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Waters KL, Spratt DE. New Discoveries on Protein Recruitment and Regulation during the Early Stages of the DNA Damage Response Pathways. Int J Mol Sci 2024; 25:1676. [PMID: 38338953 PMCID: PMC10855619 DOI: 10.3390/ijms25031676] [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: 12/19/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Maintaining genomic stability and properly repairing damaged DNA is essential to staying healthy and preserving cellular homeostasis. The five major pathways involved in repairing eukaryotic DNA include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), and homologous recombination (HR). When these pathways do not properly repair damaged DNA, genomic stability is compromised and can contribute to diseases such as cancer. It is essential that the causes of DNA damage and the consequent repair pathways are fully understood, yet the initial recruitment and regulation of DNA damage response proteins remains unclear. In this review, the causes of DNA damage, the various mechanisms of DNA damage repair, and the current research regarding the early steps of each major pathway were investigated.
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Affiliation(s)
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
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2
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Chen Y, Chen Y, Li Q, Liu H, Han J, Zhang H, Cheng L, Lin G. Short C-terminal Musashi-1 proteins regulate pluripotency states in embryonic stem cells. Cell Rep 2023; 42:113308. [PMID: 37858462 DOI: 10.1016/j.celrep.2023.113308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The RNA-binding protein Musashi-1 (MSI1) regulates the proliferation and differentiation of adult stem cells. However, its role in embryonic stem cells (ESCs) and early embryonic development remains poorly understood. Here, we report the presence of short C-terminal MSI1 (MSI1-C) proteins in early mouse embryos and mouse ESCs, but not in human ESCs, under conventional culture conditions. In mouse embryos and mESCs, deletion of MSI1-C together with full-length MSI1 causes early embryonic developmental arrest and pluripotency dissolution. MSI1-C is induced upon naive induction and facilitates hESC naive pluripotency acquisition, elevating the pluripotency of primed hESCs toward a formative-like state. MSI1-C proteins are nuclear localized and bind to RNAs involved in DNA-damage repair (including MLH1, BRCA1, and MSH2), conferring on hESCs better survival in human-mouse interspecies cell competition and prolonged ability to form blastoids. This study identifies MSI1-C as an essential regulator in ESC pluripotency states and early embryonic development.
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Affiliation(s)
- Youwei Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China
| | - Ying Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qianyan Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Huahua Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiazhen Han
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hailin Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China.
| | - Gufa Lin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China.
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3
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Jayaraj A, Thayer KM, Beveridge DL, Hingorani MM. Molecular dynamics of mismatch detection-How MutS uses indirect readout to find errors in DNA. Biophys J 2023; 122:3031-3043. [PMID: 37329136 PMCID: PMC10432192 DOI: 10.1016/j.bpj.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 04/30/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023] Open
Abstract
The mismatch repair protein MutS safeguards genomic integrity by finding and initiating repair of basepairing errors in DNA. Single-molecule studies show MutS diffusing on DNA, presumably scanning for mispaired/unpaired bases, and crystal structures show a characteristic "mismatch-recognition" complex with DNA enclosed within MutS and kinked at the site of error. But how MutS goes from scanning thousands of Watson-Crick basepairs to recognizing rare mismatches remains unanswered, largely because atomic-resolution data on the search process are lacking. Here, 10 μs all-atom molecular dynamics simulations of Thermus aquaticus MutS bound to homoduplex DNA and T-bulge DNA illuminate the structural dynamics underlying the search mechanism. MutS-DNA interactions constitute a multistep mechanism to check DNA over two helical turns for its 1) shape, through contacts with the sugar-phosphate backbone, 2) conformational flexibility, through bending/unbending engineered by large-scale motions of the clamp domain, and 3) local deformability, through basepair destabilizing contacts. Thus, MutS can localize a potential target by indirect readout due to lower energetic costs of bending mismatched DNA and identify a site that distorts easily due to weaker base stacking and pairing as a mismatch. The MutS signature Phe-X-Glu motif can then lock in the mismatch-recognition complex to initiate repair.
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Affiliation(s)
- Abhilash Jayaraj
- Chemistry Department, Wesleyan University, Middletown, Connecticut.
| | - Kelly M Thayer
- Chemistry Department, Wesleyan University, Middletown, Connecticut
| | | | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, Connecticut.
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4
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Wolf K, Kosinski J, Gibson TJ, Wesch N, Dötsch V, Genuardi M, Cordisco EL, Zeuzem S, Brieger A, Plotz G. A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation. Nucleic Acids Res 2023; 51:6307-6320. [PMID: 37224528 PMCID: PMC10325900 DOI: 10.1093/nar/gkad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.
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Affiliation(s)
- Karla Wolf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Centre for Structural Systems Biology (CSSB), Hamburg, 22607, Germany
| | - Toby J Gibson
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Maurizio Genuardi
- UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome00168, Italy
| | - Emanuela Lucci Cordisco
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome00168, Italy
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Angela Brieger
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Guido Plotz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
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5
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Oh JM, Kang Y, Park J, Sung Y, Kim D, Seo Y, Lee E, Ra J, Amarsanaa E, Park YU, Lee S, Hwang J, Kim H, Schärer O, Cho S, Lee C, Takata KI, Lee J, Myung K. MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1. Nucleic Acids Res 2023; 51:5584-5602. [PMID: 37140056 PMCID: PMC10287916 DOI: 10.1093/nar/gkad308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
DNA double-strand break (DSB) repair via homologous recombination is initiated by end resection. The extent of DNA end resection determines the choice of the DSB repair pathway. Nucleases for end resection have been extensively studied. However, it is still unclear how the potential DNA structures generated by the initial short resection by MRE11-RAD50-NBS1 are recognized and recruit proteins, such as EXO1, to DSB sites to facilitate long-range resection. We found that the MSH2-MSH3 mismatch repair complex is recruited to DSB sites through interaction with the chromatin remodeling protein SMARCAD1. MSH2-MSH3 facilitates the recruitment of EXO1 for long-range resection and enhances its enzymatic activity. MSH2-MSH3 also inhibits access of POLθ, which promotes polymerase theta-mediated end-joining (TMEJ). Collectively, we present a direct role of MSH2-MSH3 in the initial stages of DSB repair by promoting end resection and influencing the DSB repair pathway by favoring homologous recombination over TMEJ.
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Affiliation(s)
- Jung-Min Oh
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Jumi Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Yubin Sung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Dayoung Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Yuri Seo
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Enkhzul Amarsanaa
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Young-Un Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Seon Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jung Me Hwang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Orlando Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Seung Woo Cho
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Kei-ichi Takata
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Ja Yil Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
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6
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Weitao T, Grandinetti G, Guo P. Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces. EXPLORATION (BEIJING, CHINA) 2023; 3:20210056. [PMID: 37324034 PMCID: PMC10191066 DOI: 10.1002/exp.20210056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/28/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the parallel architectures of biomotors in both prokaryotic and eukaryotic systems suggest a similar revolving mechanism in the use of ATP to drive translocation of the lengthy double-stranded (ds)DNA genomes. This mechanism is exemplified by the dsDNA packaging motor of bacteriophage phi29 that operates through revolving but not rotating dsDNA to "Push through a one-way valve". This unique and novel revolving mechanism discovered in phi29 DNA packaging motor was recently reported in other systems including the dsDNA packaging motor of herpesvirus, the dsDNA ejecting motor of bacteriophage T7, the plasmid conjugation machine TraB in Streptomyces, the dsDNA translocase FtsK of gram-negative bacteria, and the genome-packaging motor in mimivirus. These motors exhibit an asymmetrical hexameric structure for transporting the genome via an inch-worm sequential action. This review intends to delineate the revolving mechanism from a perspective of conformational changes and electrostatic interactions. In phi29, the positively charged residues Arg-Lys-Arg in the N-terminus of the connector bind the negatively charged interlocking domain of pRNA. ATP binding to an ATPase subunit induces the closed conformation of the ATPase. The ATPase associates with an adjacent subunit to form a dimer facilitated by the positively charged arginine finger. The ATP-binding induces a positive charging on its DNA binding surface via an allostery mechanism and thus the higher affinity for the negatively charged dsDNA. ATP hydrolysis induces an expanded conformation of the ATPase with a lower affinity for dsDNA due to the change of the surface charge, but the (ADP+Pi)-bound subunit in the dimer undergoes a conformational change that repels dsDNA. The positively charged lysine rings of the connector attract dsDNA stepwise and periodically to keep its revolving motion along the channel wall, thus maintaining the one-way translocation of dsDNA without reversal and sliding out. The finding of the presence of the asymmetrical hexameric architectures of many ATPases that use the revolving mechanism may provide insights into the understanding of translocation of the gigantic genomes including chromosomes in complicated systems without coiling and tangling to speed up dsDNA translocation and save energy.
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Affiliation(s)
- Tao Weitao
- UT Southwestern Medical CenterCenter for the Genetics of Host DefenseDallasTXUSA
- College of Science and MathematicsSouthwest Baptist UniversityBolivarMOUSA
| | - Giovanna Grandinetti
- Center for Electron Microscopy and AnalysisThe Ohio State UniversityColumbusOHUSA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and NanomedicineDivision of Pharmaceutics and Pharmacology, College of PharmacyDorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of MedicineThe Ohio State UniversityColumbusOHUSA
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7
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Britton BM, London JA, Martin-Lopez J, Jones ND, Liu J, Lee JB, Fishel R. Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA. J Biol Chem 2022; 298:102505. [PMID: 36126773 PMCID: PMC9597889 DOI: 10.1016/j.jbc.2022.102505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022] Open
Abstract
MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.
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Affiliation(s)
- Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - James A London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Juana Martin-Lopez
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Nathan D Jones
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.
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8
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Yang XW, Han XP, Han C, London J, Fishel R, Liu J. MutS functions as a clamp loader by positioning MutL on the DNA during mismatch repair. Nat Commun 2022; 13:5808. [PMID: 36192430 PMCID: PMC9530208 DOI: 10.1038/s41467-022-33479-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Highly conserved MutS and MutL homologs operate as protein dimers in mismatch repair (MMR). MutS recognizes mismatched nucleotides forming ATP-bound sliding clamps, which subsequently load MutL sliding clamps that coordinate MMR excision. Several MMR models envision static MutS-MutL complexes bound to mismatched DNA via a positively charged cleft (PCC) located on the MutL N-terminal domains (NTD). We show MutL-DNA binding is undetectable in physiological conditions. Instead, MutS sliding clamps exploit the PCC to position a MutL NTD on the DNA backbone, likely enabling diffusion-mediated wrapping of the remaining MutL domains around the DNA. The resulting MutL sliding clamp enhances MutH endonuclease and UvrD helicase activities on the DNA, which also engage the PCC during strand-specific incision/excision. These MutS clamp-loader progressions are significantly different from the replication clamp-loaders that attach the polymerase processivity factors β-clamp/PCNA to DNA, highlighting the breadth of mechanisms for stably linking crucial genome maintenance proteins onto DNA.
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Affiliation(s)
- Xiao-Wen Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Xiao-Peng Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
- The Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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9
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Saccharomyces cerevisiae as a Model System for Eukaryotic Cell Biology, from Cell Cycle Control to DNA Damage Response. Int J Mol Sci 2022; 23:ijms231911665. [PMID: 36232965 PMCID: PMC9570374 DOI: 10.3390/ijms231911665] [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] [Received: 08/23/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in S. cerevisiae helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of S. cerevisiae and humans and discuss the challenges of using S. cerevisiae as a model system.
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10
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DuPrie ML, Palacio T, Calil FA, Kolodner RD, Putnam CD. Mlh1 interacts with both Msh2 and Msh6 for recruitment during mismatch repair. DNA Repair (Amst) 2022; 119:103405. [PMID: 36122480 PMCID: PMC9639671 DOI: 10.1016/j.dnarep.2022.103405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022]
Abstract
Eukaryotic DNA mismatch repair (MMR) initiates through mispair recognition by the MutS homologs Msh2-Msh6 and Msh2-Msh3 and subsequent recruitment of the MutL homologs Mlh1-Pms1 (human MLH1-PMS2). In bacteria, MutL is recruited by interactions with the connector domain of one MutS subunit and the ATPase and core domains of the other MutS subunit. Analysis of the S. cerevisiae and human homologs have only identified an interaction between the Msh2 connector domain and Mlh1. Here we investigated whether a conserved Msh6 ATPase/core domain-Mlh1 interaction and an Msh2-Msh6 interaction with Pms1 also act in MMR. Mutations in MLH1 affecting interactions with both the Msh2 and Msh6 interfaces caused MMR defects, whereas equivalent pms1 mutations did not cause MMR defects. Mutant Mlh1-Pms1 complexes containing Mlh1 amino acid substitutions were defective for recruitment to mispaired DNA by Msh2-Msh6, did not support MMR in reconstituted Mlh1-Pms1-dependent MMR reactions in vitro, but were proficient in Msh2-Msh6-independent Mlh1-Pms1 endonuclease activity. These results indicate that Mlh1, the common subunit of the Mlh1-Pms1, Mlh1-Mlh2, and Mlh1-Mlh3 complexes, but not Pms1, is recruited by Msh2-Msh6 through interactions with both of its subunits.
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Affiliation(s)
- Matthew L DuPrie
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Tatiana Palacio
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Felipe A Calil
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Cellular and Molecular Medicine University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Moores-UCSD Cancer Center University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Institute of Genomic Medicine University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Medicine University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA.
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11
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MutS recognition of mismatches within primed DNA replication intermediates. DNA Repair (Amst) 2022; 119:103392. [PMID: 36095926 DOI: 10.1016/j.dnarep.2022.103392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
MutS initiates mismatch repair by recognizing mismatches in newly replicated DNA. Specific interactions between MutS and mismatches within double-stranded DNA promote ADP-ATP exchange and a conformational change into a sliding clamp. Here, we demonstrated that MutS from Pseudomonas aeruginosa associates with primed DNA replication intermediates. The predicted structure of this MutS-DNA complex revealed a new DNA binding site, in which Asn 279 and Arg 272 appeared to directly interact with the 3'-OH terminus of primed DNA. Mutation of these residues resulted in a noticeable defect in the interaction of MutS with primed DNA substrates. Remarkably, MutS interaction with a mismatch within primed DNA induced a compaction of the protein structure and impaired the formation of an ATP-bound sliding clamp. Our findings reveal a novel DNA binding mode, conformational change and intramolecular signaling for MutS recognition of mismatches within primed DNA structures.
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12
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Fukui K, Inoue M, Murakawa T, Baba S, Kumasaka T, Yano T. Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction. Structure 2022; 30:973-982.e4. [DOI: 10.1016/j.str.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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13
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Resistance Mechanisms in Pediatric B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms23063067. [PMID: 35328487 PMCID: PMC8950780 DOI: 10.3390/ijms23063067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the rapid development of medicine, even nowadays, acute lymphoblastic leukemia (ALL) is still a problem for pediatric clinicians. Modern medicine has reached a limit of curability even though the recovery rate exceeds 90%. Relapse occurs in around 20% of treated patients and, regrettably, 10% of diagnosed ALL patients are still incurable. In this article, we would like to focus on the treatment resistance and disease relapse of patients with B-cell leukemia in the context of prognostic factors of ALL. We demonstrate the mechanisms of the resistance to steroid therapy and Tyrosine Kinase Inhibitors and assess the impact of genetic factors on the treatment resistance, especially TCF3::HLF translocation. We compare therapeutic protocols and decipher how cancer cells become resistant to innovative treatments—including CAR-T-cell therapies and monoclonal antibodies. The comparisons made in our article help to bring closer the main factors of resistance in hematologic malignancies in the context of ALL.
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14
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Borsellini A, Kunetsky V, Friedhoff P, Lamers MH. Cryogenic electron microscopy structures reveal how ATP and DNA binding in MutS coordinates sequential steps of DNA mismatch repair. Nat Struct Mol Biol 2022; 29:59-66. [PMID: 35013597 DOI: 10.1038/s41594-021-00707-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022]
Abstract
DNA mismatch repair detects and corrects mismatches introduced during DNA replication. The protein MutS scans for mismatches and coordinates the repair cascade. During this process, MutS undergoes multiple conformational changes in response to ATP binding, hydrolysis and release, but how ATP induces the various MutS conformations is incompletely understood. Here we present four cryogenic electron microscopy structures of Escherichia coli MutS at sequential stages of the ATP hydrolysis cycle that reveal how ATP binding and hydrolysis induce closing and opening of the MutS dimer, respectively. Biophysical analysis demonstrates how DNA binding modulates the ATPase cycle by prevention of hydrolysis during scanning and mismatch binding, while preventing ADP release in the sliding clamp state. Nucleotide release is achieved when MutS encounters single-stranded DNA that is produced during removal of the daughter strand. The combination of ATP binding and hydrolysis and its modulation by DNA enables MutS to adopt the different conformations needed to coordinate the sequential steps of the mismatch repair cascade.
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Affiliation(s)
- Alessandro Borsellini
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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15
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Yang XW, Liu J. Observing Protein One-Dimensional Sliding: Methodology and Biological Significance. Biomolecules 2021; 11:biom11111618. [PMID: 34827616 PMCID: PMC8615959 DOI: 10.3390/biom11111618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 11/28/2022] Open
Abstract
One-dimensional (1D) sliding of DNA-binding proteins has been observed by numerous kinetic studies. It appears that many of these sliding events play important roles in a wide range of biological processes. However, one challenge is to determine the physiological relevance of these motions in the context of the protein’s biological function. Here, we discuss methods of measuring protein 1D sliding by highlighting the single-molecule approaches that are capable of visualizing particle movement in real time. We also present recent findings that show how protein sliding contributes to function.
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16
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Wen J, Wang Y, Yuan M, Huang Z, Zou Q, Pu Y, Zhao B, Cai Z. Role of mismatch repair in aging. Int J Biol Sci 2021; 17:3923-3935. [PMID: 34671209 PMCID: PMC8495402 DOI: 10.7150/ijbs.64953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
A common feature of aging is the accumulation of genetic damage throughout life. DNA damage can lead to genomic instability. Many diseases associated with premature aging are a result of increased accumulation of DNA damage. In order to minimize these damages, organisms have evolved a complex network of DNA repair mechanisms, including mismatch repair (MMR). In this review, we detail the effects of MMR on genomic instability and its role in aging emphasizing on the association between MMR and the other hallmarks of aging, serving to drive or amplify these mechanisms. These hallmarks include telomere attrition, epigenetic alterations, mitochondrial dysfunction, altered nutrient sensing and cell senescence. The close relationship between MMR and these markers may provide prevention and treatment strategies, to reduce the incidence of age-related diseases and promote the healthy aging of human beings.
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Affiliation(s)
- Jie Wen
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China.,Department and Institute of Neurology, Guangdong Medical University, Guangdong, 524001, China.,Guangdong Key Laboratory of aging related cardio cerebral diseases, Guangdong, 524001, China
| | - Yangyang Wang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Minghao Yuan
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Zhenting Huang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Qian Zou
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Yinshuang Pu
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Bin Zhao
- Department and Institute of Neurology, Guangdong Medical University, Guangdong, 524001, China.,Guangdong Key Laboratory of aging related cardio cerebral diseases, Guangdong, 524001, China
| | - Zhiyou Cai
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
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17
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Furman CM, Wang TY, Zhao Q, Yugandhar K, Yu H, Alani E. Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair. Nucleic Acids Res 2021; 49:9327-9341. [PMID: 34390347 PMCID: PMC8450099 DOI: 10.1093/nar/gkab694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
The DNA mismatch repair (MMR) factor Mlh1–Pms1 contains long intrinsically disordered regions (IDRs) whose exact functions remain elusive. We performed cross-linking mass spectrometry to identify interactions within Mlh1–Pms1 and used this information to insert FRB and FKBP dimerization domains into their IDRs. Baker's yeast strains bearing these constructs were grown with rapamycin to induce dimerization. A strain containing FRB and FKBP domains in the Mlh1 IDR displayed a complete defect in MMR when grown with rapamycin. but removing rapamycin restored MMR functions. Strains in which FRB was inserted into the IDR of one MLH subunit and FKBP into the other subunit were also MMR defective. The MLH complex containing FRB and FKBP domains in the Mlh1 IDR displayed a rapamycin-dependent defect in Mlh1–Pms1 endonuclease activity. In contrast, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization inappropriately activated Mlh1–Pms1 endonuclease activity. We conclude that dynamic and coordinated rearrangements of the MLH IDRs both positively and negatively regulate how the MLH complex acts in MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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18
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Abstract
The pathogenic consequences of 369 unique human HsMLH1 missense variants has been hampered by the lack of a detailed function in mismatch repair (MMR). Here single-molecule images show that HsMSH2-HsMSH6 provides a platform for HsMLH1-HsPMS2 to form a stable sliding clamp on mismatched DNA. The mechanics of sliding clamp progression solves a significant operational puzzle in MMR and provides explicit predictions for the distribution of clinically relevant HsMLH1 missense mutations.
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19
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Elez M. Mismatch Repair: From Preserving Genome Stability to Enabling Mutation Studies in Real-Time Single Cells. Cells 2021; 10:cells10061535. [PMID: 34207040 PMCID: PMC8235422 DOI: 10.3390/cells10061535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Mismatch Repair (MMR) is an important and conserved keeper of the maintenance of genetic information. Miroslav Radman's contributions to the field of MMR are multiple and tremendous. One of the most notable was to provide, along with Bob Wagner and Matthew Meselson, the first direct evidence for the existence of the methyl-directed MMR. The purpose of this review is to outline several aspects and biological implications of MMR that his work has helped unveil, including the role of MMR during replication and recombination editing, and the current understanding of its mechanism. The review also summarizes recent discoveries related to the visualization of MMR components and discusses how it has helped shape our understanding of the coupling of mismatch recognition to replication. Finally, the author explains how visualization of MMR components has paved the way to the study of spontaneous mutations in living cells in real time.
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Affiliation(s)
- Marina Elez
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Laboratoire Jean Perrin (LJP), Institut de Biologie Paris-Seine (IBPS), CNRS, Sorbonne Université, F-75005 Paris, France
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20
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Effects of a Novel Thiadiazole Derivative with High Anticancer Activity on Cancer Cell Immunogenic Markers: Mismatch Repair System, PD-L1 Expression, and Tumor Mutation Burden. Pharmaceutics 2021; 13:pharmaceutics13060885. [PMID: 34203761 PMCID: PMC8232699 DOI: 10.3390/pharmaceutics13060885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
Microsatellite instability (MSI), tumor mutation burden (TMB), and programmed cell death ligand-1 (PD-L1) are particularly known as immunotherapy predictive biomarkers. MSI and TMB are closely related to DNA mismatch repair (MMR) pathway functionality, while the PD-L1 checkpoint mediates cancer cell evasion from immune surveillance via the PD-L1/PD-1 axis. Among all the novel triazolo[3,4-b]thiadiazole derivatives, the compound KA39 emerged as the most potent anticancer agent. In the present study, potential alterations in MSI, TMB, and/or PD-L1 expression upon cell treatment with KA39 are explored. We tested three MMR-deficient (DLD-1, LS174T, and DU-145) and two MMR-proficient (HT-29 and PC-3) human cancer cell lines. Our findings support KA39-induced PD-L1 overexpression in all cancer cell lines, although the most outstanding increase was observed in MMR-proficient HT-29 cells. MSI analysis showed that KA39 affects the MMR system, impairing its recognition or repair activity, particularly in MMR-deficient DLD-1 and DU-145 cells, enhancing oligonucleotide production. There were no remarkable alterations in the TMB between untreated and treated cells, indicating that KA39 does not belong to mutagenic agents. Taking together the significant in vitro anticancer activity with PD-L1 upregulation and MSI increase, KA39 should be investigated further for its implication in chemo-immunotherapy of cancer.
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21
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Ortega J, Lee GS, Gu L, Yang W, Li GM. Mispair-bound human MutS-MutL complex triggers DNA incisions and activates mismatch repair. Cell Res 2021; 31:542-553. [PMID: 33510387 PMCID: PMC8089094 DOI: 10.1038/s41422-021-00468-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
DNA mismatch repair (MMR) relies on MutS and MutL ATPases for mismatch recognition and strand-specific nuclease recruitment to remove mispaired bases in daughter strands. However, whether the MutS-MutL complex coordinates MMR by ATP-dependent sliding on DNA or protein-protein interactions between the mismatch and strand discrimination signal is ambiguous. Using functional MMR assays and systems preventing proteins from sliding, we show that sliding of human MutSα is required not for MMR initiation, but for final mismatch removal. MutSα recruits MutLα to form a mismatch-bound complex, which initiates MMR by nicking the daughter strand 5' to the mismatch. Exonuclease 1 (Exo1) is then recruited to the nick and conducts 5' → 3' excision. ATP-dependent MutSα dissociation from the mismatch is necessary for Exo1 to remove the mispaired base when the excision reaches the mismatch. Therefore, our study has resolved a long-standing puzzle, and provided new insights into the mechanism of MMR initiation and mispair removal.
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Affiliation(s)
- Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Grace Sanghee Lee
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY USA ,Present Address: Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX USA ,Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY USA
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22
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Cowman S, Pizer B, Sée V. Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines. PeerJ 2021; 9:e11275. [PMID: 33986995 PMCID: PMC8092103 DOI: 10.7717/peerj.11275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/24/2021] [Indexed: 01/11/2023] Open
Abstract
Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.
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Affiliation(s)
- Sophie Cowman
- Institute of Systems, Molecular and Integrative Biology, Department of Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, Merseyside, United Kingdom.,Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt-Lake-City, Utah, United States
| | - Barry Pizer
- Paediatric Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, Merseyside, United Kingdom
| | - Violaine Sée
- Institute of Systems, Molecular and Integrative Biology, Department of Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool, Merseyside, United Kingdom
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23
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The selection process of licensing a DNA mismatch for repair. Nat Struct Mol Biol 2021; 28:373-381. [PMID: 33820992 DOI: 10.1038/s41594-021-00577-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 02/19/2021] [Indexed: 01/04/2023]
Abstract
DNA mismatch repair detects and removes mismatches from DNA by a conserved mechanism, reducing the error rate of DNA replication by 100- to 1,000-fold. In this process, MutS homologs scan DNA, recognize mismatches and initiate repair. How the MutS homologs selectively license repair of a mismatch among millions of matched base pairs is not understood. Here we present four cryo-EM structures of Escherichia coli MutS that provide snapshots, from scanning homoduplex DNA to mismatch binding and MutL activation via an intermediate state. During scanning, the homoduplex DNA forms a steric block that prevents MutS from transitioning into the MutL-bound clamp state, which can only be overcome through kinking of the DNA at a mismatch. Structural asymmetry in all four structures indicates a division of labor between the two MutS monomers. Together, these structures reveal how a small conformational change from the homoduplex- to heteroduplex-bound MutS acts as a licensing step that triggers a dramatic conformational change that enables MutL binding and initiation of the repair cascade.
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24
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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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25
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Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
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Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
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26
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Young SJ, Sebald M, Shah Punatar R, Larin M, Masino L, Rodrigo-Brenni MC, Liang CC, West SC. MutSβ Stimulates Holliday Junction Resolution by the SMX Complex. Cell Rep 2020; 33:108289. [PMID: 33086055 DOI: 10.1016/j.celrep.2020.108289] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/02/2020] [Accepted: 09/29/2020] [Indexed: 12/20/2022] Open
Abstract
MutSα and MutSβ play important roles in DNA mismatch repair and are linked to inheritable cancers and degenerative disorders. Here, we show that MSH2 and MSH3, the two components of MutSβ, bind SLX4 protein, a scaffold for the assembly of the SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX) trinuclease complex. SMX promotes the resolution of Holliday junctions (HJs), which are intermediates in homologous recombinational repair. We find that MutSβ binds HJs and stimulates their resolution by SLX1-SLX4 or SMX in reactions dependent upon direct interactions between MutSβ and SLX4. In contrast, MutSα does not stimulate HJ resolution. MSH3-depleted cells exhibit reduced sister chromatid exchanges and elevated levels of homologous recombination ultrafine bridges (HR-UFBs) at mitosis, consistent with defects in the processing of recombination intermediates. These results demonstrate a role for MutSβ in addition to its established role in the pathogenic expansion of CAG/CTG trinucleotide repeats, which is causative of myotonic dystrophy and Huntington's disease.
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Affiliation(s)
- Sarah J Young
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Marie Sebald
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Meghan Larin
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Laura Masino
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Chih-Chao Liang
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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27
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Furman CM, Elbashir R, Alani E. Expanded roles for the MutL family of DNA mismatch repair proteins. Yeast 2020; 38:39-53. [PMID: 32652606 DOI: 10.1002/yea.3512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
The MutL family of DNA mismatch repair proteins plays a critical role in excising and repairing misincorporation errors during DNA replication. In many eukaryotes, members of this family have evolved to modulate and resolve recombination intermediates into crossovers during meiosis. In these organisms, such functions promote the accurate segregation of chromosomes during the meiosis I division. What alterations occurred in MutL homolog (MLH) family members that enabled them to acquire these new roles? In this review, we present evidence that the yeast Mlh1-Mlh3 and Mlh1-Mlh2 complexes have evolved novel enzymatic and nonenzymatic activities and protein-protein interactions that are critical for their meiotic functions. Curiously, even with these changes, these complexes retain backup and accessory roles in DNA mismatch repair during vegetative growth.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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28
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Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby. Proc Natl Acad Sci U S A 2020; 117:17775-17784. [PMID: 32669440 DOI: 10.1073/pnas.1918517117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA resynthesis. Dominant MMR models posit that after mismatch recognition, ATP converts MutS to a hydrolysis-independent, diffusive mobile clamp that no longer recognizes the mismatch. Little is known about the postrecognition MutS mobile clamp and its interactions with MutL. Two disparate frameworks have been proposed: One in which MutS-MutL complexes remain mobile on the DNA, and one in which MutL stops MutS movement. Here we use single-molecule FRET to follow the postrecognition states of MutS and the impact of MutL on its properties. In contrast to current thinking, we find that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA. Notably, ATP hydrolysis is required to alter the conformation of MutS such that it can recognize the mismatch again instead of bypassing it; thus, ATP hydrolysis licenses the MutS mobile clamp to rebind the mismatch. Moreover, interaction with MutL can both trap MutS at the mismatch en route to mobile clamp formation and stop movement of the mobile clamp on DNA. MutS's frequent rebinding of the mismatch, which increases its residence time in the vicinity of the mismatch, coupled with MutL's ability to trap MutS, should increase the probability that MutS-MutL MMR initiation complexes localize near the mismatch.
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29
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Dynamic human MutSα-MutLα complexes compact mismatched DNA. Proc Natl Acad Sci U S A 2020; 117:16302-16312. [PMID: 32586954 DOI: 10.1073/pnas.1918519117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA mismatch repair (MMR) corrects errors that occur during DNA replication. In humans, mutations in the proteins MutSα and MutLα that initiate MMR cause Lynch syndrome, the most common hereditary cancer. MutSα surveilles the DNA, and upon recognition of a replication error it undergoes adenosine triphosphate-dependent conformational changes and recruits MutLα. Subsequently, proliferating cell nuclear antigen (PCNA) activates MutLα to nick the error-containing strand to allow excision and resynthesis. The structure-function properties of these obligate MutSα-MutLα complexes remain mostly unexplored in higher eukaryotes, and models are predominately based on studies of prokaryotic proteins. Here, we utilize atomic force microscopy (AFM) coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα-MutLα-DNA complexes. We find that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. On the timescale of a few minutes, these complexes rearrange, folding and compacting the DNA. These observations contrast with dominant models of MMR initiation that envision diffusive MutS-MutL complexes that move away from the mismatch. Our results suggest MutSα localizes MutLα near the mismatch and promotes DNA configurations that could enhance MMR efficiency by facilitating MutLα nicking the DNA at multiple sites around the mismatch. In addition, such complexes may also protect the mismatch region from nucleosome reassembly until repair occurs, and they could potentially remodel adjacent nucleosomes.
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30
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Mardenborough YSN, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada-Vial A, Winterwerp HHK, Sixma TK, Kanaar R, Friedhoff P, Strick TR, Lebbink JHG. The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair. Nucleic Acids Res 2020; 47:11667-11680. [PMID: 31598722 PMCID: PMC6902014 DOI: 10.1093/nar/gkz834] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
DNA mismatch repair (MMR) maintains genome stability through repair of DNA replication errors. In Escherichia coli, initiation of MMR involves recognition of the mismatch by MutS, recruitment of MutL, activation of endonuclease MutH and DNA strand incision at a hemimethylated GATC site. Here, we studied the mechanism of communication that couples mismatch recognition to daughter strand incision. We investigated the effect of catalytically-deficient Cas9 as well as stalled RNA polymerase as roadblocks placed on DNA in between the mismatch and GATC site in ensemble and single molecule nanomanipulation incision assays. The MMR proteins were observed to incise GATC sites beyond a roadblock, albeit with reduced efficiency. This residual incision is completely abolished upon shortening the disordered linker regions of MutL. These results indicate that roadblock bypass can be fully attributed to the long, disordered linker regions in MutL and establish that communication during MMR initiation occurs along the DNA backbone.
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Affiliation(s)
| | - Katerina Nitsenko
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Charlie Laffeber
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Camille Duboc
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Enes Sahin
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Audrey Quessada-Vial
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | | | - Titia K Sixma
- Oncode Institute, the Netherlands.,Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Terence R Strick
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.,Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Superieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,Programme "Equipe Labellisée", Ligue Nationale contre le Cancer
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, the Netherlands
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31
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Paul Solomon Devakumar LJ, Gaubitz C, Lundblad V, Kelch BA, Kubota T. Effective mismatch repair depends on timely control of PCNA retention on DNA by the Elg1 complex. Nucleic Acids Res 2020; 47:6826-6841. [PMID: 31114918 PMCID: PMC6648347 DOI: 10.1093/nar/gkz441] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 11/14/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp that acts as a central co-ordinator for mismatch repair (MMR) as well as DNA replication. Loss of Elg1, the major subunit of the PCNA unloader complex, causes over-accumulation of PCNA on DNA and also increases mutation rate, but it has been unclear if the two effects are linked. Here we show that timely removal of PCNA from DNA by the Elg1 complex is important to prevent mutations. Although premature unloading of PCNA generally increases mutation rate, the mutator phenotype of elg1Δ is attenuated by PCNA mutants PCNA-R14E and PCNA-D150E that spontaneously fall off DNA. In contrast, the elg1Δ mutator phenotype is exacerbated by PCNA mutants that accumulate on DNA due to enhanced electrostatic PCNA–DNA interactions. Epistasis analysis suggests that PCNA over-accumulation on DNA interferes with both MMR and MMR-independent process(es). In elg1Δ, over-retained PCNA hyper-recruits the Msh2–Msh6 mismatch recognition complex through its PCNA-interacting peptide motif, causing accumulation of MMR intermediates. Our results suggest that PCNA retention controlled by the Elg1 complex is critical for efficient MMR: PCNA needs to be on DNA long enough to enable MMR, but if it is retained too long it interferes with downstream repair steps.
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Affiliation(s)
- Lovely Jael Paul Solomon Devakumar
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Takashi Kubota
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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32
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Liu J, Lee R, Britton BM, London JA, Yang K, Hanne J, Lee JB, Fishel R. MutL sliding clamps coordinate exonuclease-independent Escherichia coli mismatch repair. Nat Commun 2019; 10:5294. [PMID: 31757945 PMCID: PMC6876574 DOI: 10.1038/s41467-019-13191-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023] Open
Abstract
A shared paradigm of mismatch repair (MMR) across biology depicts extensive exonuclease-driven strand-specific excision that begins at a distant single-stranded DNA (ssDNA) break and proceeds back past the mismatched nucleotides. Historical reconstitution studies concluded that Escherichia coli (Ec) MMR employed EcMutS, EcMutL, EcMutH, EcUvrD, EcSSB and one of four ssDNA exonucleases to accomplish excision. Recent single-molecule images demonstrated that EcMutS and EcMutL formed cascading sliding clamps on a mismatched DNA that together assisted EcMutH in introducing ssDNA breaks at distant newly replicated GATC sites. Here we visualize the complete strand-specific excision process and find that long-lived EcMutL sliding clamps capture EcUvrD helicase near the ssDNA break, significantly increasing its unwinding processivity. EcSSB modulates the EcMutL–EcUvrD unwinding dynamics, which is rarely accompanied by extensive ssDNA exonuclease digestion. Together these observations are consistent with an exonuclease-independent MMR strand excision mechanism that relies on EcMutL–EcUvrD helicase-driven displacement of ssDNA segments between adjacent EcMutH–GATC incisions. The mechanics of MMR strand specific excision that begins at a distant ssDNA break are not yet clear. Here the authors have used multiple single molecule imaging techniques to visualize the behavior of MMR components on mismatched DNA substrates and reveal an exonuclease-independent mechanism for E.coli MMR.
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Affiliation(s)
- Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Ryanggeun Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Korea
| | - Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - James A London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Keunsang Yang
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Gyeongbuk, 37673, Korea
| | - Jeungphill Hanne
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Korea. .,School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Gyeongbuk, 37673, Korea.
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
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33
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Tarry MJ, Harmel C, Taylor JA, Marczynski GT, Schmeing TM. Structures of GapR reveal a central channel which could accommodate B-DNA. Sci Rep 2019; 9:16679. [PMID: 31723182 PMCID: PMC6853979 DOI: 10.1038/s41598-019-52964-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/25/2019] [Indexed: 12/04/2022] Open
Abstract
GapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α helix and two shorter α helices, and assembles into a tetrameric ring with a closed, positively charged, central channel. In contrast to the conclusions drawn from the published structures, we observe that the central channel of the tetramer presented here could freely accommodate B-DNA. Mutation of six conserved lysine residues lining the cavity and electrophoretic mobility gel shift experiments confirmed their role in DNA binding and the channel as the site of DNA binding. Although present in our crystals, DNA could not be observed in the electron density maps, suggesting that DNA binding is non-specific, which could be important for tetramer-ring translocation along the chromosome. In conjunction with previous GapR structures we propose a model for DNA binding and translocation that explains key published observations on GapR and its biological functions.
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Affiliation(s)
- Michael J Tarry
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Christoph Harmel
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - James A Taylor
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth 15 Road, Ottawa, ON, K1H 8L1, Canada
| | - Gregory T Marczynski
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada.
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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34
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Goellner EM. Chromatin remodeling and mismatch repair: Access and excision. DNA Repair (Amst) 2019; 85:102733. [PMID: 31698199 DOI: 10.1016/j.dnarep.2019.102733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/06/2019] [Accepted: 10/09/2019] [Indexed: 01/03/2023]
Abstract
DNA mismatch repair (MMR) increases replication fidelity and genome stability by correcting DNA polymerase errors that remain after replication. Defects in MMR result in the accumulation of mutations and lead to human tumor development. Germline mutations in MMR cause the hereditary cancer syndrome, Lynch syndrome. After replication, DNA is reorganized into its chromatin structure and wrapped around histone octamers. DNA MMR is thought to be less efficient in recognizing and repairing mispairs packaged in chromatin, in which case MMR must either compete for access to naked DNA before histone deposition or actively move nucleosomes to access the mispair. This article reviews studies into the mechanistic and physical interactions between MMR and various chromatin-associated factors, including the histone deposition complex CAF1. Recent Xenopus and Saccharomyces cerevisiae studies describe a physical interaction between Msh2 and chromatin-remodeling ATPase Fun30/SMARCAD1, with potential mechanistic roles for SMARCAD1 in moving histones for both mispair access and excision tract elongation. The RSC complex, another histone remodeling complex, also potentially influences excision tract length. Deletion mutations of RSC2 point to mechanistic interactions with the MMR pathways. Together, these studies paint a picture of complex interactions between MMR and the chromatin environment that will require numerous additional genetic, biochemical, and cell biology experiments to fully understand. Understanding how these pathways interconnect is essential in fully understanding eukaryotic MMR and has numerous implications in human tumor formation and treatment.
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Affiliation(s)
- Eva M Goellner
- Department of Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
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35
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LeBlanc SJ, Gauer JW, Hao P, Case BC, Hingorani MM, Weninger KR, Erie DA. Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS. Nucleic Acids Res 2019; 46:10782-10795. [PMID: 30272207 PMCID: PMC6237781 DOI: 10.1093/nar/gky865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein–DNA and DNA–DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jacob W Gauer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Brandon C Case
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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36
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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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37
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Thirumal Kumar D, Susmita B, Judith E, Priyadharshini Christy J, George Priya Doss C, Zayed H. Elucidating the role of interacting residues of the MSH2-MSH6 complex in DNA repair mechanism: A computational approach. DNA Repair (Amst) 2019; 115:325-350. [DOI: 10.1016/bs.apcsb.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Kim D, Fishel R, Lee JB. Coordinating Multi-Protein Mismatch Repair by Managing Diffusion Mechanics on the DNA. J Mol Biol 2018; 430:4469-4480. [PMID: 29792877 PMCID: PMC6388638 DOI: 10.1016/j.jmb.2018.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
Abstract
DNA mismatch repair (MMR) corrects DNA base-pairing errors that occur during DNA replication. MMR catalyzes strand-specific DNA degradation and resynthesis by dynamic molecular coordination of sequential downstream pathways. The temporal and mechanistic order of molecular events is essential to insure interactions in MMR that occur over long distances on the DNA. Biophysical real-time studies of highly conserved components on mismatched DNA have shed light on the mechanics of MMR. Single-molecule imaging has visualized stochastically coordinated MMR interactions that are based on thermal fluctuation-driven motions. In this review, we describe the role of diffusivity and stochasticity in MMR beginning with mismatch recognition through strand-specific excision. We conclude with a perspective of the possible research directions that should solve the remaining questions in MMR.
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Affiliation(s)
- Daehyung Kim
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea; Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 37673, Korea.
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39
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Graham WJ, Putnam CD, Kolodner RD. The properties of Msh2-Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair. J Biol Chem 2018; 293:18055-18070. [PMID: 30237169 PMCID: PMC6254361 DOI: 10.1074/jbc.ra118.005439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/17/2018] [Indexed: 11/30/2022] Open
Abstract
DNA mismatch repair (MMR) corrects mispaired DNA bases and small insertion/deletion loops generated by DNA replication errors. After binding a mispair, the eukaryotic mispair recognition complex Msh2–Msh6 binds ATP in both of its nucleotide-binding sites, which induces a conformational change resulting in the formation of an Msh2–Msh6 sliding clamp that releases from the mispair and slides freely along the DNA. However, the roles that Msh2–Msh6 sliding clamps play in MMR remain poorly understood. Here, using Saccharomyces cerevisiae, we created Msh2 and Msh6 Walker A nucleotide–binding site mutants that have defects in ATP binding in one or both nucleotide-binding sites of the Msh2–Msh6 heterodimer. We found that these mutations cause a complete MMR defect in vivo. The mutant Msh2–Msh6 complexes exhibited normal mispair recognition and were proficient at recruiting the MMR endonuclease Mlh1–Pms1 to mispaired DNA. At physiological (2.5 mm) ATP concentration, the mutant complexes displayed modest partial defects in supporting MMR in reconstituted Mlh1–Pms1-independent and Mlh1–Pms1-dependent MMR reactions in vitro and in activation of the Mlh1–Pms1 endonuclease and showed a more severe defect at low (0.1 mm) ATP concentration. In contrast, five of the mutants were completely defective and one was mostly defective for sliding clamp formation at high and low ATP concentrations. These findings suggest that mispair-dependent sliding clamp formation triggers binding of additional Msh2–Msh6 complexes and that further recruitment of additional downstream MMR proteins is required for signal amplification of mispair binding during MMR.
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Affiliation(s)
| | - Christopher D Putnam
- From the Ludwig Institute for Cancer Research San Diego,; Departments of Medicine and
| | - Richard D Kolodner
- From the Ludwig Institute for Cancer Research San Diego,; Cellular and Molecular Medicine,; Moores-UCSD Cancer Center, and; Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, California 92093-0669.
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40
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Hanne J, Britton BM, Park J, Liu J, Martín-López J, Jones N, Schoffner M, Klajner P, Bundschuh R, Lee JB, Fishel R. MutS homolog sliding clamps shield the DNA from binding proteins. J Biol Chem 2018; 293:14285-14294. [PMID: 30072380 DOI: 10.1074/jbc.ra118.002264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/31/2018] [Indexed: 11/06/2022] Open
Abstract
Sliding clamps on DNA consist of evolutionarily conserved enzymes that coordinate DNA replication, repair, and the cellular DNA damage response. MutS homolog (MSH) proteins initiate mismatch repair (MMR) by recognizing mispaired nucleotides and in the presence of ATP form stable sliding clamps that randomly diffuse along the DNA. The MSH sliding clamps subsequently load MutL homolog (MLH/PMS) proteins that form a second extremely stable sliding clamp, which together coordinate downstream MMR components with the excision-initiation site that may be hundreds to thousands of nucleotides distant from the mismatch. Specific or nonspecific binding of other proteins to the DNA between the mismatch and the distant excision-initiation site could conceivably obstruct the free diffusion of these MMR sliding clamps, inhibiting their ability to initiate repair. Here, we employed bulk biochemical analysis, single-molecule fluorescence imaging, and mathematical modeling to determine how sliding clamps might overcome such hindrances along the DNA. Using both bacterial and human MSH proteins, we found that increasing the number of MSH sliding clamps on a DNA decreased the association of the Escherichia coli transcriptional repressor LacI to its cognate promoter LacO. Our results suggest a simple mechanism whereby thermal diffusion of MSH sliding clamps along the DNA alters the association kinetics of other DNA-binding proteins over extended distances. These observations appear generally applicable to any stable sliding clamp that forms on DNA.
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Affiliation(s)
- Jeungphill Hanne
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Brooke M Britton
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Jonghyun Park
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea
| | - Jiaquan Liu
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Juana Martín-López
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Nathan Jones
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210.,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Matthew Schoffner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Piotr Klajner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Ralf Bundschuh
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, .,Department of Physics, The Ohio State University, Columbus, Ohio 43210.,Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, and
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea, .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784 Korea
| | - Richard Fishel
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, .,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
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41
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Markoš P, Brčić I, Brčić L, Jakić-Razumović J, Pulanić R. Microsatellite instability in metaplasia-dysplasia-adenocarcinoma sequence of Barrett esophagus: a retrospective study. Croat Med J 2018; 59:100-107. [PMID: 29972732 PMCID: PMC6045894 DOI: 10.3325/cmj.2018.59.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim To analyze the loss of mismatch repair (MMR) system protein expression in metaplasia-dysplasia-adenocarcinoma sequence of Barrett esophagus (BE). Methods This study retrospectively analyzed the data from 70 patients with pathohistological diagnosis of BE or esophageal adenocarcinoma (EAC) treated at the Clinical Department of Pathology and Cytology, University Hospital Center Zagreb, from January 2009 to January 2011. Patients were divided into three groups: BE without dysplasia (22 patients), BE with dysplasia (37 patients), and EAC (11 patients). Immunohistochemical expression of MutL homologue 1 (MLH1), MutS homologue 2 (MSH2), postmeiotic segregation increased 2 (PMS2), and MutS homologue 6 (MSH6) of DNA MMR system was measured and compared with tumor protein p53 expression. Results A total of 81.8% and 81.8% patients with EAC, 32.4% and 35.1% patients with dysplasia, and 50% and 54.5% patients without dysplasia had loss of MLH1 and PMS2 expression, respectively. Patients with EAC and patients with dysplasia did not have loss of MSH2 and MSH6 expression, and 18.2% patients without dysplasia had loss of MSH2 and MSH6 expression. There was a strong positive correlation between MLH1 and PMS2 expression (Spearman ρ 0.97; P < 0.001) and between MSH2 and MSH6 expression (Spearman ρ 0.90, P < 0.001) in the entire sample and in all BE groups. No significant correlations of MLH1 and PMS2 with p53 expression were found, except in dysplasia group (φ 0.402, P = 0.030 for MSH1; φ 0.371, P = 0.042 for PMS2). Conclusion Although we demonstrated considerable loss of MLH1 and PMS2 expression in BE-associated carcinoma sequence, due to the retrospective study design and low number of patients we cannot conclude that MLH1 and PMS2 can be used as biomarkers for patient surveillance and therapy-making decisions. Oxford Centre for Evidence-based Medicine level of evidence: 3
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Affiliation(s)
- Pave Markoš
- Pave Markoš, Division of Gastroenterology and Hepatology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia,
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42
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Stochastic Processes and Component Plasticity Governing DNA Mismatch Repair. J Mol Biol 2018; 430:4456-4468. [PMID: 29864444 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] [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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43
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Meier B, Volkova NV, Hong Y, Schofield P, Campbell PJ, Gerstung M, Gartner A. Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers. Genome Res 2018; 28:666-675. [PMID: 29636374 PMCID: PMC5932607 DOI: 10.1101/gr.226845.117] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022]
Abstract
Throughout their lifetime, cells are subject to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the genome. DNA mismatch repair (MMR) deficiency leads to hypermutation and is found in different cancer types. Although it is possible to associate mutational signatures extracted from human cancers with possible mutational processes, the exact causation is often unknown. Here, we use C. elegans genome sequencing of pms-2 and mlh-1 knockouts to reveal the mutational patterns linked to C. elegans MMR deficiency and their dependency on endogenous replication errors and errors caused by deletion of the polymerase ε subunit pole-4 Signature extraction from 215 human colorectal and 289 gastric adenocarcinomas revealed three MMR-associated signatures, one of which closely resembles the C. elegans MMR spectrum and strongly discriminates microsatellite stable and unstable tumors (AUC = 98%). A characteristic difference between human and C. elegans MMR deficiency is the lack of elevated levels of NCG > NTG mutations in C. elegans, likely caused by the absence of cytosine (CpG) methylation in worms. The other two human MMR signatures may reflect the interaction between MMR deficiency and other mutagenic processes, but their exact cause remains unknown. In summary, combining information from genetically defined models and cancer samples allows for better aligning mutational signatures to causal mutagenic processes.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Nadezda V Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Pieta Schofield
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
- Division of Computational Biology, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Department of Haematology, Addenbrooke's Hospital, Cambridge CB2 0XY, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
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44
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Ohshita K, Fukui K, Sato M, Morisawa T, Hakumai Y, Morono Y, Inagaki F, Yano T, Ashiuchi M, Wakamatsu T. Archaeal MutS5 tightly binds to Holliday junction similarly to eukaryotic MutSγ. FEBS J 2017; 284:3470-3483. [PMID: 28834211 DOI: 10.1111/febs.14204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/28/2017] [Accepted: 08/17/2017] [Indexed: 01/15/2023]
Abstract
Archaeal DNA recombination mechanism and the related proteins are similar to those in eukaryotes. However, no functional homolog of eukaryotic MutSγ, which recognizes Holliday junction to promote homologous recombination, has been identified in archaea. Hence, the whole molecular mechanism of archaeal homologous recombination has not yet been revealed. In this study, to identify the archaeal functional homolog of MutSγ, we focused on a functionally uncharacterized MutS homolog, MutS5, from a hyperthermophilic archaeon Pyrococcus horikoshii (phMutS5). Archaeal MutS5 has a Walker ATPase motif-containing amino acid sequence that shows similarity to the ATPase domain of MutSγ. It is known that the ATPase domain of MutS homologs is also a dimerization domain. Chemical cross-linking revealed that purified phMutS5 has an ability to dimerize in solution. phMutS5 bound to Holliday junction with a higher affinity than to other branched and linear DNAs, which resembles the DNA-binding specificities of MutSγ and bacterial MutS2, a Holliday junction-resolving MutS homolog. However, phMutS5 has no nuclease activity against branched DNA unlike MutS2. The ATPase activity of phMutS5 was significantly stimulated by the presence of Holliday junction similarly to MutSγ. Furthermore, site-directed mutagenesis revealed that the ATPase activity is dependent on the Walker ATPase motif of the protein. These results suggest that archaeal MutS5 should stabilize the Holliday junction and play a role in homologous recombination, which is analogous to the function of eukaryotic MutSγ.
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Affiliation(s)
- Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Kenji Fukui
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
| | - Mizuki Sato
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Takashi Morisawa
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Yuichi Hakumai
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Japan.,Geobio-Engineering and Technology Group, Submarine Resources Research Project, JAMSTEC, Nankoku, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Japan.,Geobio-Engineering and Technology Group, Submarine Resources Research Project, JAMSTEC, Nankoku, Japan.,Research and Development Center for Ocean Drilling Science, Yokohama, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
| | - Makoto Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Taisuke Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
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45
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Girelli Zubani G, Zivojnovic M, De Smet A, Albagli-Curiel O, Huetz F, Weill JC, Reynaud CA, Storck S. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs. J Exp Med 2017; 214:1169-1180. [PMID: 28283534 PMCID: PMC5379981 DOI: 10.1084/jem.20161576] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022] Open
Abstract
Girelli Zubani et al. show that the Pms2 component of the mismatch repair complex and multiple uracil glycosylases contribute, each with a distinct strand bias, to enlarge the Ig gene mutation spectrum from G-C to A-T bases. During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung−/−Pms2−/− mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases.
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Affiliation(s)
- Giulia Girelli Zubani
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Marija Zivojnovic
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Annie De Smet
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Olivier Albagli-Curiel
- Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Faculté de Médecine-Site Cochin, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - François Huetz
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France.,Département d'Immunologie, Institut Pasteur, 75015 Paris, France
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Sébastien Storck
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
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46
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Hopfner KP. Invited review: Architectures and mechanisms of ATP binding cassette proteins. Biopolymers 2017; 105:492-504. [PMID: 27037766 DOI: 10.1002/bip.22843] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
ATP binding cassette (ABC) ATPases form chemo-mechanical engines and switches that function in a broad range of biological processes. Most prominently, a very large family of integral membrane NTPases-ABC transporters-catalyzes the import or export of a diverse molecules across membranes. ABC proteins are also important components of the chromosome segregation, recombination, and DNA repair machineries and regulate or catalyze critical steps of ribosomal protein synthesis. Recent structural and mechanistic studies draw interesting architectural and mechanistic parallels between diverse ABC proteins. Here, I review this state of our understanding how NTP-dependent conformational changes of ABC proteins drive diverse biological processes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 492-504, 2016.
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Affiliation(s)
- Karl-Peter Hopfner
- Department Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Center for Integrated Protein Science Munich, Ludwigs-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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47
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Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J. Proteomic Analysis Reveals a Novel Mutator S (MutS) Partner Involved in Mismatch Repair Pathway. Mol Cell Proteomics 2016; 15:1299-308. [PMID: 27037360 DOI: 10.1074/mcp.m115.056093] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 01/08/2023] Open
Abstract
The mismatch repair (MMR) family is a highly conserved group of proteins that function in correcting base-base and insertion-deletion mismatches generated during DNA replication. Disruption of this process results in characteristic microsatellite instability (MSI), repair defects, and susceptibility to cancer. However, a significant fraction of MSI-positive cancers express MMR genes at normal levels and do not carry detectable mutation in known MMR genes, suggesting that additional factors and/or mechanisms may exist to explain these MSI phenotypes in patients. To systematically investigate the MMR pathway, we conducted a proteomic analysis and identified MMR-associated protein complexes using tandem-affinity purification coupled with mass spectrometry (TAP-MS) method. The mass spectrometry data have been deposited to the ProteomeXchange with identifier PXD003014 and DOI 10.6019/PXD003014. We identified 230 high-confidence candidate interaction proteins (HCIPs). We subsequently focused on MSH2, an essential component of the MMR pathway and uncovered a novel MSH2-binding partner, WDHD1. We further demonstrated that WDHD1 forms a stable complex with MSH2 and MSH3 or MSH6,i.e.the MutS complexes. The specific MSH2/WDHD1 interaction is mediated by the second lever domain of MSH2 and Ala(1123)site of WDHD1. Moreover, we showed that, just like MSH2-deficient cells, depletion of WDHD1 also led to 6-thioguanine (6-TG) resistance, indicating that WDHD1 likely contributes to the MMR pathway. Taken together, our study uncovers new components involved in the MMR pathway, which provides candidate genes that may be responsible for the development of MSI-positive cancers.
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Affiliation(s)
- Zhen Chen
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Mykim Tran
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Mengfan Tang
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Wenqi Wang
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Zihua Gong
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Junjie Chen
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
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48
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Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J. Proteomic Analysis Reveals a Novel Mutator S (MutS) Partner Involved in Mismatch Repair Pathway. Mol Cell Proteomics 2016. [PMID: 27037360 DOI: 10.1074/mcp.m115.056093+] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mismatch repair (MMR) family is a highly conserved group of proteins that function in correcting base-base and insertion-deletion mismatches generated during DNA replication. Disruption of this process results in characteristic microsatellite instability (MSI), repair defects, and susceptibility to cancer. However, a significant fraction of MSI-positive cancers express MMR genes at normal levels and do not carry detectable mutation in known MMR genes, suggesting that additional factors and/or mechanisms may exist to explain these MSI phenotypes in patients. To systematically investigate the MMR pathway, we conducted a proteomic analysis and identified MMR-associated protein complexes using tandem-affinity purification coupled with mass spectrometry (TAP-MS) method. The mass spectrometry data have been deposited to the ProteomeXchange with identifier PXD003014 and DOI 10.6019/PXD003014. We identified 230 high-confidence candidate interaction proteins (HCIPs). We subsequently focused on MSH2, an essential component of the MMR pathway and uncovered a novel MSH2-binding partner, WDHD1. We further demonstrated that WDHD1 forms a stable complex with MSH2 and MSH3 or MSH6,i.e.the MutS complexes. The specific MSH2/WDHD1 interaction is mediated by the second lever domain of MSH2 and Ala(1123)site of WDHD1. Moreover, we showed that, just like MSH2-deficient cells, depletion of WDHD1 also led to 6-thioguanine (6-TG) resistance, indicating that WDHD1 likely contributes to the MMR pathway. Taken together, our study uncovers new components involved in the MMR pathway, which provides candidate genes that may be responsible for the development of MSI-positive cancers.
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Affiliation(s)
- Zhen Chen
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Mykim Tran
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Mengfan Tang
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Wenqi Wang
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Zihua Gong
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
| | - Junjie Chen
- From the ‡Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Boulevard, Houston, TX 77030
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49
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Liu J, Hanne J, Britton BM, Bennett J, Kim D, Lee JB, Fishel R. Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair. Nature 2016; 539:583-587. [PMID: 27851738 PMCID: PMC5845140 DOI: 10.1038/nature20562] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Mismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis. Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10-40% of related sporadic tumours. However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism. We visualized Escherichia coli (Ec) ensemble mismatch repair and confirmed that EcMutS mismatch recognition results in the formation of stable ATP-bound sliding clamps that randomly diffuse along the DNA with intermittent backbone contact. The EcMutS sliding clamps act as a platform to recruit EcMutL onto the mismatched DNA, forming an EcMutS-EcMutL search complex that then closely follows the DNA backbone. ATP binding by EcMutL establishes a second long-lived DNA clamp that oscillates between the principal EcMutS-EcMutL search complex and unrestricted EcMutS and EcMutL sliding clamps. The EcMutH endonuclease that targets mismatch repair excision only binds clamped EcMutL, increasing its DNA association kinetics by more than 1,000-fold. The assembly of an EcMutS-EcMutL-EcMutH search complex illustrates how sequential stable sliding clamps can modulate one-dimensional diffusion mechanics along the DNA to direct mismatch repair.
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Affiliation(s)
- Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Jeungphill Hanne
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Jared Bennett
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Daehyung Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk 790-784, Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk 790-784, Korea
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Kyungbuk, 790-784, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
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50
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Wielders E, Delzenne-Goette E, Dekker R, van der Valk M, Te Riele H. Truncation of the MSH2 C-terminal 60 amino acids disrupts effective DNA mismatch repair and is causative for Lynch syndrome. Fam Cancer 2016; 16:221-229. [PMID: 27873144 DOI: 10.1007/s10689-016-9945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Missense variants of DNA mismatch repair (MMR) genes pose a problem in clinical genetics as long as they cannot unambiguously be assigned as the cause of Lynch syndrome (LS). To study such variants of uncertain clinical significance, we have developed a functional assay based on direct measurement of MMR activity in mouse embryonic stem cells expressing mutant protein from the endogenous alleles. We have applied this protocol to a specific truncation mutant of MSH2 that removes 60 C-terminal amino acids and has been found in suspected LS families. We show that the stability of the MSH2/MSH6 heterodimer is severely perturbed, causing attenuated MMR in in vitro assays and cancer predisposition in mice. This mutation can therefore unambiguously be considered as deleterious and causative for LS.
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Affiliation(s)
- Eva Wielders
- Division of Biological Stress Response, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Elly Delzenne-Goette
- Division of Biological Stress Response, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Rob Dekker
- Division of Biological Stress Response, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Martin van der Valk
- Division of Biological Stress Response, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Biological Stress Response, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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