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      SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements

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          Abstract

          Mms21, a subunit of the Smc5/6 complex, possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier (SUMO). Here we show that the mms21-CH mutation, which inactivates Mms21 ligase activity, causes increased accumulation of gross chromosomal rearrangements (GCRs) selected in the dGCR assay. These dGCRs are formed by non-allelic homologous recombination between divergent DNA sequences mediated by Rad52-, Rrm3- and Pol32-dependent break-induced replication. Combining mms21-CH with sgs1Δ caused a synergistic increase in GCRs rates, indicating the distinct roles of Mms21 and Sgs1 in suppressing GCRs. The mms21-CH mutation also caused increased rates of accumulating uGCRs mediated by breakpoints in unique sequences as revealed by whole genome sequencing. Consistent with the accumulation of endogenous DNA lesions, mms21-CH mutants accumulate increased levels of spontaneous Rad52 and Ddc2 foci and had a hyper-activated DNA damage checkpoint. Together, these findings support that Mms21 prevents the accumulation of spontaneous DNA lesions that cause diverse GCRs.

          Author summary

          Chromosomal rearrangement is a hallmark of cancer. Saccharomyces cerevisiae Mms21 is an E3 ligase for S mall U biquitin like MO difer (SUMO), which has been shown to have a major role in preventing chromosomal rearrangement. Despite extensive studies about the function of Mms21 in regulating the repair of exogenously induced DNA damage, how Mms21, and its human ortholog NSMCE2, prevents spontaneous chromosomal rearrangement in unperturbed cells has been unknown. In this study, we provided genetic evidences supporting a novel role of Mms21 in preventing the accumulation of spontaneous DNA breaks, which are likely caused by defective DNA replication, without appreciably affecting how they are repaired. Our findings highlight the central role of faithful DNA replication in preventing spontaneous chromosomal rearrangement, and further suggest that the study of the role of Mms21 dependent sumoylation in DNA replication could yield important insights into how the SUMO pathway prevents chromosomal rearrangement in human disease.

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          Most cited references71

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          The BioGRID interaction database: 2017 update

          The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.
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            Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends.

            Formation of single-strand DNA (ssDNA) tails at a double-strand break (DSB) is a key step in homologous recombination and DNA-damage signaling. The enzyme(s) producing ssDNA at DSBs in eukaryotes remain unknown. We monitored 5'-strand resection at inducible DSB ends in yeast and identified proteins required for two stages of resection: initiation and long-range 5'-strand resection. We show that the Mre11-Rad50-Xrs2 complex (MRX) initiates 5' degradation, whereas Sgs1 and Dna2 degrade 5' strands exposing long 3' strands. Deletion of SGS1 or DNA2 reduces resection and DSB repair by single-strand annealing between distant repeats while the remaining long-range resection activity depends on the exonuclease Exo1. In exo1Deltasgs1Delta double mutants, the MRX complex together with Sae2 nuclease generate, in a stepwise manner, only few hundred nucleotides of ssDNA at the break, resulting in inefficient gene conversion and G2/M damage checkpoint arrest. These results provide important insights into the early steps of DSB repair in eukaryotes.
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              Protein modification by SUMO.

              Small ubiquitin-related modifier (SUMO) family proteins function by becoming covalently attached to other proteins as post-translational modifications. SUMO modifies many proteins that participate in diverse cellular processes, including transcriptional regulation, nuclear transport, maintenance of genome integrity, and signal transduction. Reversible attachment of SUMO is controlled by an enzyme pathway that is analogous to the ubiquitin pathway. The functional consequences of SUMO attachment vary greatly from substrate to substrate, and in many cases are not understood at the molecular level. Frequently SUMO alters interactions of substrates with other proteins or with DNA, but SUMO can also act by blocking ubiquitin attachment sites. An unusual feature of SUMO modification is that, for most substrates, only a small fraction of the substrate is sumoylated at any given time. This review discusses our current understanding of how SUMO conjugation is controlled, as well as the roles of SUMO in a number of biological processes.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: Validation
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: Validation
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                5 March 2018
                March 2018
                : 14
                : 3
                : e1007250
                Affiliations
                [1 ] Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                [2 ] Departments of Chemistry and Biochemistry, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                [3 ] Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                [4 ] Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                [5 ] Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                [6 ] Department of Medicine, University of California School of Medicine, San Diego, La Jolla, California, United States of America
                Columbia University, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-4806-8384
                http://orcid.org/0000-0002-6145-1265
                http://orcid.org/0000-0002-1350-4430
                Article
                PGENETICS-D-18-00016
                10.1371/journal.pgen.1007250
                5860785
                29505562
                39602fc3-d635-4e64-9c6d-506a452101de
                © 2018 Liang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 5 January 2018
                : 12 February 2018
                Page count
                Figures: 7, Tables: 0, Pages: 28
                Funding
                Funded by: Ludwig Institute for Cancer Research (US)
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: GM116897
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: GM26017
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: T32 CA009523
                Award Recipient :
                These studies were supported by the Ludwig Institute for Cancer Research (RDK, CDP and HZ), NIH grants GM26017 (RDK) and GM116897 (HZ), and NCI grant T32 CA009523 (JL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Genetics
                DNA
                DNA damage
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA damage
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and life sciences
                Biochemistry
                Proteins
                Post-translational modification
                SUMOylation
                Biology and Life Sciences
                Genetics
                Mutation
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomal Aberrations
                Chromosomal Translocations
                Biology and life sciences
                Genetics
                DNA
                DNA replication
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA replication
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomes
                Chromosome Structure and Function
                Telomeres
                Biology and life sciences
                Genetics
                DNA
                DNA repair
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
                DNA repair
                Custom metadata
                vor-update-to-uncorrected-proof
                2018-03-20
                All relevant data are within the paper and its Supporting Information files.

                Genetics
                Genetics

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