
Cejka P., Plank J.L., Bachrati C.Z., Hickson I.D., Kowalczykowski S.C. Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1–Top3. Nat. Struct. Mol. Biol. 2010;17:1377–1382. PubMed PMC
Bergink S., Ammon T., Kern M., Schermelleh L., Leonhardt H., Jentsch S. Role of Cdc48/p97 as a SUMO-targeted segregase curbing Rad51–Rad52 interaction. Nat Cell Biol. 2013;15:526–532. PubMed
Song J., Zhang Z., Hu W., Chen Y. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J. Biol. Chem. 2005;280:40122–40129. PubMed
Psakhye I., Jentsch S. Protein group modification and synergy in the SUMO pathway as exemplified in DNA repair. Cell. 151:807–820. PubMed
Jentsch S., Psakhye I. Control of nuclear activities by substrate-selective and protein-group SUMOylation. Annu. Rev. Genet. 2013;47:167–186. PubMed
Kolesar P., Altmannova V., Silva S., Lisby M., Krejci L. Pro-recombination role of Srs2 protein requires SUMO (small ubiquitin-like modifier) but Is independent of PCNA (proliferating cell nuclear antigen) interaction. J. Biol. Chem. 2016;291:7594–7607. PubMed PMC
Ryu T., Spatola B., Delabaere L., Bowlin K., Hopp H., Kunitake R., Karpen G.H., Chiolo I. Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat. Cell Biol. 2015;17:1401–1411. PubMed PMC
Gomes X.V., Burgers P.M.J. Two modes of FEN1 binding to PCNA regulated by DNA. EMBO J. 2000;19:3811–3821. PubMed PMC
Tom S., Henricksen L.A., Bambara R.A. Mechanism whereby proliferating cell nuclear antigen stimulates flap endonuclease 1. J. Biol. Chem. 2000;275:10498–10505. PubMed
Cho I.-T., Kim D.-H., Kang Y.-H., Lee C.-H., Amangyelid T., Nguyen T.A., Hurwitz J., Seo Y.-S. Human replication factor C stimulates flap endonuclease 1. J. Biol. Chem. 2009;284:10387–10399. PubMed PMC
Mazina O.M., Mazin A.V. Human Rad54 protein stimulates human Mus81-Eme1 endonuclease. Proc. Natl. Acad. Sci. U.S.A. 2008;105:18249–18254. PubMed PMC
Chavdarova M., Marini V., Sisakova A., Sedlackova H., Vigasova D., Brill S.J., Lisby M., Krejci L. Srs2 promotes Mus81–Mms4-mediated resolution of recombination intermediates. Nucleic Acids Res. 2015;43:3626–3642. PubMed PMC
Wu L., Hickson I.D. The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nat. Cell Biol. 2003;426:870–874. PubMed
Cejka P., Plank J.L., Dombrowski C.C., Kowalczykowski S.C. Decatenation of DNA by the S. cerevisiae Sgs1-Top3-Rmi1 and RPA complex: a mechanism for disentangling chromosomes. Mol. Cell. 2012;47:886–896. PubMed PMC
Fricke W.M., Brill S.J. Slx1—Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1—Top3. Genes Dev. 2003;17:1768–1778. PubMed PMC
Zakharyevich K., Tang S., Ma Y., Hunter N. Delineation of joint molecule resolution pathways in meiosis identifies a crossover-specific resolvase. Cell. 2012;149:334–347. PubMed PMC
Ranjha L., Anand R., Cejka P. The Saccharomyces cerevisiae Mlh1-Mlh3 heterodimer Is an endonuclease that preferentially binds to Holliday junctions. J. Biol. Chem. 2014;289:5674–5686. PubMed PMC
Bellaoui M., Chang M., Ou J., Xu H., Boone C., Brown G.W. Elg1 forms an alternative RFC complex important for DNA replication and genome integrity. EMBO J. 2003;22:4304–4313. PubMed PMC
West S.C., Blanco M.G., Chan Y.W., Matos J., Sarbajna S., Wyatt H.D.M. Resolution of Recombination Intermediates: Mechanisms and Regulation. Cold Spring Harb. Symp. Quant. Biol. 2015;80:103–109. PubMed