1
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. CDK-independent role of D-type cyclins in regulating DNA mismatch repair. Mol Cell 2024; 84:1224-1242.e13. [PMID: 38458201 PMCID: PMC10997477 DOI: 10.1016/j.molcel.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/10/2024]
Abstract
Although mismatch repair (MMR) is essential for correcting DNA replication errors, it can also recognize other lesions, such as oxidized bases. In G0 and G1, MMR is kept in check through unknown mechanisms as it is error-prone during these cell cycle phases. We show that in mammalian cells, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins inhibit the proteasomal degradation of p21, which competes with MMR proteins for binding to PCNA, thereby inhibiting MMR. The ability of D-type cyclins to limit MMR is CDK4- and CDK6-independent and is conserved in G0 and G1. At the G1/S transition, the timely, cullin-RING ubiquitin ligase (CRL)-dependent degradation of D-type cyclins and p21 enables MMR activity to efficiently repair DNA replication errors. Persistent expression of D-type cyclins during S-phase inhibits the binding of MMR proteins to PCNA, increases the mutational burden, and promotes microsatellite instability.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel J Laverty
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cortt G Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged 6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA.
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2
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Singh R, Jaiswal A, Singh RP. Simulated microgravity induces DNA damage concurrent with impairment of DNA repair and activation of cell-type specific DNA damage response in microglial and glioblastoma cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119679. [PMID: 38272357 DOI: 10.1016/j.bbamcr.2024.119679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/31/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Long-term spaceflights affect the structural changes in brain, alter motor or cognitive function and associated development of neuro-optic syndrome in astronauts. Studies addressing the impact of microgravity on brain cells are very limited. Herein, we employed microglial (CHME3) and glioblastoma (U87MG and A172) cells to study their molecular and functional adaptations under simulated microgravity (SMG) exposure. A reduction in cell viability and proliferation with decreased levels of PCNA were observed in these cells. SMG caused extensive DNA damage with an increase in γH2A.X (ser139) phosphorylation and differential activation/expression of DNA damage response (DDR) proteins including ATM, ATR, Chk1, Chk2 and p53 in all the three cell lines. Unlike CHME3, the ATM/Chk2-dependent DDR pathway was activated in glioblastoma cells suggesting a marked difference in the adaptation between normal and cancer cells to SMG. Five different classes of DNA repair pathways including BER, NER, MMR, NHEJ and HR were suppressed in both cell lines with the notable exception of NHEJ (Ku70/80 and DNA-PK) activation in U87MG cells. SMG induced mitochondrial apoptosis with increased expression of Bax, cleaved caspase-3 and cleaved poly-(ADP-ribose) polymerase, and reduced Bcl-2 level. SMG triggered apoptosis simultaneously via ERK1/2 and AKT activation, and inhibition of GSK3β activity which was reversed by MEK1 and PI3K inhibitors. Taken together, our study revealed that microgravity is a strong stressor to trigger DNA damage and apoptosis through activation of ERK1/2 and AKT, and impairment of DNA repair capacity, albeit with a cell-type difference in DDR and NHEJ regulation, in microglial and glioblastoma cells.
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Affiliation(s)
- Ragini Singh
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aishwarya Jaiswal
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rana P Singh
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India; Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA.
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3
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575420. [PMID: 38260436 PMCID: PMC10802603 DOI: 10.1101/2024.01.12.575420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The large majority of oxidative DNA lesions occurring in the G1 phase of the cell cycle are repaired by base excision repair (BER) rather than mismatch repair (MMR) to avoid long resections that can lead to genomic instability and cell death. However, the molecular mechanisms dictating pathway choice between MMR and BER have remained unknown. Here, we show that, during G1, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins shield p21 from its two ubiquitin ligases CRL1SKP2 and CRL4CDT2 in a CDK4/6-independent manner. In turn, p21 competes through its PCNA-interacting protein degron with MMR components for their binding to PCNA. This inhibits MMR while not affecting BER. At the G1/S transition, the CRL4AMBRA1-dependent degradation of D-type cyclins renders p21 susceptible to proteolysis. These timely degradation events allow the proper binding of MMR proteins to PCNA, enabling the repair of DNA replication errors. Persistent expression of cyclin D1 during S-phase increases the mutational burden and promotes microsatellite instability. Thus, the expression of D-type cyclins inhibits MMR in G1, whereas their degradation is necessary for proper MMR function in S.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V. Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A. Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B. Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W. Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A. Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Cortt G. Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S. Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, University of Szeged, Szeged, H-6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D. Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
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4
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Li J, Wang H, Yang W. Tandem MutSβ binding to long extruded DNA trinucleotide repeats underpins pathogenic expansions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571350. [PMID: 38168405 PMCID: PMC10760016 DOI: 10.1101/2023.12.12.571350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Expansion of trinucleotide repeats causes Huntington's disease, Fragile X syndrome and over twenty other monogenic disorders1. How mismatch repair protein MutSβ and large repeats of CNG (N=A, T, C or G) cooperate to drive the expansion is poorly understood. Contrary to expectations, we find that MutSβ prefers to bind the stem of an extruded (CNG) hairpin rather than the hairpin end or hairpin-duplex junction. Structural analyses reveal that in the presence of MutSβ, CNG repeats with N:N mismatches adopt a B form-like pseudo-duplex, with one or two CNG repeats slipped out forming uneven bubbles that partly mimic insertion-deletion loops of mismatched DNA2. When the extruded hairpin exceeds 40-45 repeats, it can be bound by three or more MutSβ molecules, which are resistant to ATP-dependent dissociation. We envision that such MutSβ-CNG complexes recruit MutLγ endonuclease to nick DNA and initiate the repeat expansion process3,4. To develop drugs against the expansion diseases, we have identified lead compounds that prevent MutSβ binding to CNG repeats but not to mismatched DNA.
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Affiliation(s)
- Jun Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
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5
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The mismatch recognition protein MutSα promotes nascent strand degradation at stalled replication forks. Proc Natl Acad Sci U S A 2022; 119:e2201738119. [PMID: 36161943 PMCID: PMC9546528 DOI: 10.1073/pnas.2201738119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA mismatch repair (MMR) is well known for its role in maintaining replication fidelity by correcting mispairs generated during replication. Here, we identify an unusual MMR function to promote genome instability in the replication stress response. Under replication stress, binding of the mismatch recognition protein MutSα to replication forks blocks the loading of fork protection factors FANCD2 and BRCA1 to replication forks and promotes the recruitment of exonuclease MRE11 onto DNA to nascent strand degradation. This MutSα-dependent MRE11-catalyzed DNA degradation causes DNA breaks and chromosome abnormalities, contributing to an ultramutator phenotype. Mismatch repair (MMR) is a replication-coupled DNA repair mechanism and plays multiple roles at the replication fork. The well-established MMR functions include correcting misincorporated nucleotides that have escaped the proofreading activity of DNA polymerases, recognizing nonmismatched DNA adducts, and triggering a DNA damage response. In an attempt to determine whether MMR regulates replication progression in cells expressing an ultramutable DNA polymerase ɛ (Polɛ), carrying a proline-to-arginine substitution at amino acid 286 (Polɛ-P286R), we identified an unusual MMR function in response to hydroxyurea (HU)-induced replication stress. Polɛ-P286R cells treated with hydroxyurea exhibit increased MRE11-catalyzed nascent strand degradation. This degradation by MRE11 depends on the mismatch recognition protein MutSα and its binding to stalled replication forks. Increased MutSα binding at replication forks is also associated with decreased loading of replication fork protection factors FANCD2 and BRCA1, suggesting blockage of these fork protection factors from loading to replication forks by MutSα. We find that the MutSα-dependent MRE11-catalyzed fork degradation induces DNA breaks and various chromosome abnormalities. Therefore, unlike the well-known MMR functions of ensuring replication fidelity, the newly identified MMR activity of promoting genome instability may also play a role in cancer avoidance by eliminating rogue cells.
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6
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Orc6 is a component of the replication fork and enables efficient mismatch repair. Proc Natl Acad Sci U S A 2022; 119:e2121406119. [PMID: 35622890 DOI: 10.1073/pnas.2121406119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance Origin recognition complex (ORC) is required for the initiation of DNA replication. Unlike other ORC components, the role of human Orc6 in replication remains to be resolved. We identified an unexpected role for hOrc6, which is to promote S-phase progression after prereplication complex assembly and DNA damage response. Orc6 localizes at the replication fork, is an accessory factor of the mismatch repair complex, and plays a fundamental role in genome surveillance during S phase.
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Young SJ, West SC. Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability. Crit Rev Biochem Mol Biol 2021; 56:157-177. [PMID: 33596761 PMCID: PMC7610648 DOI: 10.1080/10409238.2021.1881433] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/06/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
SLX4 provides a molecular scaffold for the assembly of multiple protein complexes required for the maintenance of genome stability. It is involved in the repair of DNA crosslinks, the resolution of recombination intermediates, the response to replication stress and the maintenance of telomere length. To carry out these diverse functions, SLX4 interacts with three structure-selective endonucleases, MUS81-EME1, SLX1 and XPF-ERCC1, as well as the telomere binding proteins TRF2, RTEL1 and SLX4IP. Recently, SLX4 was shown to interact with MutSβ, a heterodimeric protein involved in DNA mismatch repair, trinucleotide repeat instability, crosslink repair and recombination. Importantly, MutSβ promotes the pathogenic expansion of CAG/CTG trinucleotide repeats, which is causative of myotonic dystrophy and Huntington's disease. The colocalization and specific interaction of MutSβ with SLX4, together with their apparently overlapping functions, are suggestive of a common role in reactions that promote DNA maintenance and genome stability. This review will focus on the role of SLX4 in DNA repair, the interplay between MutSβ and SLX4, and detail how they cooperate to promote recombinational repair and DNA crosslink repair. Furthermore, we speculate that MutSβ and SLX4 may provide an alternative cellular mechanism that modulates trinucleotide instability.
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Affiliation(s)
- Sarah J Young
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK
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8
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da Silva Sergio LP, Mencalha AL, de Souza da Fonseca A, de Paoli F. DNA repair and genomic stability in lungs affected by acute injury. Biomed Pharmacother 2019; 119:109412. [PMID: 31514069 PMCID: PMC9170240 DOI: 10.1016/j.biopha.2019.109412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
Acute pulmonary injury, or acute respiratory distress syndrome, has a high incidence in elderly individuals and high mortality in its most severe degree, becoming a challenge to public health due to pathophysiological complications and increased economic burden. Acute pulmonary injury can develop from sepsis, septic shock, and pancreatitis causing reduction of alveolar airspace due to hyperinflammatory response. Oxidative stress acts directly on the maintenance of inflammation, resulting in tissue injury, as well as inducing DNA damages. Once the DNA is damaged, enzymatic DNA repair mechanisms act on lesions in order to maintain genomic stability and, consequently, contribute to cell viability and homeostasis. Although palliative treatment based on mechanical ventilation and antibiotic using have a kind of efficacy, therapies based on modulation of DNA repair and genomic stability could be effective for improving repair and recovery of lung tissue in patients with acute pulmonary injury.
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Affiliation(s)
- Luiz Philippe da Silva Sergio
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil.
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil; Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rua Frei Caneca, 94, Rio de Janeiro, 20211040, Brazil; Centro de Ciências da Saúde, Centro Universitário Serra dos Órgãos, Avenida Alberto Torres, 111, Teresópolis, Rio de Janeiro, 25964004, Brazil
| | - Flavia de Paoli
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer - s/n, Campus Universitário, São Pedro, Juiz de Fora, Minas Gerais, 36036900, Brazil
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9
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Matsuno Y, Atsumi Y, Shimizu A, Katayama K, Fujimori H, Hyodo M, Minakawa Y, Nakatsu Y, Kaneko S, Hamamoto R, Shimamura T, Miyano S, Tsuzuki T, Hanaoka F, Yoshioka KI. Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro. Nat Commun 2019; 10:3925. [PMID: 31477700 PMCID: PMC6718401 DOI: 10.1038/s41467-019-11760-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. However, it remains unclear how MSI and hypermutation arise and contribute to cancer development. Here, we show that MSI and hypermutation are triggered by replication stress in an MMR-deficient background, enabling clonal expansion of cells harboring ARF/p53-module mutations and cells that are resistant to the anti-cancer drug camptothecin. While replication stress-associated DNA double-strand breaks (DSBs) caused chromosomal instability (CIN) in an MMR-proficient background, they induced MSI with concomitant suppression of CIN via a PARP-mediated repair pathway in an MMR-deficient background. This was associated with the induction of mutations, including cancer-driver mutations in the ARF/p53 module, via chromosomal deletions and base substitutions. Immortalization of MMR-deficient mouse embryonic fibroblasts (MEFs) in association with ARF/p53-module mutations was ~60-fold more efficient than that of wild-type MEFs. Thus, replication stress-triggered MSI and hypermutation efficiently lead to clonal expansion of cells with abrogated defense systems. Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. Here authors reveal a mechanism by which replication stress induces MSI and associated induction of mutations in vitro.
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Affiliation(s)
- Yusuke Matsuno
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Yuko Atsumi
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Atsuhiro Shimizu
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kotoe Katayama
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Haruka Fujimori
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mai Hyodo
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yusuke Minakawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, 103-0027, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Tsurumai-cho, Syouwa-ku, Nagoya, 466-8550, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.,National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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10
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Tamura K, Kaneda M, Futagawa M, Takeshita M, Kim S, Nakama M, Kawashita N, Tatsumi-Miyajima J. Genetic and genomic basis of the mismatch repair system involved in Lynch syndrome. Int J Clin Oncol 2019; 24:999-1011. [PMID: 31273487 DOI: 10.1007/s10147-019-01494-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022]
Abstract
Lynch syndrome is a cancer-predisposing syndrome inherited in an autosomal-dominant manner, wherein colon cancer and endometrial cancer develop frequently in the family, it results from a loss-of-function mutation in one of four different genes (MLH1, MSH2, MSH6, and PMS2) encoding mismatch repair proteins. Being located immediately upstream of the MSH2 gene, EPCAM abnormalities can affect MSH2 and cause Lynch syndrome. Mismatch repair proteins are involved in repairing of incorrect pairing (point mutations and deletion/insertion of simple repetitive sequences, so-called microsatellites) that can arise during DNA replication. MSH2 forms heterodimers with MSH6 or MSH3 (MutSα, MutSβ, respectively) and is involved in mismatch-pair recognition and initiation of repair. MLH1 forms a complex with PMS2, and functions as an endonuclease. If the mismatch repair system is thoroughly working, genome integrity is maintained completely. Lynch syndrome is a state of mismatch repair deficiency due to a monoallelic abnormality of any mismatch repair genes. The phenotype indicating the mismatch repair deficiency can be frequently shown as a microsatellite instability in tumors. Children with germline biallelic mismatch repair gene abnormalities were reported to develop conditions such as gastrointestinal polyposis, colorectal cancer, brain cancer, leukemia, etc., and so on, demonstrating the need to respond with new concepts in genetic counseling. In promoting cancer genome medicine in a new era, such as by utilizing immune checkpoints, it is important to understand the genetic and genomic molecular background, including the status of mismatch repair deficiency.
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Affiliation(s)
- Kazuo Tamura
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan.
| | - Motohide Kaneda
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
| | - Mashu Futagawa
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
| | - Miho Takeshita
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
| | - Sanghyuk Kim
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
| | - Mina Nakama
- Division of Clinical Genetics, Gifu University Hospital, Gifu, Japan
| | - Norihito Kawashita
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
| | - Junko Tatsumi-Miyajima
- Division of Medical Genetics, Master of Science, Graduate School of Science and Engineering Research, Kindai University, Higashiosaka, Japan
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11
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Bhardwaj V, Purohit R. Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway. J Biomol Struct Dyn 2019; 38:1963-1974. [PMID: 31138032 DOI: 10.1080/07391102.2019.1621210] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijay Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India.,Biotechnology division, CSIR-IHBT, Palampur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India.,Biotechnology division, CSIR-IHBT, Palampur, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, India
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12
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Peng B, Ortega J, Gu L, Chang Z, Li GM. Phosphorylation of proliferating cell nuclear antigen promotes cancer progression by activating the ATM/Akt/GSK3β/Snail signaling pathway. J Biol Chem 2019; 294:7037-7045. [PMID: 30858175 PMCID: PMC6497965 DOI: 10.1074/jbc.ra119.007897] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/03/2019] [Indexed: 12/19/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) and its posttranslational modifications regulate DNA metabolic reactions, including DNA replication and repair, at replication forks. PCNA phosphorylation at Tyr-211 (PCNA-Y211p) inhibits DNA mismatch repair and induces misincorporation during DNA synthesis. Here, we describe an unexpected role of PCNA-Y211p in cancer promotion and development. Cells expressing phosphorylation-mimicking PCNA, PCNA-Y211D, show elevated hallmarks specific to the epithelial-mesenchymal transition (EMT), including the up-regulation of the EMT-promoting factor Snail and the down-regulation of EMT-inhibitory factors E-cadherin and GSK3β. The PCNA-Y211D-expressing cells also exhibited active cell migration and underwent G2/M arrest. Interestingly, all of these EMT-associated activities required the activation of ATM and Akt kinases, as inactivating these protein kinases by gene knockdown or inhibitors blocked EMT-associated signaling and cell migration. We concluded that PCNA phosphorylation promotes cancer progression via the ATM/Akt/GSK3β/Snail signaling pathway. In conclusion, this study identifies a novel PCNA function and reveals the molecular basis of phosphorylated PCNA-mediated cancer development and progression.
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Affiliation(s)
- Bo Peng
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, China 100084 and
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Zhijie Chang
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, China 100084 and
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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13
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Gupta D, Heinen CD. The mismatch repair-dependent DNA damage response: Mechanisms and implications. DNA Repair (Amst) 2019; 78:60-69. [PMID: 30959407 DOI: 10.1016/j.dnarep.2019.03.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/25/2019] [Accepted: 03/16/2019] [Indexed: 12/22/2022]
Abstract
An important role for the DNA mismatch repair (MMR) pathway in maintaining genomic stability is embodied in its conservation through evolution and the link between loss of MMR function and tumorigenesis. The latter is evident as inheritance of mutations within the major MMR genes give rise to the cancer predisposition condition, Lynch syndrome. Nonetheless, how MMR loss contributes to tumorigenesis is not completely understood. In addition to preventing the accumulation of mutations, MMR also directs cellular responses, such as cell cycle checkpoint or apoptosis activation, to different forms of DNA damage. Understanding this MMR-dependent DNA damage response may provide insight into the full tumor suppressing capabilities of the MMR pathway. Here, we delve into the proposed mechanisms for the MMR-dependent response to DNA damaging agents. We discuss how these pre-clinical findings extend to the clinical treatment of cancers, emphasizing MMR status as a crucial variable in selection of chemotherapeutic regimens. Also, we discuss how loss of the MMR-dependent damage response could promote tumorigenesis via the establishment of a survival advantage to endogenous levels of stress in MMR-deficient cells.
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Affiliation(s)
- Dipika Gupta
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030, USA
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14
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Liu J, Lee JB, Fishel R. Stochastic Processes and Component Plasticity Governing DNA Mismatch Repair. J Mol Biol 2018; 430:4456-4468. [PMID: 29864444 PMCID: PMC6461355 DOI: 10.1016/j.jmb.2018.05.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/09/2018] [Accepted: 05/28/2018] [Indexed: 02/06/2023]
Abstract
DNA mismatch repair (MMR) is a DNA excision-resynthesis process that principally enhances replication fidelity. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologs initiate MMR and in higher eukaryotes act as DNA damage sensors that can trigger apoptosis. MSH proteins recognize mismatched nucleotides, whereas the MLH/PMS proteins mediate multiple interactions associated with downstream MMR events including strand discrimination and strand-specific excision that are initiated at a significant distance from the mismatch. Remarkably, the biophysical functions of the MLH/PMS proteins have been elusive for decades. Here we consider recent observations that have helped to define the mechanics of MLH/PMS proteins and their role in choreographing MMR. We highlight the stochastic nature of DNA interactions that have been visualized by single-molecule analysis and the plasticity of protein complexes that employ thermal diffusion to complete the progressions of MMR.
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Affiliation(s)
- Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, 43210, OH, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), 790-784, Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, 790-784, Pohang, Korea.
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, 43210, OH, USA.
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15
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DNA mismatch repair and its many roles in eukaryotic cells. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:174-187. [PMID: 28927527 DOI: 10.1016/j.mrrev.2017.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/01/2017] [Accepted: 07/06/2017] [Indexed: 02/06/2023]
Abstract
DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore, the mechanism by which the eukaryotic MMR machinery discriminates between the parental (template) and the daughter (nascent) DNA strand is incompletely understood and how cells choose between the EXO1-dependent and the EXO1-independent subpathways of MMR is not known. This review summarizes recent literature on eukaryotic MMR, with emphasis on the diverse cellular roles of eukaryotic MMR proteins, the mechanism of strand discrimination and cross-talk/interactions between and co-regulation of MMR and other DNA repair pathways in eukaryotic cells. The main conclusion of the review is that MMR proteins contribute to genome stability through their ability to recognize and promote an appropriate cellular response to aberrant DNA structures, especially when they arise during DNA replication. Although the molecular mechanism of MMR in the eukaryotic cell is still not completely understood, increased used of single-molecule analyses in the future may yield new insight into these unsolved questions.
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16
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Wang KY, Chen CC, Tsai SF, Shen CKJ. Epigenetic Enhancement of the Post-replicative DNA Mismatch Repair of Mammalian Genomes by a Hemi- mCpG-Np95-Dnmt1 Axis. Sci Rep 2016; 6:37490. [PMID: 27886214 PMCID: PMC5122852 DOI: 10.1038/srep37490] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/26/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation at C of CpG dyads (mCpG) in vertebrate genomes is essential for gene regulation, genome stability and development. We show in this study that proper functioning of post-replicative DNA mismatch repair (MMR) in mammalian cells relies on the presence of genomic mCpG, as well as on the maintenance DNA methyltransferase Dnmt1 independently of its catalytic activity. More importantly, high efficiency of mammalian MMR surveillance is achieved through a hemi-mCpG-Np95(Uhrf1)-Dnmt1 axis, in which the MMR surveillance complex(es) is recruited to post-replicative DNA by Dnmt1, requiring its interactions with MutSα, as well as with Np95 bound at the hemi-methylated CpG sites. Thus, efficiency of MMR surveillance over the mammalian genome in vivo is enhanced at the epigenetic level. This synergy endows vertebrate CpG methylation with a new biological significance and, consequently, an additional mechanism for the maintenance of vertebrate genome stability.
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Affiliation(s)
- Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Shih-Feng Tsai
- Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
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17
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Affiliation(s)
- Guo-Min Li
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90033.
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18
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Kolodner RD. A personal historical view of DNA mismatch repair with an emphasis on eukaryotic DNA mismatch repair. DNA Repair (Amst) 2016; 38:3-13. [PMID: 26698650 PMCID: PMC4740188 DOI: 10.1016/j.dnarep.2015.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 10/30/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute for Molecular Medicine, University of CA, San Diego School of Medicine, La Jolla, CA 92093-0669, United States.
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19
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Activation of the DNA Damage Response by RNA Viruses. Biomolecules 2016; 6:2. [PMID: 26751489 PMCID: PMC4808796 DOI: 10.3390/biom6010002] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 12/11/2022] Open
Abstract
RNA viruses are a genetically diverse group of pathogens that are responsible for some of the most prevalent and lethal human diseases. Numerous viruses introduce DNA damage and genetic instability in host cells during their lifecycles and some species also manipulate components of the DNA damage response (DDR), a complex and sophisticated series of cellular pathways that have evolved to detect and repair DNA lesions. Activation and manipulation of the DDR by DNA viruses has been extensively studied. It is apparent, however, that many RNA viruses can also induce significant DNA damage, even in cases where viral replication takes place exclusively in the cytoplasm. DNA damage can contribute to the pathogenesis of RNA viruses through the triggering of apoptosis, stimulation of inflammatory immune responses and the introduction of deleterious mutations that can increase the risk of tumorigenesis. In addition, activation of DDR pathways can contribute positively to replication of viral RNA genomes. Elucidation of the interactions between RNA viruses and the DDR has provided important insights into modulation of host cell functions by these pathogens. This review summarises the current literature regarding activation and manipulation of the DDR by several medically important RNA viruses.
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20
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The Eukaryotic Mismatch Recognition Complexes Track with the Replisome during DNA Synthesis. PLoS Genet 2015; 11:e1005719. [PMID: 26684201 PMCID: PMC4684283 DOI: 10.1371/journal.pgen.1005719] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 11/10/2015] [Indexed: 01/06/2023] Open
Abstract
During replication, mismatch repair proteins recognize and repair mispaired bases that escape the proofreading activity of DNA polymerase. In this work, we tested the model that the eukaryotic mismatch recognition complex tracks with the advancing replisome. Using yeast, we examined the dynamics during replication of the leading strand polymerase Polε using Pol2 and the eukaryotic mismatch recognition complex using Msh2, the invariant protein involved in mismatch recognition. Specifically, we synchronized cells and processed samples using chromatin immunoprecipitation combined with custom DNA tiling arrays (ChIP-chip). The Polε signal was not detectable in G1, but was observed at active origins and replicating DNA throughout S-phase. The Polε signal provided the resolution to track origin firing timing and efficiencies as well as replisome progression rates. By detecting Polε and Msh2 dynamics within the same strain, we established that the mismatch recognition complex binds origins and spreads to adjacent regions with the replisome. In mismatch repair defective PCNA mutants, we observed that Msh2 binds to regions of replicating DNA, but the distribution and dynamics are altered, suggesting that PCNA is not the sole determinant for the mismatch recognition complex association with replicating regions, but may influence the dynamics of movement. Using biochemical and genomic methods, we provide evidence that both MutS complexes are in the vicinity of the replisome to efficiently repair the entire spectrum of mutations during replication. Our data supports the model that the proximity of MutSα/β to the replisome for the efficient repair of the newly synthesized strand before chromatin reassembles. During replication, errors that escape the replication machinery are identified and repaired by DNA mismatch repair proteins. A mismatch in the helix is recognized by MutS homologs and subsequent events include excision of the error-containing strand followed by re-synthesis. A critical step in this process is directing repair to the newly synthesized strand. Current data suggest that transient discontinuities in the DNA backbone, known as nicks, generated during replication serve as the strand discrimination signals. Additionally, proteins that package DNA have the capacity to block mismatch recognition and are known to rapidly assemble behind the replication fork. Thus, there must be a short window of opportunity for the mismatch recognition complexes to scan for mismatches and access the strand discrimination signals. To address these issues, we tested the model that the mismatch recognition complexes track with the replisome. We employed high resolution genomic methods to determine that during replication, the mismatch recognition complexes bind origins of replication and advances with the replisome. The findings support the hypothesis that the mismatch recognition proteins track with the DNA replication machinery to accurately survey and repair the newly synthesized strands while the DNA is unpackaged and strand specificity signals are accessible.
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21
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A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae. Genetics 2015; 202:525-40. [PMID: 26680658 DOI: 10.1534/genetics.115.184093] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/07/2015] [Indexed: 11/18/2022] Open
Abstract
Single-strand annealing (SSA) is an important homologous recombination mechanism that repairs DNA double strand breaks (DSBs) occurring between closely spaced repeat sequences. During SSA, the DSB is acted upon by exonucleases to reveal complementary sequences that anneal and are then repaired through tail clipping, DNA synthesis, and ligation steps. In baker's yeast, the Msh DNA mismatch recognition complex and the Sgs1 helicase act to suppress SSA between divergent sequences by binding to mismatches present in heteroduplex DNA intermediates and triggering a DNA unwinding mechanism known as heteroduplex rejection. Using baker's yeast as a model, we have identified new factors and regulatory steps in heteroduplex rejection during SSA. First we showed that Top3-Rmi1, a topoisomerase complex that interacts with Sgs1, is required for heteroduplex rejection. Second, we found that the replication processivity clamp proliferating cell nuclear antigen (PCNA) is dispensable for heteroduplex rejection, but is important for repairing mismatches formed during SSA. Third, we showed that modest overexpression of Msh6 results in a significant increase in heteroduplex rejection; this increase is due to a compromise in Msh2-Msh3 function required for the clipping of 3' tails. Thus 3' tail clipping during SSA is a critical regulatory step in the repair vs. rejection decision; rejection is favored before the 3' tails are clipped. Unexpectedly, Msh6 overexpression, through interactions with PCNA, disrupted heteroduplex rejection between divergent sequences in another recombination substrate. These observations illustrate the delicate balance that exists between repair and replication factors to optimize genome stability.
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22
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Friedhoff P, Li P, Gotthardt J. Protein-protein interactions in DNA mismatch repair. DNA Repair (Amst) 2015; 38:50-57. [PMID: 26725162 DOI: 10.1016/j.dnarep.2015.11.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022]
Abstract
The principal DNA mismatch repair proteins MutS and MutL are versatile enzymes that couple DNA mismatch or damage recognition to other cellular processes. Besides interaction with their DNA substrates this involves transient interactions with other proteins which is triggered by the DNA mismatch or damage and controlled by conformational changes. Both MutS and MutL proteins have ATPase activity, which adds another level to control their activity and interactions with DNA substrates and other proteins. Here we focus on the protein-protein interactions, protein interaction sites and the different levels of structural knowledge about the protein complexes formed with MutS and MutL during the mismatch repair reaction.
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Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
| | - Pingping Li
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Julia Gotthardt
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
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23
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Khanam T, Rai N, Ramachandran R. Mycobacterium tuberculosis class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β-clamp. Mol Microbiol 2015; 98:46-68. [PMID: 26103519 DOI: 10.1111/mmi.13102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 11/30/2022]
Abstract
The class-II AP-endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239 QLRFPKK245 motif in the DNA-binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of β-clamp located on different domains interact with XthA. The β-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β-clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β-clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
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Tong D, Ortega J, Kim C, Huang J, Gu L, Li GM. Arsenic Inhibits DNA Mismatch Repair by Promoting EGFR Expression and PCNA Phosphorylation. J Biol Chem 2015; 290:14536-41. [PMID: 25907674 DOI: 10.1074/jbc.m115.641399] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 01/04/2023] Open
Abstract
Both genotoxic and non-genotoxic chemicals can act as carcinogens. However, while genotoxic compounds lead directly to mutations that promote unregulated cell growth, the mechanism by which non-genotoxic carcinogens lead to cellular transformation is poorly understood. Using a model non-genotoxic carcinogen, arsenic, we show here that exposure to arsenic inhibits mismatch repair (MMR) in human cells, possibly through its ability to stimulate epidermal growth factor receptor (EGFR)-dependent tyrosine phosphorylation of proliferating cellular nuclear antigen (PCNA). HeLa cells exposed to exogenous arsenic demonstrate a dose- and time-dependent increase in the levels of EGFR and tyrosine 211-phosphorylated PCNA. Cell extracts derived from arsenic-treated HeLa cells are defective in MMR, and unphosphorylated recombinant PCNA restores normal MMR activity to these extracts. These results suggest a model in which arsenic induces expression of EGFR, which in turn phosphorylates PCNA, and phosphorylated PCNA then inhibits MMR, leading to increased susceptibility to carcinogenesis. This study suggests a putative novel mechanism of action for arsenic and other non-genotoxic carcinogens.
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Affiliation(s)
- Dan Tong
- From the College of Life Sciences, Wuhan University, Wuhan, China 430072, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536, and Tsinghua University School of Medicine, Beijing, China 100084
| | - Janice Ortega
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536, and
| | - Christine Kim
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536, and
| | - Jian Huang
- From the College of Life Sciences, Wuhan University, Wuhan, China 430072
| | - Liya Gu
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536, and
| | - Guo-Min Li
- From the College of Life Sciences, Wuhan University, Wuhan, China 430072, Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536, and Tsinghua University School of Medicine, Beijing, China 100084
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Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesis. Proc Natl Acad Sci U S A 2015; 112:5667-72. [PMID: 25825764 DOI: 10.1073/pnas.1417711112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) plays essential roles in eukaryotic cells during DNA replication, DNA mismatch repair (MMR), and other events at the replication fork. Earlier studies show that PCNA is regulated by posttranslational modifications, including phosphorylation of tyrosine 211 (Y211) by the epidermal growth factor receptor (EGFR). However, the functional significance of Y211-phosphorylated PCNA remains unknown. Here, we show that PCNA phosphorylation by EGFR alters its interaction with mismatch-recognition proteins MutSα and MutSβ and interferes with PCNA-dependent activation of MutLα endonuclease, thereby inhibiting MMR at the initiation step. Evidence is also provided that Y211-phosphorylated PCNA induces nucleotide misincorporation during DNA synthesis. These findings reveal a novel mechanism by which Y211-phosphorylated PCNA promotes cancer development and progression via facilitating error-prone DNA replication and suppressing the MMR function.
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Guarné A, Charbonnier JB. Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:149-156. [PMID: 25701376 DOI: 10.1016/j.pbiomolbio.2015.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 01/31/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
DNA mismatch repair (MMR) is a conserved pathway that safeguards genome integrity by correcting replication errors. The coordinated actions of two proteins (MutS and MutL) initiate the mismatch repair response and defects in the genes encoding for these proteins have been linked to sporadic and hereditary cancers. The basic steps to repair a mismatch include recognizing the mismatch, discriminating the newly synthesized from the parental strand, removing and re-synthesizing the erroneous strand. Although the DNA mismatch repair pathway has been extensively studied over the last four decades, the strand discrimination mechanism has remained elusive in most organisms. Work over the last decade has brought significant progress onto this step of the pathway, in turn ascribing new and critical roles to the MutL protein. In this review, we describe biochemical, biophysical and structural analyses that have clarified how MutL aids at discriminating the newly synthesized strand from its template and marking it for removal.
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Affiliation(s)
- Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| | - Jean-Baptiste Charbonnier
- CEA, IBITECS, Laboratoire de Biologie Structurale et Radiobiologie, CE-Saclay, F-91191 Gif sur Yvette, France; CNRS, URA 2096, F-91191 Gif sur Yvette, France.
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27
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Lee JB, Cho WK, Park J, Jeon Y, Kim D, Lee SH, Fishel R. Single-molecule views of MutS on mismatched DNA. DNA Repair (Amst) 2014; 20:82-93. [PMID: 24629484 PMCID: PMC4245035 DOI: 10.1016/j.dnarep.2014.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/11/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023]
Abstract
Base-pair mismatches that occur during DNA replication or recombination can reduce genetic stability or conversely increase genetic diversity. The genetics and biophysical mechanism of mismatch repair (MMR) has been extensively studied since its discovery nearly 50 years ago. MMR is a strand-specific excision-resynthesis reaction that is initiated by MutS homolog (MSH) binding to the mismatched nucleotides. The MSH mismatch-binding signal is then transmitted to the immediate downstream MutL homolog (MLH/PMS) MMR components and ultimately to a distant strand scission site where excision begins. The mechanism of signal transmission has been controversial for decades. We have utilized single molecule Forster Resonance Energy Transfer (smFRET), Fluorescence Tracking (smFT) and Polarization Total Internal Reflection Fluorescence (smP-TIRF) to examine the interactions and dynamic behaviors of single Thermus aquaticus MutS (TaqMutS) particles on mismatched DNA. We determined that TaqMutS forms an incipient clamp to search for a mismatch in ~1 s intervals by 1-dimensional (1D) thermal fluctuation-driven rotational diffusion while in continuous contact with the helical duplex DNA. When MutS encounters a mismatch it lingers for ~3 s to exchange bound ADP for ATP (ADP→ATP exchange). ATP binding by TaqMutS induces an extremely stable clamp conformation (~10 min) that slides off the mismatch and moves along the adjacent duplex DNA driven simply by 1D thermal diffusion. The ATP-bound sliding clamps rotate freely while in discontinuous contact with the DNA. The visualization of a train of MSH proteins suggests that dissociation of ATP-bound sliding clamps from the mismatch permits multiple mismatch-dependent loading events. These direct observations have provided critical clues into understanding the molecular mechanism of MSH proteins during MMR.
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Affiliation(s)
- Jong-Bong Lee
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea; School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea.
| | - Won-Ki Cho
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Jonghyun Park
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Yongmoon Jeon
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Daehyung Kim
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Seung Hwan Lee
- School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, United States; Physics Department, The Ohio State University, Columbus, OH 43210, United States.
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Goellner EM, Smith CE, Campbell CS, Hombauer H, Desai A, Putnam CD, Kolodner RD. PCNA and Msh2-Msh6 activate an Mlh1-Pms1 endonuclease pathway required for Exo1-independent mismatch repair. Mol Cell 2014; 55:291-304. [PMID: 24981171 DOI: 10.1016/j.molcel.2014.04.034] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/09/2014] [Accepted: 04/28/2014] [Indexed: 11/17/2022]
Abstract
Genetic evidence has implicated multiple pathways in eukaryotic DNA mismatch repair (MMR) downstream of mispair recognition and Mlh1-Pms1 recruitment, including Exonuclease 1 (Exo1)-dependent and -independent pathways. We identified 14 mutations in POL30, which encodes PCNA in Saccharomyces cerevisiae, specific to Exo1-independent MMR. The mutations identified affected amino acids at three distinct sites on the PCNA structure. Multiple mutant PCNA proteins had defects either in trimerization and Msh2-Msh6 binding or in activation of the Mlh1-Pms1 endonuclease that initiates excision during MMR. The latter class of mutations led to hyperaccumulation of repair intermediate Mlh1-Pms1 foci and were enhanced by an msh6 mutation that disrupted the Msh2-Msh6 interaction with PCNA. These results reveal a central role for PCNA in the Exo1-independent MMR pathway and suggest that Msh2-Msh6 localizes PCNA to repair sites after mispair recognition to activate the Mlh1-Pms1 endonuclease for initiating Exo1-dependent repair or for driving progressive excision in Exo1-independent repair.
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Affiliation(s)
- Eva M Goellner
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA
| | - Catherine E Smith
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA
| | - Christopher S Campbell
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA
| | - Hans Hombauer
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arshad Desai
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Moores-UCSD Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA; Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0669, USA.
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29
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Xiao X, Melton DW, Gourley C. Mismatch repair deficiency in ovarian cancer — Molecular characteristics and clinical implications. Gynecol Oncol 2014; 132:506-12. [DOI: 10.1016/j.ygyno.2013.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/24/2023]
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30
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Chang YW, Mai RT, Fang WH, Lin CC, Chiu CC, Wu Lee YH. YB-1 disrupts mismatch repair complex formation, interferes with MutSα recruitment on mismatch and inhibits mismatch repair through interacting with PCNA. Oncogene 2013; 33:5065-77. [PMID: 24141788 DOI: 10.1038/onc.2013.450] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 09/04/2013] [Accepted: 09/20/2013] [Indexed: 12/17/2022]
Abstract
Y-box binding protein-1 (YB-1) is highly expressed in tumors and it participates in various cellular processes. Previous studies indicated that YB-1 binds to mispaired DNA and interacts with several mismatch repair (MMR)-related factors. However, its role in the MMR system remains undefined. Here, we found that YB-1 represses mutS homolog 6 (MSH6)-containing MMR complex formation and reduces MutSα mismatch binding activity by disrupting interactions among MMR-related factors. In an effort to elucidate how YB-1 exerts this inhibitory effect, we have identified two functional proliferating cell nuclear antigen (PCNA)-interacting protein (PIP)-boxes that mediate YB-1/PCNA interaction and locate within the C-terminal region of YB-1. This interaction is critical for the regulatory role of YB-1 in repressing MutSα mismatch binding activity, disrupting MutSα/PCNA/G/T heteroduplex ternary complex formation and inhibiting in vitro MMR activity. The differential regulation of 3' and 5' nick-directed MMR activity by YB-1 was also observed. Moreover, YB-1 overexpression is associated with the alteration of microsatellite pattern and the enhancement of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced and spontaneous mutations. Furthermore, upregulation of other PIP-box-containing proteins, such as myeloid cell leukemia-1 (Mcl-1) and inhibitor of growth protein 1b (ING1b), has no impact on MMR complex formation and mutation accumulation, thus revealing the significant effect of YB-1 on regulating the MMR system. In conclusion, our study suggests that YB-1 functions as a PCNA-interacting factor to exert its regulatory role on the MMR process and involves in the induction of genome instability, which may partially account for the oncogenic potential of YB-1.
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Affiliation(s)
- Y-W Chang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - R-T Mai
- 1] Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan [2] Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao-Tung University, Hsinchu, Taiwan
| | - W-H Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Hospital, Taipei, Taiwan
| | - C-C Lin
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - C-C Chiu
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Y-H Wu Lee
- 1] Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan [2] Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao-Tung University, Hsinchu, Taiwan
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31
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Dieckman LM, Boehm EM, Hingorani MM, Washington MT. Distinct structural alterations in proliferating cell nuclear antigen block DNA mismatch repair. Biochemistry 2013; 52:5611-9. [PMID: 23869605 DOI: 10.1021/bi400378e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During DNA replication, mismatches and small loops in the DNA resulting from insertions or deletions are repaired by the mismatch repair (MMR) machinery. Proliferating cell nuclear antigen (PCNA) plays an important role in both mismatch-recognition and resynthesis stages of MMR. Previously, two mutant forms of PCNA were identified that cause defects in MMR with little, if any, other defects. The C22Y mutant PCNA protein completely blocks MutSα-dependent MMR, and the C81R mutant PCNA protein partially blocks both MutSα-dependent and MutSβ-dependent MMR. In order to understand the structural and mechanistic basis by which these two amino acid substitutions in PCNA proteins block MMR, we solved the X-ray crystal structures of both mutant proteins and carried out further biochemical studies. We found that these amino acid substitutions lead to subtle, distinct structural changes in PCNA. The C22Y substitution alters the positions of the α-helices lining the central hole of the PCNA ring, whereas the C81R substitution creates a distortion in an extended loop near the PCNA subunit interface. We conclude that the structural integrity of the α-helices lining the central hole and this loop are both necessary to form productive complexes with MutSα and mismatch-containing DNA.
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Affiliation(s)
- Lynne M Dieckman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Abstract
SIGNIFICANCE Living organisms are under constant assault by a combination of environmental and endogenous oxidative DNA damage, inducing the modification of proteins, lipids, and DNA. Failure to resolve these oxidative modifications is associated with genome instability and the development of many disease states. To maintain genomic integrity, oxidative lesions must be precisely targeted and efficiently resolved. For this, cells have evolved an intricate network of DNA repair mechanisms to detect and repair oxidative DNA damage. RECENT ADVANCES Emerging evidence suggests that in addition to the base excision repair and nucleotide excision repair pathways, the DNA mismatch repair (MMR) pathway plays an important role in mediating oxidative DNA damage repair. Studies in lower organisms and mammalian cells have enabled us to further dissect this critical role and elucidate the precise mechanisms of repair. CRITICAL ISSUES Identification of synthetic lethal interactions between MMR deficiency and the accumulation of oxidative DNA damage raises the tantalizing prospect that oxidative DNA-damaging agents may be utilized to selectively target MMR-deficient cancers and potentially other tumor types deficient for oxidative DNA repair molecules. FUTURE DIRECTIONS In this review, we emphasize the clinical relevance and potential translation of exploiting this oxidative DNA repair mechanism using synthetic lethality studies in MMR-deficient cells, to develop improved treatment strategies that will benefit cancer patients.
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Affiliation(s)
- David J Brierley
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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33
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Lenhart JS, Sharma A, Hingorani MM, Simmons LA. DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication. Mol Microbiol 2012; 87:553-68. [PMID: 23228104 DOI: 10.1111/mmi.12115] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2012] [Indexed: 11/30/2022]
Abstract
Mismatch repair (MMR) increases the fidelity of DNA replication by identifying and correcting replication errors. Processivity clamps are vital components of DNA replication and MMR, yet the mechanism and extent to which they participate in MMR remains unclear. We investigated the role of the Bacillus subtilis processivity clamp DnaN, and found that it serves as a platform for mismatch detection and coupling of repair to DNA replication. By visualizing functional MutS fluorescent fusions in vivo, we find that MutS forms foci independent of mismatch detection at sites of replication (i.e. the replisome). These MutS foci are directed to the replisome by DnaN clamp zones that aid mismatch detection by targeting the search to nascent DNA. Following mismatch detection, MutS disengages from the replisome, facilitating repair. We tested the functional importance of DnaN-mediated mismatch detection for MMR, and found that it accounts for 90% of repair. This high dependence on DnaN can be bypassed by increasing MutS concentration within the cell, indicating a secondary mode of detection in vivo whereby MutS directly finds mismatches without associating with the replisome. Overall, our results provide new insight into the mechanism by which DnaN couples mismatch recognition to DNA replication in living cells.
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Affiliation(s)
- Justin S Lenhart
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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Hassen S, Ali N, Chowdhury P. Molecular signaling mechanisms of apoptosis in hereditary non-polyposis colorectal cancer. World J Gastrointest Pathophysiol 2012; 3:71-9. [PMID: 22737591 PMCID: PMC3382705 DOI: 10.4291/wjgp.v3.i3.71] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 05/31/2012] [Accepted: 06/12/2012] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is the second most leading cause of cancer related deaths in the western countries. One of the forms of colorectal cancer is hereditary non-polyposis colorectal cancer (HNPCC), also known as “Lynch syndrome”. It is the most common hereditary form of cancer accounting for 5%-10% of all colon cancers. HNPCC is a dominant autosomal genetic disorder caused by germ line mutations in mismatch repair genes. Human mismatch repair genes play a crucial role in genetic stability of DNA, the inactivation of which results in an increased rate of mutation and often a loss of mismatch repair function. Recent studies have shown that certain mismatch repair genes are involved in the regulation of key cellular processes including apoptosis. Thus, differential expression of mismatch repair genes particularly the contributions of MLH1 and MSH2 play important roles in therapeutic resistance to certain cytotoxic drugs such as cisplatin that is used normally as chemoprevention. An understanding of the role of mismatch repair genes in molecular signaling mechanism of apoptosis and its involvement in HNPCC needs attention for further work into this important area of cancer research, and this review article is intended to accomplish that goal of linkage of apoptosis with HNPCC. The current review was not intended to provide a comprehensive enumeration of the entire body of literature in the area of HNPCC or mismatch repair system or apoptosis; it is rather intended to focus primarily on the current state of knowledge of the role of mismatch repair proteins in molecular signaling mechanism of apoptosis as it relates to understanding of HNPCC.
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Functional analysis of the interaction between the mismatch repair protein MutS and the replication processivity factor β clamp in Pseudomonas aeruginosa. DNA Repair (Amst) 2012; 11:463-9. [DOI: 10.1016/j.dnarep.2012.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/19/2012] [Accepted: 01/26/2012] [Indexed: 11/17/2022]
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37
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Hombauer H, Campbell CS, Smith CE, Desai A, Kolodner RD. Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell 2012; 147:1040-53. [PMID: 22118461 DOI: 10.1016/j.cell.2011.10.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/22/2011] [Accepted: 10/07/2011] [Indexed: 11/17/2022]
Abstract
DNA mismatch repair (MMR) increases replication fidelity by eliminating mispaired bases resulting from replication errors. In Saccharomyces cerevisiae, mispairs are primarily detected by the Msh2-Msh6 complex and corrected following recruitment of the Mlh1-Pms1 complex. Here, we visualized functional fluorescent versions of Msh2-Msh6 and Mlh1-Pms1 in living cells. We found that the Msh2-Msh6 complex is an S phase component of replication centers independent of mispaired bases; this localized pool accounted for 10%-15% of MMR in wild-type cells but was essential for MMR in the absence of Exo1. Unexpectedly, Mlh1-Pms1 formed nuclear foci that, although dependent on Msh2-Msh6 for formation, rarely colocalized with Msh2-Msh6 replication-associated foci. Mlh1-Pms1 foci increased when the number of mispaired bases was increased; in contrast, Msh2-Msh6 foci were unaffected. These findings suggest the presence of replication machinery-coupled and -independent pathways for mispair recognition by Msh2-Msh6, which direct formation of superstoichiometric Mlh1-Pms1 foci that represent sites of active MMR.
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Affiliation(s)
- Hans Hombauer
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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The functions of MutL in mismatch repair: the power of multitasking. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:41-70. [PMID: 22749142 DOI: 10.1016/b978-0-12-387665-2.00003-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA mismatch repair enhances genomic stability by correcting errors that have escaped polymerase proofreading. One of the critical steps in DNA mismatch repair is discriminating the new from the parental DNA strand as only the former needs repair. In Escherichia coli, the latent endonuclease MutH carries out this function. However, most prokaryotes and all eukaryotes lack a mutH gene. MutL is a key component of this system that mediates protein-protein interactions during mismatch recognition, strand discrimination, and strand removal. Hence, it had long been thought that the primary function of MutL was coordinating sequential mismatch repair steps. However, recent studies have revealed that most MutL homologs from organisms lacking MutH encode a conserved metal-binding motif associated with a weak endonuclease activity. As MutL homologs bearing this activity are found only in organisms relying on MutH-independent DNA mismatch repair, this finding unveils yet another crucial function of the MutL protein at the strand discrimination step. In this chapter, we review recent functional and structural work aimed at characterizing the multiple functions of MutL and discuss how the endonuclease activity of MutL is regulated by other repair factors.
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Hassen S, Boman BM, Ali N, Parker M, Somerman C, Ali-Khan Catts ZJ, Ali AA, Fields JZ. Detection of DNA mismatch repair proteins in fresh human blood lymphocytes--towards a novel method for hereditary non-polyposis colorectal cancer (Lynch syndrome) screening. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2011; 30:100. [PMID: 22017758 PMCID: PMC3216249 DOI: 10.1186/1756-9966-30-100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 10/21/2011] [Indexed: 12/22/2022]
Abstract
BACKGROUND A broad population-based assay to detect individuals with Lynch Syndrome (LS) before they develop cancer would save lives and healthcare dollars via cancer prevention. LS is caused by a germline mutation in a DNA mismatch repair (MMR) gene, especially protein truncation-causing mutations involving MSH2 or MLH1. We showed that immortalized lymphocytes from LS patients have reduced levels of full-length MLH1 or MSH2 proteins. Thus, it may be feasible to identify LS patients in a broad population-based assay by detecting reduced levels of MMR proteins in lymphocytes. METHODS Accordingly, we determined whether MSH2 and MLH1 proteins can also be detected in fresh lymphocytes. A quantitative western blot assay was developed using two commercially available monoclonal antibodies that we showed are specific for detecting full-length MLH1 or MSH2. To directly determine the ratio of the levels of these MMR proteins, we used both antibodies in a multiplex-type western blot. RESULTS MLH1 and MSH2 levels were often not detectable in fresh lymphocytes, but were readily detectable if fresh lymphocytes were first stimulated with PHA. In fresh lymphocytes from normal controls, the MMR ratio was ~1.0. In fresh lymphocytes from patients (N > 50) at elevated risk for LS, there was a bimodal distribution of MMR ratios (range: 0.3-1.0). CONCLUSIONS Finding that MMR protein levels can be measured in fresh lymphocytes, and given that cells with heterozygote MMR mutations have reduced levels of full-length MMR proteins, suggests that our immunoassay could be advanced to a quantitative test for screening populations at high risk for LS.
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Gao Q, Xiang Y, Zeng L, Ma XT, Lee WH, Zhang Y. Characterization of the βγ-crystallin domains of βγ-CAT, a non-lens βγ-crystallin and trefoil factor complex, from the skin of the toad Bombina maxima. Biochimie 2011; 93:1865-72. [PMID: 21784123 DOI: 10.1016/j.biochi.2011.07.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Accepted: 07/06/2011] [Indexed: 12/15/2022]
Abstract
βγ-CAT is a naturally existing 72-kDa complex of a non-lens βγ-crystallin (α-subunit, CAT-α) and a trefoil factor (β-subunit, CAT-β) that contains a non-covalently linked form of αβ(2) and was isolated from the skin secretions of the toad Bombina maxima. The N-terminal region of CAT-α (CAT-αN, residues 1-170) contains two βγ-crystallin domains while the C-terminal region (CAT-αC) has sequence homology to the membrane insertion domain of the Clostridium perfringens epsilon toxin. To examine the biochemical characteristics of the βγ-crystallin domains of βγ-CAT, CAT-αN, CAT-αC and CAT-β were expressed in Escherichia coli. Co-immunoprecipitation of the naturally assembled βγ-CAT confirmed that the CAT-α and CAT-β complex always exists. Furthermore, recombinant CAT-β bound recombinant CAT-αN. Ca(2+)-binding motifs were identified in CAT-αN, and recombinant CAT-αN was able to bind the calcium probe terbium. However, the conformation of CAT-αN was not significantly altered upon Ca(2+) binding. βγ-CAT possesses strong hemolytic activity toward human erythrocytes, and treatment of erythrocytes with βγ-CAT resulted in a rapid Ca(2+) influx, eventually leading to hemolysis. However, in the absence of extracellular Ca(2+), no significant hemolysis was detected, even though the binding and oligomerization of βγ-CAT in the erythrocyte membrane was observed. Our data demonstrate the binding of CAT-β (a trefoil factor) to CAT-αN (βγ-crystallin domains) and provide a basis for the formation of a βγ-crystallin and trefoil factor complex in vivo. Furthermore, the βγ-crystallin domains of βγ-CAT are able to bind Ca(2+), and βγ-CAT-induced hemolysis is Ca(2+) dependent.
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Affiliation(s)
- Qian Gao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, The Chinese Academy of Sciences, 32 East Jiao Chang Road, Kunming 650223, China
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Pillon MC, Miller JH, Guarné A. The endonuclease domain of MutL interacts with the β sliding clamp. DNA Repair (Amst) 2010; 10:87-93. [PMID: 21050827 DOI: 10.1016/j.dnarep.2010.10.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
Abstract
Mismatch repair corrects errors that have escaped polymerase proofreading enhancing replication fidelity by at least two orders of magnitude. The β and PCNA sliding clamps increase the polymerase processivity during DNA replication and are important at several stages of mismatch repair. Both MutS and MutL, the two proteins that initiate the mismatch repair response, interact with β. Binding of MutS to β is important to recruit MutS and MutL to foci. Moreover, the endonuclease activity of human and yeast MutLα is stimulated by PCNA. However, the concrete functions of the processivity clamp in the repair steps preceding DNA resynthesis remain obscure. Here, we demonstrate that the C-terminal domain of MutL encompasses a bona fide β-binding motif that mediates a weak, yet specific, interaction between the two proteins. Mutation of this conserved motif correlates with defects in mismatch repair, demonstrating that the direct interaction with β is important for MutL function. The interaction between the C-terminal domain of MutL and β is conserved in both Bacillus subtilis and Escherichia coli, but the repair defects associated with mutation of this β-binding motif are more severe in the former, suggesting that this interaction may have a more prominent role in methyl-independent than methyl-directed mismatch repair systems. Together with previously published data, our work strongly suggests that β may stimulate the endonuclease activity of MutL through its direct interaction with the C-terminal domain of MutL.
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Affiliation(s)
- Monica C Pillon
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
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Liberti SE, Andersen SD, Wang J, May A, Miron S, Perderiset M, Keijzers G, Nielsen FC, Charbonnier JB, Bohr VA, Rasmussen LJ. Bi-directional routing of DNA mismatch repair protein human exonuclease 1 to replication foci and DNA double strand breaks. DNA Repair (Amst) 2010; 10:73-86. [PMID: 20970388 DOI: 10.1016/j.dnarep.2010.09.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 09/26/2010] [Accepted: 09/28/2010] [Indexed: 01/23/2023]
Abstract
Human exonuclease 1 (hEXO1) is implicated in DNA metabolism, including replication, recombination and repair, substantiated by its interactions with PCNA, DNA helicases BLM and WRN, and several DNA mismatch repair (MMR) proteins. We investigated the sub-nuclear localization of hEXO1 during S-phase progression and in response to laser-induced DNA double strand breaks (DSBs). We show that hEXO1 and PCNA co-localize in replication foci. This apparent interaction is sustained throughout S-phase. We also demonstrate that hEXO1 is rapidly recruited to DNA DSBs. We have identified a PCNA interacting protein (PIP-box) region on hEXO1 located in its COOH-terminal ((788)QIKLNELW(795)). This motif is essential for PCNA binding and co-localization during S-phase. Recruitment of hEXO1 to DNA DSB sites is dependent on the MMR protein hMLH1. We show that two distinct hMLH1 interaction regions of hEXO1 (residues 390-490 and 787-846) are required to direct the protein to the DNA damage site. Our results reveal that protein domains in hEXO1 in conjunction with specific protein interactions control bi-directional routing of hEXO1 between on-going DNA replication and repair processes in living cells.
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Affiliation(s)
- Sascha E Liberti
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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Iyer RR, Pluciennik A, Genschel J, Tsai MS, Beese LS, Modrich P. MutLalpha and proliferating cell nuclear antigen share binding sites on MutSbeta. J Biol Chem 2010; 285:11730-9. [PMID: 20154325 PMCID: PMC2857047 DOI: 10.1074/jbc.m110.104125] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MutSbeta (MSH2-MSH3) mediates repair of insertion-deletion heterologies but also triggers triplet repeat expansions that cause neurological diseases. Like other DNA metabolic activities, MutSbeta interacts with proliferating cell nuclear antigen (PCNA) via a conserved motif (QXX(L/I)XXFF). We demonstrate that MutSbeta-PCNA complex formation occurs with an affinity of approximately 0.1 microM and a preferred stoichiometry of 1:1. However, up to 20% of complexes are multivalent under conditions where MutSbeta is in molar excess over PCNA. Conformational studies indicate that the two proteins associate in an end-to-end fashion in solution. Surprisingly, mutation of the PCNA-binding motif of MutSbeta not only abolishes PCNA binding, but unlike MutSalpha, also dramatically attenuates MutSbeta-MutLalpha interaction, MutLalpha endonuclease activation, and bidirectional mismatch repair. As predicted by these findings, PCNA competes with MutLalpha for binding to MutSbeta, an effect that is blocked by the cell cycle regulator p21(CIP1). We propose that MutSbeta-MutLalpha interaction is mediated in part by residues ((L/I)SRFF) embedded within the MSH3 PCNA-binding motif. To our knowledge this is the first case where residues important for PCNA binding also mediate interaction with a second protein. These findings also indicate that MutSbeta- and MutSalpha-initiated repair events differ in fundamental ways.
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Affiliation(s)
- Ravi R Iyer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Mastrocola AS, Heinen CD. Nuclear reorganization of DNA mismatch repair proteins in response to DNA damage. DNA Repair (Amst) 2010; 9:120-33. [PMID: 20004149 PMCID: PMC2819642 DOI: 10.1016/j.dnarep.2009.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 10/16/2009] [Accepted: 11/04/2009] [Indexed: 12/16/2022]
Abstract
The DNA mismatch repair (MMR) system is highly conserved and vital for preserving genomic integrity. Current mechanistic models for MMR are mainly derived from in vitro assays including reconstitution of strand-specific MMR and DNA binding assays using short oligonucleotides. However, fundamental questions regarding the mechanism and regulation in the context of cellular DNA replication remain. Using synchronized populations of HeLa cells we demonstrated that hMSH2, hMLH1 and PCNA localize to the chromatin during S-phase, and accumulate to a greater extent in cells treated with a DNA alkylating agent. In addition, using small interfering RNA to deplete hMSH2, we demonstrated that hMLH1 localization to the chromatin is hMSH2-dependent. hMSH2/hMLH1/PCNA proteins, when associated with the chromatin, form a complex that is greatly enhanced by DNA damage. The DNA damage caused by high doses of alkylating agents leads to a G(2) arrest after only one round of replication. In these G(2)-arrested cells, an hMSH2/hMLH1 complex persists on chromatin, however, PCNA is no longer in the complex. Cells treated with a lower dose of alkylating agent require two rounds of replication before cells arrest in G(2). In the first S-phase, the MMR proteins form a complex with PCNA, however, during the second S-phase PCNA is missing from that complex. The distinction between these complexes may suggest separate functions for the MMR proteins in damage repair and signaling. Additionally, using confocal immunofluorescence, we observed a population of hMSH6 that localized to the nucleolus. This population is significantly reduced after DNA damage suggesting that the protein is shuttled out of the nucleolus in response to damage. In contrast, hMLH1 is excluded from the nucleolus at all times. Thus, the nucleolus may act to segregate a population of hMSH2-hMSH6 from hMLH1-hPMS2 such that, in the absence of DNA damage, an inappropriate response is not invoked.
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Affiliation(s)
- Adam S. Mastrocola
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Christopher D. Heinen
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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Mukherjee S, Law SM, Feig M. Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis. Biophys J 2009; 96:1707-20. [PMID: 19254532 DOI: 10.1016/j.bpj.2008.10.071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 10/24/2008] [Indexed: 11/24/2022] Open
Abstract
Postreplication DNA mismatch repair is essential for maintaining the integrity of genomic information in prokaryotes and eukaryotes. The first step in mismatch repair is the recognition of base-base mismatches and insertions/deletions by bacterial MutS or eukaryotic MSH2-MSH6. Crystal structures of both proteins bound to mismatch DNA reveal a similar molecular architecture but provide limited insight into the detailed molecular mechanism of long-range allostery involved in mismatch recognition and repair initiation. This study describes normal-mode calculations of MutS and MSH2-MSH6 with and without DNA. The results reveal similar protein flexibilities and suggest common dynamic and functional characteristics. A strongly correlated motion is present between the lever domain and ATPase domains, which suggests a pathway for long-range allostery from the N-terminal DNA binding domain to the C-terminal ATPase domains, as indicated by experimental studies. A detailed analysis of individual low-frequency modes of both MutS and MSH2-MSH6 shows changes in the DNA-binding domains coupled to the ATPase sites, which are interpreted in the context of experimental data to arrive at a complete molecular-level mismatch recognition cycle. Distinct conformational states are proposed for DNA scanning, mismatch recognition, repair initiation, and sliding along DNA after mismatch recognition. Hypotheses based on the results presented here form the basis for further experimental and computational studies.
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Affiliation(s)
- Shayantani Mukherjee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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Larson ED, Bednarski DW, Maizels N. High-fidelity correction of genomic uracil by human mismatch repair activities. BMC Mol Biol 2008; 9:94. [PMID: 18954457 PMCID: PMC2606688 DOI: 10.1186/1471-2199-9-94] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 10/27/2008] [Indexed: 11/25/2022] Open
Abstract
Background Deamination of cytosine to produce uracil is a common and potentially mutagenic lesion in genomic DNA. U•G mismatches occur spontaneously throughout the genome, where they are repaired by factors associated with the base excision repair pathway. U•G mismatches are also the initiating lesion in immunoglobulin gene diversification, where they undergo mutagenic processing by redundant pathways, one dependent upon uracil excision and the other upon mismatch recognition by MutSα. While UNG is well known to initiate repair of uracil in DNA, the ability of MutSα to direct correction of this base has not been directly demonstrated. Results Using a biochemical assay for mismatch repair, we show that MutSα can promote efficient and faithful repair of U•G mismatches, but does not repair U•A pairs in DNA. This contrasts with UNG, which readily excises U opposite either A or G. Repair of U•G by MutSα depends upon DNA polymerase δ (pol δ), ATP, and proliferating cell nuclear antigen (PCNA), all properties of canonical mismatch repair. Conclusion These results show that faithful repair of U•G can be carried out by either the mismatch repair or base excision repair pathways. Thus, the redundant functions of these pathways in immunoglobulin gene diversification reflect their redundant functions in faithful repair. Faithful repair by either pathway is comparably efficient, suggesting that mismatch repair and base excision repair share the task of faithful repair of genomic uracil.
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Affiliation(s)
- Erik D Larson
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195-7650, USA.
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Hsieh P, Yamane K. DNA mismatch repair: molecular mechanism, cancer, and ageing. Mech Ageing Dev 2008; 129:391-407. [PMID: 18406444 PMCID: PMC2574955 DOI: 10.1016/j.mad.2008.02.012] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 02/22/2008] [Accepted: 02/28/2008] [Indexed: 02/09/2023]
Abstract
DNA mismatch repair (MMR) proteins are ubiquitous players in a diverse array of important cellular functions. In its role in post-replication repair, MMR safeguards the genome correcting base mispairs arising as a result of replication errors. Loss of MMR results in greatly increased rates of spontaneous mutation in organisms ranging from bacteria to humans. Mutations in MMR genes cause hereditary nonpolyposis colorectal cancer, and loss of MMR is associated with a significant fraction of sporadic cancers. Given its prominence in mutation avoidance and its ability to target a range of DNA lesions, MMR has been under investigation in studies of ageing mechanisms. This review summarizes what is known about the molecular details of the MMR pathway and the role of MMR proteins in cancer susceptibility and ageing.
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Affiliation(s)
- Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Beta clamp directs localization of mismatch repair in Bacillus subtilis. Mol Cell 2008; 29:291-301. [PMID: 18280235 DOI: 10.1016/j.molcel.2007.10.036] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 09/28/2007] [Accepted: 10/31/2007] [Indexed: 11/20/2022]
Abstract
MutS homologs function in several cellular pathways including mismatch repair (MMR), the process by which mismatches introduced during DNA replication are corrected. We demonstrate that the C terminus of Bacillus subtilis MutS is necessary for an interaction with beta clamp. This interaction is required for MutS-GFP focus formation in response to mismatches. Reciprocally, we show that a mutant of the beta clamp causes elevated mutation frequencies and is reduced for MutS-GFP focus formation. MutS mutants defective for interaction with beta clamp failed to support the next step of MMR, MutL-GFP focus formation. We conclude that the interaction between MutS and beta is the major molecular interaction facilitating focus formation and that beta clamp aids in the stabilization of MutS at a mismatch in vivo. The striking ability of the MutS C terminus to direct focus formation at replisomes by itself, suggests that it is mismatch recognition that licenses MutS's interaction with beta clamp.
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Iyer RR, Pohlhaus TJ, Chen S, Hura GL, Dzantiev L, Beese LS, Modrich P. The MutSalpha-proliferating cell nuclear antigen interaction in human DNA mismatch repair. J Biol Chem 2008; 283:13310-9. [PMID: 18326858 PMCID: PMC2423938 DOI: 10.1074/jbc.m800606200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined the interaction parameters, conformation, and functional significance of the human MutSalpha(.) proliferating cell nuclear antigen (PCNA) complex in mismatch repair. The two proteins associate with a 1:1 stoichiometry and a K(D) of 0.7 microm in the absence or presence of heteroduplex DNA. PCNA does not influence the affinity of MutSalpha for a mismatch, and mismatch-bound MutSalpha binds PCNA. Small angle x-ray scattering studies have established the molecular parameters of the complex, which are consistent with an elongated conformation in which the two proteins associate in an end-to-end fashion in a manner that does not involve an extended unstructured tether, as has been proposed for yeast MutSalpha and PCNA ( Shell, S. S., Putnam, C. D., and Kolodner, R. D. (2007) Mol. Cell 26, 565-578 ). MutSalpha variants lacking the PCNA interaction motif are functional in 3'- or 5'-directed mismatch-provoked excision, but display a partial defect in 5'-directed mismatch repair. This finding is consistent with the modest mutability conferred by inactivation of the MutSalpha PCNA interaction motif and suggests that interaction of the replication clamp with other repair protein(s) accounts for the essential role of PCNA in MutSalpha-dependent mismatch repair.
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Affiliation(s)
- Ravi R Iyer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Kulkarni A, Wilson DM. The involvement of DNA-damage and -repair defects in neurological dysfunction. Am J Hum Genet 2008; 82:539-66. [PMID: 18319069 PMCID: PMC2427185 DOI: 10.1016/j.ajhg.2008.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 12/17/2007] [Accepted: 01/03/2008] [Indexed: 10/22/2022] Open
Abstract
A genetic link between defects in DNA repair and neurological abnormalities has been well established through studies of inherited disorders such as ataxia telangiectasia and xeroderma pigmentosum. In this review, we present a comprehensive summary of the major types of DNA damage, the molecular pathways that function in their repair, and the connection between defective DNA-repair responses and specific neurological disease. Particular attention is given to describing the nature of the repair defect and its relationship to the manifestation of the associated neurological dysfunction. Finally, the review touches upon the role of oxidative stress, a leading precursor to DNA damage, in the development of certain neurodegenerative pathologies, such as Alzheimer's and Parkinson's.
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Affiliation(s)
- Avanti Kulkarni
- Laboratory of Molecular Gerontology, National Institute of Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M. Wilson
- Laboratory of Molecular Gerontology, National Institute of Aging, National Institutes of Health, Baltimore, MD 21224, USA
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