Distinct Roles of Mus81, Yen1, Slx1-Slx4, and Rad1 Nucleases in the Repair of Replication-Born Double-Strand Breaks by Sister Chromatid Exchange

ABSTRACT Most spontaneous DNA double-strand breaks (DSBs) arise during replication and are repaired by homologous recombination (HR) with the sister chromatid. Many proteins participate in HR, but it is often difficult to determine their in vivo functions due to the existence of alternative pathways. Here we take advantage of an in vivo assay to assess repair of a specific replication-born DSB by sister chromatid recombination (SCR). We analyzed the functional relevance of four structure-selective endonucleases (SSEs), Yen1, Mus81-Mms4, Slx1-Slx4, and Rad1, on SCR in Saccharomyces cerevisiae. Physical and genetic analyses showed that ablation of any of these SSEs leads to a specific SCR decrease that is not observed in general HR. Our work suggests that Yen1, Mus81-Mms4, Slx4, and Rad1, but not Slx1, function independently in the cleavage of intercrossed DNA structures to reconstitute broken replication forks via HR with the sister chromatid. These unique effects, which have not been detected in other studies unless double mutant combinations were used, indicate the formation of distinct alternatives for the repair of replication-born DSBs that require specific SSEs.

[1]  W. Heyer,et al.  Erratum to: Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes , 2011, Chromosoma.

[2]  S. West,et al.  Aberrant chromosome morphology in human cells defective for Holliday junction resolution , 2011, Nature.

[3]  W. Heyer,et al.  Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes , 2011, Chromosoma.

[4]  L. Symington,et al.  Mus81 and Yen1 promote reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. , 2010, Molecular cell.

[5]  W. Heyer,et al.  Regulation of homologous recombination in eukaryotes. , 2010, Annual review of genetics.

[6]  S. Kowalczykowski,et al.  Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1–Top3 , 2010, Nature Structural &Molecular Biology.

[7]  S. West,et al.  Mechanism of Holliday junction resolution by the human GEN1 protein. , 2010, Genes & development.

[8]  S. West,et al.  Functional overlap between the structure-specific nucleases Yen1 and Mus81-Mms4 for DNA-damage repair in S. cerevisiae. , 2010, DNA repair.

[9]  Y. Tay,et al.  Overlapping Roles for Yen1 and Mus81 in Cellular Holliday Junction Processing* , 2010, The Journal of Biological Chemistry.

[10]  S. West,et al.  The human Holliday junction resolvase GEN1 rescues the meiotic phenotype of a Schizosaccharomyces pombe mus81 mutant , 2009, Nucleic acids research.

[11]  S. Boulton,et al.  Caenorhabditis elegans HIM-18/SLX-4 Interacts with SLX-1 and XPF-1 and Maintains Genomic Integrity in the Germline by Processing Recombination Intermediates , 2009, PLoS genetics.

[12]  J. Yates,et al.  Human SLX4 Is a Holliday Junction Resolvase Subunit that Binds Multiple DNA Repair/Recombination Endonucleases , 2009, Cell.

[13]  C. Ponting,et al.  Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. , 2009, Molecular cell.

[14]  J. Sekelsky,et al.  Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. , 2009, Molecular cell.

[15]  Steven P. Gygi,et al.  Mammalian BTBD12/SLX4 Assembles A Holliday Junction Resolvase and Is Required for DNA Repair , 2009, Cell.

[16]  W. Heyer,et al.  A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4 , 2009, Nucleic acids research.

[17]  A. Aguilera,et al.  DNA double-strand break repair: how to fix a broken relationship , 2009 .

[18]  A. Aguilera,et al.  DNA Repair in Mammalian Cells , 2009, Cellular and Molecular Life Sciences.

[19]  S. West,et al.  Identification of Holliday junction resolvases from humans and yeast , 2008, Nature.

[20]  Michael Lichten,et al.  Mus81/Mms4 endonuclease and Sgs1 helicase collaborate to ensure proper recombination intermediate metabolism during meiosis. , 2008, Molecular cell.

[21]  Neil Hunter,et al.  RecQ helicase, Sgs1, and XPF family endonuclease, Mus81-Mms4, resolve aberrant joint molecules during meiotic recombination. , 2008, Molecular cell.

[22]  S. West,et al.  Structural and functional relationships of the XPF/MUS81 family of proteins. , 2008, Annual review of biochemistry.

[23]  P. Russell,et al.  Mus81 is essential for sister chromatid recombination at broken replication forks , 2008, The EMBO journal.

[24]  C. McGowan,et al.  Cleavage mechanism of human Mus81–Eme1 acting on Holliday-junction structures , 2008, Proceedings of the National Academy of Sciences.

[25]  B. Gómez-González,et al.  Genome instability: a mechanistic view of its causes and consequences , 2008, Nature Reviews Genetics.

[26]  W. Heyer,et al.  Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease , 2008, Nucleic Acids Research.

[27]  R. Kanaar,et al.  The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks , 2007, Nature Structural &Molecular Biology.

[28]  S. Lindquist,et al.  A suite of Gateway® cloning vectors for high‐throughput genetic analysis in Saccharomyces cerevisiae , 2007, Yeast.

[29]  A. Aguilera,et al.  Different genetic requirements for repair of replication-born double-strand breaks by sister-chromatid recombination and break-induced replication , 2007, Nucleic acids research.

[30]  J. Haber,et al.  Phosphorylation of Slx4 by Mec1 and Tel1 Regulates the Single-Strand Annealing Mode of DNA Repair in Budding Yeast , 2007, Molecular and Cellular Biology.

[31]  M. Whitby,et al.  Mus81 cleavage of Holliday junctions: a failsafe for processing meiotic recombination intermediates? , 2007, The EMBO journal.

[32]  A. Aguilera,et al.  Double‐strand breaks arising by replication through a nick are repaired by cohesin‐dependent sister‐chromatid exchange , 2006, EMBO reports.

[33]  J. Haber,et al.  Smc5–Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination , 2006, Nature Cell Biology.

[34]  S. Keeney,et al.  Crossover Homeostasis in Yeast Meiosis , 2006, Cell.

[35]  S. Brill,et al.  Substrate specificity of the Saccharomyces cerevisiae Mus81-Mms4 endonuclease. , 2005, DNA repair.

[36]  J. Yates,et al.  Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. , 2003, Molecular biology of the cell.

[37]  Ian D. Hickson,et al.  The Bloom's syndrome helicase suppresses crossing over during homologous recombination , 2003, Nature.

[38]  P. Russell,et al.  Fission yeast Mus81.Eme1 Holliday junction resolvase is required for meiotic crossing over but not for gene conversion. , 2003, Genetics.

[39]  M. Whitby,et al.  Generating crossovers by resolution of nicked Holliday junctions: a role for Mus81-Eme1 in meiosis. , 2003, Molecular cell.

[40]  S. Brill,et al.  Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3. , 2003, Genes & development.

[41]  A. Aguilera,et al.  Equal sister chromatid exchange is a major mechanism of double-strand break repair in yeast. , 2003, Molecular cell.

[42]  Stephen C. West,et al.  Molecular views of recombination proteins and their control , 2003, Nature Reviews Molecular Cell Biology.

[43]  S. Brill,et al.  The Mechanism of Mus81-Mms4 Cleavage Site Selection Distinguishes It from the Homologous Endonuclease Rad1-Rad10 , 2003, Molecular and Cellular Biology.

[44]  F. Fabre,et al.  Alternate pathways involving Sgs1/Top3, Mus81/ Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  J. Sekelsky,et al.  Drosophila MUS312 interacts with the nucleotide excision repair endonuclease MEI-9 to generate meiotic crossovers. , 2002, Molecular cell.

[46]  A. Aguilera,et al.  Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae. , 2002, Genetics.

[47]  M. Whitby,et al.  Mus81-Eme1 and Rqh1 Involvement in Processing Stalled and Collapsed Replication Forks* , 2002, The Journal of Biological Chemistry.

[48]  J. Yates,et al.  Mus81-Eme1 Are Essential Components of a Holliday Junction Resolvase , 2001, Cell.

[49]  I. Hickson,et al.  Topoisomerase III Acts Upstream of Rad53p in the S-Phase DNA Damage Checkpoint , 2001, Molecular and Cellular Biology.

[50]  S. Brill,et al.  Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease. , 2001, Genes & development.

[51]  S. Brill,et al.  Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae. , 2001, Genetics.

[52]  W. Heyer,et al.  MUS81 encodes a novel Helix-hairpin-Helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae , 2000, Molecular and General Genetics MGG.

[53]  J. Haber,et al.  Multiple Pathways of Recombination Induced by Double-Strand Breaks in Saccharomyces cerevisiae , 1999, Microbiology and Molecular Biology Reviews.

[54]  J. Sekelsky,et al.  The Drosophila meiotic recombination gene mei-9 encodes a homologue of the yeast excision repair protein Rad1. , 1995, Genetics.

[55]  E. Louis,et al.  Sgs1: A eukaryotic homolog of E. coil RecQ that interacts with topoisomerase II in vivo and is required for faithful chromosome segregation , 1995, Cell.

[56]  S Gangloff,et al.  The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase , 1994, Molecular and cellular biology.

[57]  P. Sung,et al.  Holliday junction cleavage by yeast Rad1 protein , 1994, Nature.