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Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, Brieba LG. Expansion of the MutS Gene Family in Plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603841. [PMID: 39071318 PMCID: PMC11275761 DOI: 10.1101/2024.07.17.603841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Viraj Muthye
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alejandro Peñafiel-Ayala
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | - Jennifer R Marron
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Luis G Brieba
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
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2
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Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe G. H3K4me1 recruits DNA repair proteins in plants. THE PLANT CELL 2024; 36:2410-2426. [PMID: 38531669 PMCID: PMC11132887 DOI: 10.1093/plcell/koae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
Abstract
DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined 2 proteins which, in plants, contain Tudor histone reader domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved in homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch repair protein. The MSH6 Tudor domain of Arabidopsis (Arabidopsis thaliana) binds to H3K4me1 as previously demonstrated for PDS5C, which localizes to H3K4me1-rich gene bodies and essential genes. Mutations revealed by ultradeep sequencing of wild-type and msh6 knockout lines in Arabidopsis show that functional MSH6 is critical for the reduced rate of single-base substitution (SBS) mutations in gene bodies and H3K4me1-rich regions. We explored the breadth of these mechanisms among plants by examining a large rice (Oryza sativa) mutation data set. H3K4me1-associated hypomutation is conserved in rice as are the H3K4me1-binding residues of MSH6 and PDS5C Tudor domains. Recruitment of DNA repair proteins by H3K4me1 in plants reveals convergent, but distinct, epigenome-recruited DNA repair mechanisms from those well described in humans. The emergent model of H3K4me1-recruited repair in plants is consistent with evolutionary theory regarding mutation modifier systems and offers mechanistic insight into intragenomic mutation rate variation in plants.
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Affiliation(s)
- Daniela Quiroz
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
| | - Satoyo Oya
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Diego Lopez-Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Kehan Zhao
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Lissandro Ortega
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Alissza Ali
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
- Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-0814, Japan
| | - Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Integrative Genetics and Genomics, University of California Davis, Davis, CA 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, CA 95616, USA
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3
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Ozturk S. Genetic variants underlying spermatogenic arrests in men with non-obstructive azoospermia. Cell Cycle 2023; 22:1021-1061. [PMID: 36740861 PMCID: PMC10081088 DOI: 10.1080/15384101.2023.2171544] [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: 10/17/2022] [Revised: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Spermatogenic arrest is a severe form of non-obstructive azoospermia (NOA), which occurs in 10-15% of infertile men. Interruption in spermatogenic progression at premeiotic, meiotic, or postmeiotic stage can lead to arrest in men with NOA. Recent studies have intensively focused on defining genetic variants underlying these spermatogenic arrests by making genome/exome sequencing. A number of variants were discovered in the genes involving in mitosis, meiosis, germline differentiation and other basic cellular events. Herein, defined variants in NOA cases with spermatogenic arrests and created knockout mouse models for the related genes are comprehensively reviewed. Also, importance of gene panel-based screening for NOA cases was discussed. Screening common variants in these infertile men with spermatogenic arrests may contribute to elucidating the molecular background and designing novel treatment strategies.
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Affiliation(s)
- Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey
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Madden-Hennessey K, Gupta D, Radecki AA, Guild C, Rath A, Heinen CD. Loss of mismatch repair promotes a direct selective advantage in human stem cells. Stem Cell Reports 2022; 17:2661-2673. [PMID: 36368329 PMCID: PMC9768573 DOI: 10.1016/j.stemcr.2022.10.009] [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: 03/04/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
Lynch syndrome (LS) is the most common hereditary form of colon cancer, resulting from a germline mutation in a DNA mismatch repair (MMR) gene. Loss of MMR in cells establishes a mutator phenotype, which may underlie its link to cancer. Acquired downstream mutations that provide the cell a selective advantage would contribute to tumorigenesis. It is unclear, however, whether loss of MMR has other consequences that would directly result in a selective advantage. We found that knockout of the MMR gene MSH2 results in an immediate survival advantage in human stem cells grown under standard cell culture conditions. This advantage results, in part, from an MMR-dependent response to oxidative stress. We also found that loss of MMR gives rise to enhanced formation and growth of human colonic organoids. These results suggest that loss of MMR may affect cells in ways beyond just increasing mutation frequency that could influence tumorigenesis.
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Affiliation(s)
| | - Dipika Gupta
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101, USA
| | | | - Caroline Guild
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101, USA
| | - Abhijit Rath
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101, USA
| | - Christopher D. Heinen
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101, USA,Corresponding author
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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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D'Arcy BM, Arrington J, Weisman J, McClellan SB, Vandana , Yang Z, Deivanayagam C, Blount J, Prakash A. PMS2 variant results in loss of ATPase activity without compromising mismatch repair. Mol Genet Genomic Med 2022; 10:e1908. [PMID: 35189042 PMCID: PMC9034662 DOI: 10.1002/mgg3.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
Hereditary cancer syndromes account for approximately 5%-10% of all diagnosed cancer cases. Lynch syndrome (LS) is an autosomal dominant hereditary cancer condition that predisposes individuals to an elevated lifetime risk for developing colorectal, endometrial, and other cancers. LS results from a pathogenic mutation in one of four mismatch repair (MMR) genes (MSH2, MSH6, MLH1, and PMS2). The diagnosis of LS is often challenged by the identification of missense mutations, termed variants of uncertain significance, whose functional effect on the protein is not known. Of the eight PMS2 variants initially selected for this study, we identified a variant within the N-terminal domain where asparagine 335 is mutated to serine, p.Asn335Ser, which lacked ATPase activity, yet appears to be proficient in MMR. To expand our understanding of this functional dichotomy, we performed biophysical and structural studies, and noted that p.Asn335Ser binds to ATP but is unable to hydrolyze it to ADP. To examine the impact of p.Asn335Ser on MMR, we developed a novel in-cell fluorescent-based microsatellite instability reporter that revealed p.Asn335Ser maintained genomic stability. We conclude that in the absence of gross structural changes, PMS2 ATP hydrolysis is not necessary for proficient MMR and that the ATPase deficient p.Asn335Ser variant is likely benign.
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Affiliation(s)
- Brandon M. D'Arcy
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Jennifer Arrington
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Justin Weisman
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Steven B. McClellan
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Flow Cytometry Shared Resource LabMitchell Cancer InstituteMobileAlabamaUSA
| | - Vandana
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Zhengrong Yang
- Department of Biochemistry and Molecular GeneticsSchool of Medicine University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular GeneticsSchool of Medicine University of Alabama at BirminghamBirminghamAlabamaUSA
| | | | - Aishwarya Prakash
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
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Katju V, Konrad A, Deiss TC, Bergthorsson U. Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2. G3 GENES|GENOMES|GENETICS 2022; 12:6407146. [PMID: 34849777 PMCID: PMC8727991 DOI: 10.1093/g3journal/jkab364] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
DNA mismatch repair (MMR), an evolutionarily conserved repair pathway shared by prokaryotic and eukaryotic species alike, influences molecular evolution by detecting and correcting mismatches, thereby protecting genetic fidelity, reducing the mutational load, and preventing lethality. Herein we conduct the first genome-wide evaluation of the alterations to the mutation rate and spectrum under impaired activity of the MutSα homolog, msh-2, in Caenorhabditis elegans male–female fog-2(lf) lines. We performed mutation accumulation (MA) under RNAi-induced knockdown of msh-2 for up to 50 generations, followed by next-generation sequencing of 19 MA lines and the ancestral control. msh-2 impairment in the male–female background substantially increased the frequency of nuclear base substitutions (∼23×) and small indels (∼328×) relative to wildtype hermaphrodites. However, we observed no increase in the mutation rates of mtDNA, and copy-number changes of single-copy genes. There was a marked increase in copy-number variation of rDNA genes under MMR impairment. In C. elegans, msh-2 repairs transitions more efficiently than transversions and increases the AT mutational bias relative to wildtype. The local sequence context, including sequence complexity, G + C-content, and flanking bases influenced the mutation rate. The X chromosome exhibited lower substitution and higher indel rates than autosomes, which can either result from sex-specific mutation rates or a nonrandom distribution of mutable sites between chromosomes. Provided the observed difference in mutational pattern is mostly due to MMR impairment, our results indicate that the specificity of MMR varies between taxa, and is more efficient in detecting and repairing small indels in eukaryotes relative to prokaryotes.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
- Faculdade de Ciência da Universidade de Lisboa (FCUL), CE3C—Centre for Ecology, Evolution and Environmental Changes, 1749-016 Lisboa, Portugal
| | - Thaddeus C Deiss
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
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Pandya N, Bhagwat SR, Kumar A. Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in Cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188594. [PMID: 34303788 DOI: 10.1016/j.bbcan.2021.188594] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
DNA has the ability to form polymorphic structures like canonical duplex DNA and non-canonical triplex DNA, Cruciform, Z-DNA, G-quadruplex (G4), i-motifs, and hairpin structures. The alteration in the form of DNA polymorphism in the response to environmental changes influences the gene expression. Non-canonical structures are engaged in various biological functions, including chromatin epigenetic and gene expression regulation via transcription and translation, as well as DNA repair and recombination. The presence of non-canonical structures in the regulatory region of the gene alters the gene expression and affects the cellular machinery. Formation of non-canonical structure in the regulatory site of cancer-related genes either inhibits or dysregulate the gene function and promote tumour formation. In the current article, we review the influence of non-canonical structure on the regulatory mechanisms in human genome. Moreover, we have also discussed the relevance of non-canonical structures in cancer and provided information on the drugs used for their treatment by targeting these structures.
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Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Sonali R Bhagwat
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
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Haupt S, Gleim N, Ahadova A, Bläker H, Knebel Doeberitz M, Kloor M, Heuveline V. A computational model for investigating the evolution of colonic crypts during Lynch syndrome carcinogenesis. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Saskia Haupt
- Engineering Mathematics and Computing Lab (EMCL) Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Heidelberg Germany
- Data Mining and Uncertainty Quantification (DMQ) Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
| | - Nils Gleim
- Engineering Mathematics and Computing Lab (EMCL) Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Heidelberg Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology (ATB) Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- Clinical Cooperation Unit Applied Tumor Biology German Cancer Research Center Heidelberg Germany
| | - Hendrik Bläker
- Institute of Pathology University Hospital Leipzig Leipzig Germany
| | - Magnus Knebel Doeberitz
- Department of Applied Tumor Biology (ATB) Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- Clinical Cooperation Unit Applied Tumor Biology German Cancer Research Center Heidelberg Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology (ATB) Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- Clinical Cooperation Unit Applied Tumor Biology German Cancer Research Center Heidelberg Germany
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL) Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Heidelberg Germany
- Data Mining and Uncertainty Quantification (DMQ) Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
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10
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Kim SY, Kim GY, You HJ, Kang MJ. Relationship between DNA mismatch repair and CRISPR/Cas9-mediated knock-in in the bovine β-casein gene locus. Anim Biosci 2021; 35:126-137. [PMID: 34293843 PMCID: PMC8738927 DOI: 10.5713/ab.21.0117] [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: 03/16/2021] [Accepted: 06/16/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Efficient gene editing technology is critical for successful knock-in in domestic animals. RAD51 recombinase (RAD51) gene plays an important role in strand invasion during homologous recombination (HR) in mammals, and is regulated by checkpoint kinase 1 (CHK1) and CHK2 genes, which are upstream elements of RAD51 recombinase (RAD51). In addition, mismatch repair (MMR) system is inextricably linked to HR-related pathways and regulates HR via heteroduplex rejection. Thus, the aim of this study was to investigate whether clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9)-mediated knock-in efficiency of human lactoferrin (hLF) knock-in vector in the bovine β-casein gene locus can be increased by suppressing DNA MMR-related genes (MSH2, MSH3, MSH6, MLH1, and PMS2) and overexpressing DNA double-strand break (DSB) repair-related genes (RAD51, CHK1, CHK2). Methods Bovine mammary epithelial (MAC-T) cells were transfected with a knock-in vector, RAD51, CHK1, or CHK2 overexpression vector and CRISPR/sgRNA expression vector to target the bovine β-casein gene locus, followed by treatment of the cells with CdCl2 for 24 hours. After 3 days of CdCl2 treatment, the knock-in efficiency was confirmed by polymerase chain reaction (PCR). The mRNA expression levels of DNA MMR-related and DNA DSB repair-related genes were assessed by quantitative real-time PCR (RT-qPCR). Results Treatment with CdCl2 decreased the mRNA expression of RAD51 and MMR-related genes but did not increase the knock-in efficiency in MAC-T cells. Also, the overexpression of DNA DSB repair-related genes in MAC-T cells did not significantly affect the mRNA expression of MMR-related genes and failed to increase the knock-in efficiency. Conclusion Treatment with CdCl2 inhibited the mRNA levels of RAD51 and DNA MMR-related genes in MAC-T cells. However, the function of MMR pathway in relation to HR may differ in various cell types or species.
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Affiliation(s)
- Seung-Yeon Kim
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
| | - Ga-Yeon Kim
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
| | - Hyeong-Ju You
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
| | - Man-Jong Kang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Korea
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11
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Haupt S, Zeilmann A, Ahadova A, Bläker H, von Knebel Doeberitz M, Kloor M, Heuveline V. Mathematical modeling of multiple pathways in colorectal carcinogenesis using dynamical systems with Kronecker structure. PLoS Comput Biol 2021; 17:e1008970. [PMID: 34003820 PMCID: PMC8162698 DOI: 10.1371/journal.pcbi.1008970] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/28/2021] [Accepted: 04/16/2021] [Indexed: 01/02/2023] Open
Abstract
Like many other types of cancer, colorectal cancer (CRC) develops through multiple pathways of carcinogenesis. This is also true for colorectal carcinogenesis in Lynch syndrome (LS), the most common inherited CRC syndrome. However, a comprehensive understanding of the distribution of these pathways of carcinogenesis, which allows for tailored clinical treatment and even prevention, is still lacking. We suggest a linear dynamical system modeling the evolution of different pathways of colorectal carcinogenesis based on the involved driver mutations. The model consists of different components accounting for independent and dependent mutational processes. We define the driver gene mutation graphs and combine them using the Cartesian graph product. This leads to matrix components built by the Kronecker sum and product of the adjacency matrices of the gene mutation graphs enabling a thorough mathematical analysis and medical interpretation. Using the Kronecker structure, we developed a mathematical model which we applied exemplarily to the three pathways of colorectal carcinogenesis in LS. Beside a pathogenic germline variant in one of the DNA mismatch repair (MMR) genes, driver mutations in APC, CTNNB1, KRAS and TP53 are considered. We exemplarily incorporate mutational dependencies, such as increased point mutation rates after MMR deficiency, and based on recent experimental data, biallelic somatic CTNNB1 mutations as common drivers of LS-associated CRCs. With the model and parameter choice, we obtained simulation results that are in concordance with clinical observations. These include the evolution of MMR-deficient crypts as early precursors in LS carcinogenesis and the influence of variants in MMR genes thereon. The proportions of MMR-deficient and MMR-proficient APC-inactivated crypts as first measure for the distribution among the pathways in LS-associated colorectal carcinogenesis are compatible with clinical observations. The approach provides a modular framework for modeling multiple pathways of carcinogenesis yielding promising results in concordance with clinical observations in LS CRCs.
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Affiliation(s)
- Saskia Haupt
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
- Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Alexander Zeilmann
- Image and Pattern Analysis Group (IPA), Heidelberg University, Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology (ATB), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology (ATB), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology (ATB), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
- Data Mining and Uncertainty Quantification (DMQ), Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
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12
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Leelatian N, Hong CS, Bindra RS. The Role of Mismatch Repair in Glioblastoma Multiforme Treatment Response and Resistance. Neurosurg Clin N Am 2021; 32:171-180. [PMID: 33781500 DOI: 10.1016/j.nec.2020.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mismatch repair (MMR) is a highly conserved DNA repair pathway that is critical for the maintenance of genomic integrity. This pathway targets base substitution and insertion-deletion mismatches, which primarily arise from replication errors that escape DNA polymerase proof-reading function. Here, the authors review key concepts in the molecular mechanisms of MMR in response to alkylation damage, approaches to detect MMR status in the clinic, and the clinical relevance of this pathway in glioblastoma multiforme treatment response and resistance.
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Affiliation(s)
- Nalin Leelatian
- Department of Pathology, Yale School of Medicine, 310 Cedar Street LH 108, New Haven, CT 06510, USA
| | - Christopher S Hong
- Department of Neurosurgery, Yale School of Medicine, 333 Cedar Street Tompkins 4, New Haven, CT 06510, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale School of Medicine, 333 Cedar Street Hunter 2, New Haven, CT 06510, USA.
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13
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Verma P, Tandon R, Yadav G, Gaur V. Structural Aspects of DNA Repair and Recombination in Crop Improvement. Front Genet 2020; 11:574549. [PMID: 33024442 PMCID: PMC7516265 DOI: 10.3389/fgene.2020.574549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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14
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Engel C, Ahadova A, Seppälä TT, Aretz S, Bigirwamungu-Bargeman M, Bläker H, Bucksch K, Büttner R, de Vos Tot Nederveen Cappel WT, Endris V, Holinski-Feder E, Holzapfel S, Hüneburg R, Jacobs MAJM, Koornstra JJ, Langers AM, Lepistö A, Morak M, Möslein G, Peltomäki P, Pylvänäinen K, Rahner N, Renkonen-Sinisalo L, Schulmann K, Steinke-Lange V, Stenzinger A, Strassburg CP, van de Meeberg PC, van Kouwen M, van Leerdam M, Vangala DB, Vecht J, Verhulst ML, von Knebel Doeberitz M, Weitz J, Zachariae S, Loeffler M, Mecklin JP, Kloor M, Vasen HF. Associations of Pathogenic Variants in MLH1, MSH2, and MSH6 With Risk of Colorectal Adenomas and Tumors and With Somatic Mutations in Patients With Lynch Syndrome. Gastroenterology 2020; 158:1326-1333. [PMID: 31926173 DOI: 10.1053/j.gastro.2019.12.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/05/2019] [Accepted: 12/24/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Lynch syndrome is caused by variants in DNA mismatch repair (MMR) genes and associated with an increased risk of colorectal cancer (CRC). In patients with Lynch syndrome, CRCs can develop via different pathways. We studied associations between Lynch syndrome-associated variants in MMR genes and risks of adenoma and CRC and somatic mutations in APC and CTNNB1 in tumors in an international cohort of patients. METHODS We combined clinical and molecular data from 3 studies. We obtained clinical data from 2747 patients with Lynch syndrome associated with variants in MLH1, MSH2, or MSH6 from Germany, the Netherlands, and Finland who received at least 2 surveillance colonoscopies and were followed for a median time of 7.8 years for development of adenomas or CRC. We performed DNA sequence analyses of 48 colorectal tumors (from 16 patients with mutations in MLH1, 29 patients with mutations in MSH2, and 3 with mutations in MSH6) for somatic mutations in APC and CTNNB1. RESULTS Risk of advanced adenoma in 10 years was 17.8% in patients with pathogenic variants in MSH2 vs 7.7% in MLH1 (P < .001). Higher proportions of patients with pathogenic variants in MLH1 or MSH2 developed CRC in 10 years (11.3% and 11.4%) than patients with pathogenic variants in MSH6 (4.7%) (P = .001 and P = .003 for MLH1 and MSH2 vs MSH6, respectively). Somatic mutations in APC were found in 75% of tumors from patients with pathogenic variants in MSH2 vs 11% in MLH1 (P = .015). Somatic mutations in CTNNB1 were found in 50% of tumors from patients with pathogenic variants in MLH1 vs 7% in MSH2 (P = .002). None of the 3 tumors with pathogenic variants in MSH6 had a mutation in CTNNB1, but all had mutations in APC. CONCLUSIONS In an analysis of clinical and DNA sequence data from patients with Lynch syndrome from 3 countries, we associated pathogenic variants in MMR genes with risk of adenoma and CRC, and somatic mutations in APC and CTNNB1 in colorectal tumors. If these findings are confirmed, surveillance guidelines might be adjusted based on MMR gene variants.
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Affiliation(s)
- Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
| | - Aysel Ahadova
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Toni T Seppälä
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; University of Helsinki, Helsinki, Finland; Johns Hopkins University, Surgical Oncology, Baltimore, Maryland
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | | | - Hendrik Bläker
- Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Karolin Bucksch
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | | | - Volker Endris
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Robert Hüneburg
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Maarten A J M Jacobs
- Department of Gastroenterology & Hepatology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Jan J Koornstra
- Department of Gastroenterology & Hepatology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra M Langers
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Gabriela Möslein
- Center for Hereditary Tumors, HELIOS Klinikum Wuppertal, University Witten-Herdecke, Wuppertal, Germany
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Kirsi Pylvänäinen
- Department of Education and Science, Central Finland Hospital District, Jyväskylä, Finland
| | - Nils Rahner
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Karsten Schulmann
- Department of Hematology and Oncology, Klinikum Hochsauerland, Meschede, Germany; MVZ Arnsberg, Medical Practice for Hematology and Oncology, Arnsberg, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Albrecht Stenzinger
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian P Strassburg
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Paul C van de Meeberg
- Department of Gastroenterology & Hepatology, Slingeland Hospital, Doetinchem, The Netherlands
| | - Mariette van Kouwen
- Department of Gastroenterology & Hepatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Monique van Leerdam
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Deepak B Vangala
- Department of Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Juda Vecht
- Department of Gastroenterology & Hepatology, Isala Zwolle, Zwolle, The Netherlands
| | - Marie-Louise Verhulst
- Department of Gastroenterology & Hepatology, Maxima Medical Centre, Eindhoven, The Netherlands
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus of the Technical University Dresden, Dresden, Germany
| | - Silke Zachariae
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Jukka-Pekka Mecklin
- Department of Surgery, Central Finland Central Hospital, Jyväskylä, Finland; Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Matthias Kloor
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans F Vasen
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
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15
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Huang Y, Li GM. DNA mismatch repair in the context of chromatin. Cell Biosci 2020; 10:10. [PMID: 32025281 PMCID: PMC6996186 DOI: 10.1186/s13578-020-0379-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA mismatch repair (MMR) maintains replication fidelity by correcting mispaired nucleotides incorporated by DNA polymerases. Defects in MMR lead to cancers characterized by microsatellite instability. Recently, chromatin mechanisms that regulate MMR have been discovered, which sheds new light on MMR deficiency and its role in tumorigenesis. This review summarizes these chromatin-level mechanisms that regulate MMR and their implications for tumor development.
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Affiliation(s)
- Yaping Huang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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16
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Lahiri S, Li Y, Hingorani MM, Mukerji I. MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination. Biophys J 2018; 115:2087-2101. [PMID: 30467025 DOI: 10.1016/j.bpj.2018.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023] Open
Abstract
In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a Kd < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.
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Affiliation(s)
- Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut.
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17
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Abstract
DNA mismatch repair (MMR) is an evolutionally conserved genome maintenance pathway and is well known for its role in maintaining replication fidelity by correcting biosynthetic errors generated during DNA replication. However, recent studies have shown that MMR preferentially protects actively transcribed genes from mutation during both DNA replication and transcription. This review describes the recent discoveries in this area. Potential mechanisms by which MMR safeguards actively transcribed genes are also discussed.
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Affiliation(s)
- Yaping Huang
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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18
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Liu J, Lee JB, Fishel R. Stochastic Processes and Component Plasticity Governing DNA Mismatch Repair. J Mol Biol 2018; 430:4456-4468. [PMID: 29864444 PMCID: PMC6461355 DOI: 10.1016/j.jmb.2018.05.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/09/2018] [Accepted: 05/28/2018] [Indexed: 02/06/2023]
Abstract
DNA mismatch repair (MMR) is a DNA excision-resynthesis process that principally enhances replication fidelity. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologs initiate MMR and in higher eukaryotes act as DNA damage sensors that can trigger apoptosis. MSH proteins recognize mismatched nucleotides, whereas the MLH/PMS proteins mediate multiple interactions associated with downstream MMR events including strand discrimination and strand-specific excision that are initiated at a significant distance from the mismatch. Remarkably, the biophysical functions of the MLH/PMS proteins have been elusive for decades. Here we consider recent observations that have helped to define the mechanics of MLH/PMS proteins and their role in choreographing MMR. We highlight the stochastic nature of DNA interactions that have been visualized by single-molecule analysis and the plasticity of protein complexes that employ thermal diffusion to complete the progressions of MMR.
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Affiliation(s)
- Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, 43210, OH, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), 790-784, Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, 790-784, Pohang, Korea.
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, 43210, OH, USA.
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19
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Murmann AE, Yu J, Opal P, Peter ME. Trinucleotide Repeat Expansion Diseases, RNAi, and Cancer. Trends Cancer 2018; 4:684-700. [PMID: 30292352 DOI: 10.1016/j.trecan.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 01/12/2023]
Abstract
Many neurodegenerative diseases are caused by unstable trinucleotide repeat (TNR) expansions located in disease-associated genes. siRNAs based on CAG repeat expansions effectively kill cancer cell lines in vitro through RNAi. They also cause significant reduction in tumor growth in a human ovarian cancer mouse model with no toxicity to the treated mice. This suggests that cancer cells are particularly sensitive to CAG TNR-derived siRNAs, and explains a reported inverse correlation between the length of CAG TNRs and reduced global cancer incidences in some CAG TNR diseases. This review discusses both mutant proteins and mutant RNAs as a cause of TNR diseases, with a focus on RNAi and its role in contributing to disease pathology and in suppressing cancer.
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Affiliation(s)
- Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jindan Yu
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Puneet Opal
- Davee Department of Neurology, Northwestern University, Chicago, IL 60611, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA.
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20
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Huang Y, Gu L, Li GM. H3K36me3-mediated mismatch repair preferentially protects actively transcribed genes from mutation. J Biol Chem 2018; 293:7811-7823. [PMID: 29610279 DOI: 10.1074/jbc.ra118.002839] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
Histone H3 trimethylation at lysine 36 (H3K36me3) is an important histone mark involved in both transcription elongation and DNA mismatch repair (MMR). It is known that H3K36me3 recruits the mismatch-recognition protein MutSα to replicating chromatin via its physical interaction with MutSα's PWWP domain, but the exact role of H3K36me3 in transcription is undefined. Using ChIP combined with whole-genome DNA sequencing analysis, we demonstrate here that H3K36me3, together with MutSα, is involved in protecting against mutation, preferentially in actively transcribed genomic regions. We found that H3K36me3 and MutSα are much more co-enriched in exons and actively transcribed regions than in introns and nontranscribed regions. The H3K36me3-MutSα co-enrichment correlated with a much lower mutation frequency in exons and actively transcribed regions than in introns and nontranscribed regions. Correspondingly, depleting H3K36me3 or disrupting the H3K36me3-MutSα interaction elevated the spontaneous mutation frequency in actively transcribed genes, but it had little influence on the mutation frequency in nontranscribed or transcriptionally inactive regions. Similarly, H2O2-induced mutations, which mainly cause base oxidations, preferentially occurred in actively transcribed genes in MMR-deficient cells. The data presented here suggest that H3K36me3-mediated MMR preferentially safeguards actively transcribed genes not only during replication by efficiently correcting mispairs in early replicating chromatin but also during transcription by directly or indirectly removing DNA lesions associated with a persistently open chromatin structure.
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Affiliation(s)
- Yaping Huang
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, 100084 Beijing, China and
| | - Liya Gu
- the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Guo-Min Li
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, 100084 Beijing, China and .,the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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21
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Bologna-Molina R, Pereira-Prado V, Sánchez-Romero C, Tapia-Repetto G, Soria S, Hernandez M, Gónzalez-Gónzalez R, Molina-Frechero M, Mikami T. Expression of hMLH1 and hMSH2 proteins in ameloblastomas and tooth germs. Med Oral Patol Oral Cir Bucal 2018; 23:e126-e131. [PMID: 29476681 PMCID: PMC5911352 DOI: 10.4317/medoral.22210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/09/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mismatch repair proteins (MMRPs) are a group of nuclear enzymes that participate in the repair of base mismatches that occur during DNA replication in all proliferating cells. The most studied MMRPs are hMSH2 and hMLH1, which are known to be highly expressed in normal tissues. A loss of MMRPs leads to the accumulation of DNA replication errors in proliferating cells. Ki-67 is a biomarker regarded to be the gold-standard tool for determining cell proliferation by immunohistochemical methods. The aim of this study was to investigate the immunohistochemical expression of hMLH1, hMSH2 and Ki-67 proteins in ameloblastomas and tooth germs, to contribute to the understanding of the development of this odontogenic neoplasm. MATERIAL AND METHODS Immunohistochemical assays to determine the presence of proteins hMSH2, hMLH1 and Ki-67 were performed in 80 ameloblastomas (40 solid and 40 unicystic) and five tooth germs. RESULTS Unicystic ameloblastomas showed higher MMRP expression (hMLH1: 62.5 ± 43.4; hMSH2: 83.3 ± 47.8) than did solid ameloblastomas (hMLH1: 59.4 ± 13.5; hMSH2: 75.8 ± 40.2). Additionally, the cell proliferation index assessed by Ki-67 was inversely proportional to the expression of MMRP. Comparison between tooth germs and ameloblastoma revealed significantly higher expression of hMLH1, hMSH2 and Ki-67 in tooth germs (p=0.02). CONCLUSIONS The differences of MMRP and Ki-67 immunoexpression between ameloblastomas and tooth germ suggest that alterations in the MMRP mechanisms could participate in the biological behavior of ameloblastomas.
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Affiliation(s)
- R Bologna-Molina
- School of Dentistry, Molecular Pathology Area, Universidad de la República, Las Heras 1925, Montevideo, Uruguay,
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22
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Yuan Y, Zhao Y, Chen L, Wu J, Chen G, Li S, Zou J, Chen R, Wang J, Jiang F, Tang Z. Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G-T mismatch. Nucleic Acids Res 2017; 45:8676-8683. [PMID: 28911109 PMCID: PMC5587794 DOI: 10.1093/nar/gkx602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/04/2017] [Indexed: 12/04/2022] Open
Abstract
Riboflavin (vitamin B2) has been thought to be a promising antitumoral agent in photodynamic therapy, though the further application of the method was limited by the unclear molecular mechanism. Our work reveals that riboflavin was able to recognize G–T mismatch specifically and induce single-strand breaks in duplex DNA targets efficiently under irradiation. In the presence of riboflavin, the photo-irradiation could induce the death of tumor cells that are defective in mismatch repair system selectively, highlighting the G–T mismatch as potential drug target for tumor cells. Moreover, riboflavin is a promising leading compound for further drug design due to its inherent specific recognition of the G–T mismatch.
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Affiliation(s)
- Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.,College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Yongyun Zhao
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Lianqi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiasi Wu
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Sheng Li
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jiawei Zou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Rong Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Jian Wang
- College of pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, PR China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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23
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Liu D, Frederiksen JH, Liberti SE, Lützen A, Keijzers G, Pena-Diaz J, Rasmussen LJ. Human DNA polymerase delta double-mutant D316A;E318A interferes with DNA mismatch repair in vitro. Nucleic Acids Res 2017; 45:9427-9440. [PMID: 28934474 PMCID: PMC5766205 DOI: 10.1093/nar/gkx611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
DNA mismatch repair (MMR) is a highly-conserved DNA repair mechanism, whose primary role is to remove DNA replication errors preventing them from manifesting as mutations, thereby increasing the overall genome stability. Defects in MMR are associated with increased cancer risk in humans and other organisms. Here, we characterize the interaction between MMR and a proofreading-deficient allele of the human replicative DNA polymerase delta, PolδD316A;E318A, which has a higher capacity for strand displacement DNA synthesis than wild type Polδ. Human cell lines overexpressing PolδD316A;E318A display a mild mutator phenotype, while nuclear extracts of these cells exhibit reduced MMR activity in vitro, and these defects are complemented by overexpression or addition of exogenous human Exonuclease 1 (EXO1). By contrast, another proofreading-deficient mutant, PolδD515V, which has a weaker strand displacement activity, does not decrease the MMR activity as significantly as PolδD316A;E318A. In addition, PolδD515V does not increase the mutation frequency in MMR-proficient cells. Based on our findings, we propose that the proofreading activity restricts the strand displacement activity of Polδ in MMR. This contributes to maintain the nicks required for EXO1 entry, and in this manner ensures the dominance of the EXO1-dependent MMR pathway.
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Affiliation(s)
- Dekang Liu
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Jane H Frederiksen
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Sascha E Liberti
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Anne Lützen
- Department of Science, Systems and Models, Roskilde University, Denmark
| | - Guido Keijzers
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Javier Pena-Diaz
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Lene Juel Rasmussen
- Center for Healthy Aging, University of Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
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24
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Bailis JM, Weidmann AG, Mariano NF, Barton JK. Rhodium metalloinsertor binding generates a lesion with selective cytotoxicity for mismatch repair-deficient cells. Proc Natl Acad Sci U S A 2017; 114:6948-6953. [PMID: 28634291 PMCID: PMC5502648 DOI: 10.1073/pnas.1706665114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The DNA mismatch repair (MMR) pathway recognizes and repairs errors in base pairing and acts to maintain genome stability. Cancers that have lost MMR function are common and comprise an important clinical subtype that is resistant to many standard of care chemotherapeutics such as cisplatin. We have identified a family of rhodium metalloinsertors that bind DNA mismatches with high specificity and are preferentially cytotoxic to MMR-deficient cells. Here, we characterize the cellular mechanism of action of the most potent and selective complex in this family, [Rh(chrysi)(phen)(PPO)]2+ (Rh-PPO). We find that Rh-PPO binding induces a lesion that triggers the DNA damage response (DDR). DDR activation results in cell-cycle blockade and inhibition of DNA replication and transcription. Significantly, the lesion induced by Rh-PPO is not repaired in MMR-deficient cells, resulting in selective cytotoxicity. The Rh-PPO mechanism is reminiscent of DNA repair enzymes that displace mismatched bases, and is differentiated from other DNA-targeted chemotherapeutics such as cisplatin by its potency, cellular mechanism, and selectivity for MMR-deficient cells.
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Affiliation(s)
- Julie M Bailis
- Department of Oncology Research, Amgen, Inc., South San Francisco, CA 94080;
| | - Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Natalie F Mariano
- Department of Oncology Research, Amgen, Inc., South San Francisco, CA 94080
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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25
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Korona R. GENETIC LOAD OF THE YEAST SACCHAROMYCES CEREVISIAE UNDER DIVERSE ENVIRONMENTAL CONDITIONS. Evolution 2017; 53:1966-1971. [PMID: 28565447 DOI: 10.1111/j.1558-5646.1999.tb04577.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/1998] [Accepted: 06/10/1999] [Indexed: 11/30/2022]
Abstract
Fitness effect of spontaneous mutations accumulated in mismatch-repair deficient strains of yeast was estimated by measuring their maximum growth rate. Several environments with different energetic substrates, nutritional conditions, and temperature were tested. Genetic load of haploid strains was about 20-30% under most of these conditions. Because such a pronounced effect was caused by relatively small lesions (point mutations) affecting probably less than 1% of genes, resistance of the yeast genome to DNA damage appears to be rather limited. Fitness transitions among environments were orderly, in the sense that some strains tended to be more or less fit than others in all circumstances. One of the environments (an extremely high temperature, 38°C) was stressful to the strains that accumulated mutations, as some of them stopped to grow, whereas the mutation-free strains were only moderately affected. These results imply that the impact of random point mutations is substantial and generally not dependent on a particular environment. Under stressful conditions, however, natural selection may be especially effective in purging mutations that, if commonly met, could slow down the rate of mutation accumulation.
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Affiliation(s)
- Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, Ingardena 6, 30-060, Krakow, Poland
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26
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Cui H, Wu Q, Zhu B. Specific-Locus Amplified Fragment Sequencing Reveals Spontaneous Single-Nucleotide Mutations in Rice OsMsh6 Mutants. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4816973. [PMID: 28589142 PMCID: PMC5447274 DOI: 10.1155/2017/4816973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022]
Abstract
Genomic stability depends in part on an efficient DNA lesion recognition and correction by the DNA mismatch repair (MMR) system. We investigated mutations arising spontaneously in rice OsMsh6 mutants by specific-locus amplified fragment sequencing. Totally 994 single-nucleotide mutations were identified in three mutants and on average the mutation density is about 1/136.72 Kb per mutant line. These mutations were relatively randomly distributed in genome and might be accumulated in generation-dependent manner. All possible base transitions and base transversions could be seen and the ratio of transitions to transversions was about 3.12. We also observed the nearest-neighbor bias around the mutated base. Our data suggests that OsMsh6 (LOC_Os09g24220) is important in ensuring genome stability by recognizing mismatches that arise spontaneously and provides useful information for investigating the function of the OsMsh6 gene in DNA repair and exploiting MMR mutants in rice induced mutation breeding.
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Affiliation(s)
- Hairui Cui
- Institute of Nuclear-Agricultural Sciences/Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
- *Hairui Cui:
| | - Qiongyu Wu
- Institute of Nuclear-Agricultural Sciences/Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Bin Zhu
- Institute of Nuclear-Agricultural Sciences/Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
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27
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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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28
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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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29
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Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells. DNA Repair (Amst) 2015; 38:68-74. [PMID: 26719139 DOI: 10.1016/j.dnarep.2015.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 09/09/2015] [Accepted: 11/30/2015] [Indexed: 12/15/2022]
Abstract
DNA mismatch repair (MMR) protects genome integrity by correcting DNA replication-associated mispairs, modulating DNA damage-induced cell cycle checkpoints and regulating homeologous recombination. Loss of MMR function leads to cancer development. This review describes progress in understanding how MMR is carried out in the context of chromatin and how chromatin organization/compaction, epigenetic mechanisms and posttranslational modifications of MMR proteins influence and regulate MMR in eukaryotic cells.
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30
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Liu J, Hanne J, Britton BM, Shoffner M, Albers AE, Bennett J, Zatezalo R, Barfield R, Rabuka D, Lee JB, Fishel R. An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore. Sci Rep 2015; 5:16883. [PMID: 26582263 PMCID: PMC4652282 DOI: 10.1038/srep16883] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/07/2015] [Indexed: 11/09/2022] Open
Abstract
Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.
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Affiliation(s)
- Jiaquan Liu
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Jeungphill Hanne
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Brooke M Britton
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Matthew Shoffner
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | - Jared Bennett
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Rachel Zatezalo
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | | | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210.,Physics Department, The Ohio State University, Columbus, OH 43210
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31
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Patil S, Moeys S, von Dassow P, Huysman MJJ, Mapleson D, De Veylder L, Sanges R, Vyverman W, Montresor M, Ferrante MI. Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta. BMC Genomics 2015; 16:930. [PMID: 26572248 PMCID: PMC4647503 DOI: 10.1186/s12864-015-1983-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/04/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. RESULTS The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. CONCLUSIONS Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.
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Affiliation(s)
- Shrikant Patil
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Sara Moeys
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Peter von Dassow
- Facultad de Ciencias Biológicas, Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Chile, Santiago, Chile. .,UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de Roscoff, Roscoff, France.
| | - Marie J J Huysman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Daniel Mapleson
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Wim Vyverman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium.
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
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32
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Fang M, Pak ML, Chamberlain L, Xing W, Yu H, Green MR. The CREB Coactivator CRTC2 Is a Lymphoma Tumor Suppressor that Preserves Genome Integrity through Transcription of DNA Mismatch Repair Genes. Cell Rep 2015; 11:1350-7. [PMID: 26004186 DOI: 10.1016/j.celrep.2015.04.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/06/2015] [Accepted: 04/23/2015] [Indexed: 12/12/2022] Open
Abstract
The CREB-regulated transcription coactivator CRTC2 stimulates CREB target gene expression and has a well-established role in modulating glucose and lipid metabolism. Here, we find, unexpectedly, that loss of CRTC2, as well as CREB1 and its coactivator CREB-binding protein (CBP), results in a deficiency in DNA mismatch repair (MMR) and a resultant increased mutation frequency. We show that CRTC2, CREB1, and CBP are transcriptional activators of well-established MMR genes, including EXO1, MSH6, PMS1, and POLD2. Mining of expression profiling databases and analysis of patient samples reveal that CRTC2 and its target MMR genes are downregulated in specific T cell lymphoma subtypes, which are microsatellite unstable. The levels of acetylated histone H3 on the CRTC2 promoter are significantly reduced in lymphoma in comparison to normal tissue, explaining the decreased CRTC2 expression. Our results establish a role for CRTC2 as a lymphoma tumor suppressor gene that preserves genome integrity by stimulating transcription of MMR genes.
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Affiliation(s)
- Minggang Fang
- Howard Hughes Medical Institute, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Magnolia L Pak
- Howard Hughes Medical Institute, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lynn Chamberlain
- Howard Hughes Medical Institute, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Wei Xing
- Department of Pathology, UMass Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hongbo Yu
- Department of Pathology, UMass Memorial Medical Center and University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael R Green
- Howard Hughes Medical Institute, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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33
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Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesis. Proc Natl Acad Sci U S A 2015; 112:5667-72. [PMID: 25825764 DOI: 10.1073/pnas.1417711112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) plays essential roles in eukaryotic cells during DNA replication, DNA mismatch repair (MMR), and other events at the replication fork. Earlier studies show that PCNA is regulated by posttranslational modifications, including phosphorylation of tyrosine 211 (Y211) by the epidermal growth factor receptor (EGFR). However, the functional significance of Y211-phosphorylated PCNA remains unknown. Here, we show that PCNA phosphorylation by EGFR alters its interaction with mismatch-recognition proteins MutSα and MutSβ and interferes with PCNA-dependent activation of MutLα endonuclease, thereby inhibiting MMR at the initiation step. Evidence is also provided that Y211-phosphorylated PCNA induces nucleotide misincorporation during DNA synthesis. These findings reveal a novel mechanism by which Y211-phosphorylated PCNA promotes cancer development and progression via facilitating error-prone DNA replication and suppressing the MMR function.
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34
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Shyam K, Penketh PG, Baumann RP, Finch RA, Zhu R, Zhu YL, Sartorelli AC. Antitumor sulfonylhydrazines: design, structure-activity relationships, resistance mechanisms, and strategies for improving therapeutic utility. J Med Chem 2015; 58:3639-71. [PMID: 25612194 DOI: 10.1021/jm501459c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
1,2-Bis(sulfonyl)-1-alkylhydrazines (BSHs) were conceived as more specific DNA guanine O-6 methylating and chloroethylating agents lacking many of the undesirable toxicophores contained in antitumor nitrosoureas. O(6)-Alkylguanine-DNA alkyltransferase (MGMT) is the sole repair protein for O(6)-alkylguanine lesions in DNA and has been reported to be absent in 5-20% of most tumor types. Many BSHs exhibit highly selective cytotoxicity toward cells deficient in MGMT activity. The development of clinically useful MGMT assays should permit the identification of tumors with this vulnerability and allow for the preselection of patient subpopulations with a high probability of responding. The BSH system is highly versatile, permitting the synthesis of many prodrug types with the ability to incorporate an additional level of tumor-targeting due to preferential activation by tumor cells. Furthermore, it may be possible to expand the spectrum of activity of these agents to include tumors with MGMT activity by combining them with tumor-targeted MGMT inhibitors.
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Affiliation(s)
- Krishnamurthy Shyam
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Philip G Penketh
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Raymond P Baumann
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Rick A Finch
- ‡Department of Veterinary Sciences, The University of Texas M.D. Anderson Cancer Center, 650 Cool Water Drive, Bastrop, Texas 78602, United States
| | - Rui Zhu
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Yong-Lian Zhu
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
| | - Alan C Sartorelli
- †Department of Pharmacology and Developmental Therapeutics Program, Cancer Center, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520-8066, United States
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35
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Kanchan S, Mehrotra R, Chowdhury S. Evolutionary pattern of four representative DNA repair proteins across six model organisms: an in silico analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13721-014-0070-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Desai A, Gerson S. Exo1 independent DNA mismatch repair involves multiple compensatory nucleases. DNA Repair (Amst) 2014; 21:55-64. [PMID: 25037770 PMCID: PMC5944346 DOI: 10.1016/j.dnarep.2014.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 05/07/2014] [Accepted: 06/11/2014] [Indexed: 11/18/2022]
Abstract
Functional DNA mismatch repair (MMR) is essential for maintaining the fidelity of DNA replication and genetic stability. In hematopoiesis, loss of MMR results in methylating agent resistance and a hematopoietic stem cell (HSC) repopulation defect. Additionally MMR failure is associated with a variety of human malignancies, notably Lynch syndrome. We focus on the 5'→3' exonuclease Exo1, the primary enzyme excising the nicked strand during MMR, preceding polymerase synthesis. We found that nuclease dead Exo1 mutant cells are sensitive to the O6-methylguanine alkylating agent temozolomide when given with the MGMT inactivator, O6benzylguanine (BG). Additionally we used an MMR reporter plasmid to verify that Exo1(mut) MEFs were able to repair G:T base mismatches in vitro. We showed that unlike other MMR deficient mouse models, Exo1(mut) mouse HSC did not gain a competitive survival advantage post temozolomide/BG treatment in vivo. To determine potential nucleases implicated in MMR in the absence of Exo1 nuclease activity, but in the presence of the inactive protein, we performed gene expression analyses of several mammalian nucleases in WT and Exo1(mut) MEFs before and after temozolomide treatment and identified upregulation of Artemis, Fan1, and Mre11. Partial shRNA mediated silencing of each of these in Exo1(mut) cells resulted in decreased MMR capacity and increased resistance to temozolomide/BG. We propose that nuclease function is required for fully functional MMR, but a portfolio of nucleases is able to compensate for loss of Exo1 nuclease activity to maintain proficiency.
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Affiliation(s)
- Amar Desai
- Department of Pharmacology, University Hospitals Seidman Cancer Center and Case Western Reserve University, United States; Division of Hematology/Oncology, Center of Stem Cell and Regenerative Medicine, University Hospitals Seidman Cancer Center and Case Western Reserve University, United States
| | - Stanton Gerson
- Department of Pharmacology, University Hospitals Seidman Cancer Center and Case Western Reserve University, United States; Division of Hematology/Oncology, Center of Stem Cell and Regenerative Medicine, University Hospitals Seidman Cancer Center and Case Western Reserve University, United States; Case Comprehensive Cancer Center, University Hospitals Seidman Cancer Center and Case Western Reserve University, United States.
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Martín-López JV, Fishel R. The mechanism of mismatch repair and the functional analysis of mismatch repair defects in Lynch syndrome. Fam Cancer 2014; 12:159-68. [PMID: 23572416 DOI: 10.1007/s10689-013-9635-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of Lynch syndrome (LS), also known as hereditary non-polyposis colorectal cancer (HNPCC), has been linked to heterozygous defects in DNA mismatch repair (MMR). MMR is a highly conserved pathway that recognizes and repairs polymerase misincorporation errors and nucleotide damage as well as functioning as a damage sensor that signals apoptosis. Loss-of-heterozygosity (LOH) that retains the mutant MMR allele and epigenetic silencing of MMR genes are associated with an increased mutation rate that drives carcinogenesis as well as microsatellite instability that is a hallmark of LS/HNPCC. Understanding the biophysical functions of the MMR components is crucial to elucidating the role of MMR in human tumorigenesis and determining the pathogenetic consequences of patients that present in the clinic with an uncharacterized variant of the MMR genes. We summarize the historical association between LS/HNPCC and MMR, discuss the mechanism of the MMR and finally examine the functional analysis of MMR defects found in LS/HNPCC patients and their relationship with the severity of the disease.
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Affiliation(s)
- Juana V Martín-López
- Department of Molecular Virology, Immunology and Medical Genetics, Human Cancer Genetics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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Guo Y, Guo Y, Dong C. Ultrasensitive and label-free electrochemical DNA biosensor based on water-soluble electroactive dye azophloxine-functionalized graphene nanosheets. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bailis JM, Gordon ML, Gurgel JL, Komor AC, Barton JK, Kirsch IR. An inducible, isogenic cancer cell line system for targeting the state of mismatch repair deficiency. PLoS One 2013; 8:e78726. [PMID: 24205301 PMCID: PMC3812133 DOI: 10.1371/journal.pone.0078726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
The DNA mismatch repair system (MMR) maintains genome stability through recognition and repair of single-base mismatches and small insertion-deletion loops. Inactivation of the MMR pathway causes microsatellite instability and the accumulation of genomic mutations that can cause or contribute to cancer. In fact, 10-20% of certain solid and hematologic cancers are MMR-deficient. MMR-deficient cancers do not respond to some standard of care chemotherapeutics because of presumed increased tolerance of DNA damage, highlighting the need for novel therapeutic drugs. Toward this goal, we generated isogenic cancer cell lines for direct comparison of MMR-proficient and MMR-deficient cells. We engineered NCI-H23 lung adenocarcinoma cells to contain a doxycycline-inducible shRNA designed to suppress the expression of the mismatch repair gene MLH1, and compared single cell subclones that were uninduced (MLH1-proficient) versus induced for the MLH1 shRNA (MLH1-deficient). Here we present the characterization of these MMR-inducible cell lines and validate a novel class of rhodium metalloinsertor compounds that differentially inhibit the proliferation of MMR-deficient cancer cells.
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Affiliation(s)
- Julie M. Bailis
- Oncology Research, Amgen Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Marcia L. Gordon
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Jesse L. Gurgel
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Alexis C. Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Ilan R. Kirsch
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
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DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Proc Natl Acad Sci U S A 2013; 110:17308-13. [PMID: 24101514 DOI: 10.1073/pnas.1308595110] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA metabolism and processing frequently require transient or metastable DNA conformations that are biologically important but challenging to characterize. We use gold nanocrystal labels combined with small angle X-ray scattering to develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatch repair (MMR) system in solution. We developed a neutral PEG linker that allowed gold-labeled DNAs to be flash-cooled and stored without degradation in sample quality. The 1,000-fold increased gold nanocrystal scattering vs. DNA enabled investigations at much lower concentrations than otherwise possible to avoid concentration-dependent tetramerization of the MMR initiation enzyme MutS. We analyzed the correlation scattering functions for the nanocrystals to provide higher resolution interparticle distributions not convoluted by the intraparticle distribution. We determined that mispair-containing DNAs were bent more by MutS than complementary sequence DNA (csDNA), did not promote tetramer formation, and allowed MutS conversion to a sliding clamp conformation that eliminated the DNA bends. Addition of second protein responder MutL did not stabilize the MutS-bent forms of DNA. Thus, DNA distortion is only involved at the earliest mispair recognition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/MutL complexes as a conserved feature of MMR. The results promote a mechanism of mismatch DNA bending followed by straightening in initial MutS and MutL responses in MMR. We demonstrate that small angle X-ray scattering with gold labels is an enabling method to examine protein-induced DNA distortions key to the DNA repair, replication, transcription, and packaging.
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Ko JC, Chiu HC, Wo TY, Huang YJ, Tseng SC, Huang YC, Chen HJ, Syu JJ, Chen CY, Jian YT, Jian YJ, Lin YW. Inhibition of p38 MAPK-dependent MutS homologue-2 (MSH2) expression by metformin enhances gefitinib-induced cytotoxicity in human squamous lung cancer cells. Lung Cancer 2013; 82:397-406. [PMID: 24138903 DOI: 10.1016/j.lungcan.2013.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/12/2013] [Accepted: 09/18/2013] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Gefitinib, a quinazoline-derived tyrosine kinase inhibitor, has anti-tumor activity in vivo and in vitro. Human MutS homologue-2 (MSH2) plays a central role in promoting genetic stability by correcting DNA replication errors. The present study investigated the effects of p38 mitogen-activated protein kinase (MAPK) signal on gefitinib-induced MSH2 expression in two human non-small cell lung squamous cancer cell lines. MATERIALS AND METHODS After the gefitinib treatment, the expressions of MSH2 mRNA were determined by real-time PCR and RT-PCR analysis. Protein levels of MSH2, phospho-MKK3/6, phospho-p38 MAPK were determined by Western blot analysis. We used specific MSH2, and p38 MAPK small interfering RNA to examine the role of p38 MAPK-MSH2 signal in regulating the chemosensitivity of gefitinib. Cell viability was assessed by MTS assay, trypan blue exclusion, and colony-forming ability assay. RESULTS Exposure of gefitinib increased MSH2 protein and mRNA levels, which was accompanied by MKK3/6-p38 MAPK activation in H520 and H1703 cells. Moreover, blocking p38 MAPK activation by SB202190 significantly decreased gefitinib-induced MSH2 expression by increasing mRNA and protein instability. In contrast, enhancing p38 activation using constitutively active MKK6 (MKK6E) increased MSH2 protein and mRNA levels. Specific inhibition of MSH2 expression by siRNA enhanced gefitinib-induced cytotoxicity. Metformin, an anti-diabetic drug, might reduce cancer risk. In human lung squamous cancer cells, metformin decreased gefitinib-induced MSH2 expression and augmented the cytotoxic effect and growth inhibition by gefitinib. Transient expression of MKK6E or HA-p38 MAPK vector could abrogate metformin and gefitinib-induced synergistic cytotoxic effect in H520 and H1703 cells. CONCLUSION Together, down-regulation of MSH2 expression can be a possible strategy to enhance the sensitivity of gefitinib to human lung squamous cancer cells.
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Affiliation(s)
- Jen-Chung Ko
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Taiwan; Department of Nursing, Yuanpei University, Hsinchu, Taiwan; Institute of Technology Law, National Chiao Tung University, Hsinchu, Taiwan
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Kwok CK, Lam SL. NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:184-9. [PMID: 23892104 DOI: 10.1016/j.jmr.2013.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 05/15/2023]
Abstract
A proton chemical shift prediction scheme for B-DNA duplexes containing a T·T mismatch has been established. The scheme employs a set of T·T mismatch triplet chemical shift values, 5'- and 3'-correction factors extracted from reference sequences, and also the B-DNA chemical shift values predicted by Altona et al. The prediction scheme was tested by eight B-DNA duplexes containing T·T mismatches. Based on 560 sets of predicted and experimental proton chemical shift values, the overall prediction accuracy for non-labile protons was determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996. In addition, the prediction accuracy for 96 sets of labile protons was found to be 0.22 ppm with a correlation coefficient of 0.9961. The prediction scheme developed herein can facilitate resonance assignments of B-DNA duplexes containing T·T mismatches and be generalized for the chemical shift prediction of other DNA mismatches. Our chemical shift data will also be useful for establishing structure-chemical shift information in B-DNA containing mismatches.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Li F, Mao G, Tong D, Huang J, Gu L, Yang W, Li GM. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα. Cell 2013; 153:590-600. [PMID: 23622243 DOI: 10.1016/j.cell.2013.03.025] [Citation(s) in RCA: 432] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 02/13/2013] [Accepted: 03/18/2013] [Indexed: 12/23/2022]
Abstract
DNA mismatch repair (MMR) ensures replication fidelity by correcting mismatches generated during DNA replication. Although human MMR has been reconstituted in vitro, how MMR occurs in vivo is unknown. Here, we show that an epigenetic histone mark, H3K36me3, is required in vivo to recruit the mismatch recognition protein hMutSα (hMSH2-hMSH6) onto chromatin through direct interactions with the hMSH6 PWWP domain. The abundance of H3K36me3 in G1 and early S phases ensures that hMutSα is enriched on chromatin before mispairs are introduced during DNA replication. Cells lacking the H3K36 trimethyltransferase SETD2 display microsatellite instability (MSI) and an elevated spontaneous mutation frequency, characteristic of MMR-deficient cells. This work reveals that a histone mark regulates MMR in human cells and explains the long-standing puzzle of MSI-positive cancer cells that lack detectable mutations in known MMR genes.
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Affiliation(s)
- Feng Li
- Graduate Center for Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA
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Ahmad SS, Glatzle J, Bajaeifer K, Bühler S, Lehmann T, Königsrainer I, Vollmer JP, Sipos B, Ahmad SS, Northoff H, Königsrainer A, Zieker D. Phosphoglycerate kinase 1 as a promoter of metastasis in colon cancer. Int J Oncol 2013; 43:586-90. [PMID: 23727790 DOI: 10.3892/ijo.2013.1971] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/12/2013] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress due to intratumoral hypoxia in solid cancer has been shown to be associated with increased mortality. Phosphoglycerate kinase 1 (PGK1) is an enzyme of the glycolytic pathway, which is regulated by hypoxia-inducible factor-1α (HIF-1α) and has been described for its role in tumor progression and metastasis in several malignancies. We investigated whether the expression of PGK1 varies between metastatic and non-metastatic colon cancer. We compared PGK1 expression in colon cancer patients either with or without metastasis via polymerase chain reaction (PCR) and immunohistochemistry. Microarray analysis was performed to test altered gene expression after PGK1 silencing, using isolates from HCT116 cell lines. PCR results showed an increased expression of PGK1 in colon cancer tissue from metastatic patients in comparison to patients with no metastasis (fold change 2.6, p<0.001). Immunohistochemical staining of PGK1 showed stronger staining in metastatic tissue in comparison to non-metastatic cancer tissue according to a semi-quantitative evaluation. Microarray and subsequent pathway analysis provided 4 genes of interest (CYR61, FOS, JUN and EGR1) used for pathway proposal. The results indicate that increased expression of PGK1 in colon cancer tissue is associated with metastasis. Furthermore, we propose several genes induced by PGK1 that could account for cell migration, mainly EGR1 and CYR61 together with the transcription factors FOS and JUN.
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Affiliation(s)
- Sufian S Ahmad
- Department of General, Visceral and Transplantation Surgery, University of Tübingen, D-72076 Tübingen, Germany
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An MSH4 homolog, stpp1, from Pleurotus pulmonarius is a "silver bullet" for resolving problems caused by spores in cultivated mushrooms. Appl Environ Microbiol 2013; 79:4520-7. [PMID: 23666334 DOI: 10.1128/aem.00561-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enormous number of spores produced by fruiting bodies during cultivation of mushrooms can lead to allergic reactions of workers, reduction of commercial value, spread of mushroom disease, pollution of facilities, and depletion of genetic diversity in natural populations. A cultivar harboring a sporulation-deficient (sporeless) mutation would be very useful for preventing these problems, but sporeless commercial cultivars are very limited in usefulness because sporeless traits are often linked with traits that are unfavorable for commercial cultivation. Thus, identifying a causal gene of a sporeless phenotype not linked to the adverse traits in breeding and cultivation is crucial for the establishment of sporeless breeding using a strategy employing targeting induced local lesions in genomes (TILLING) in cultivated mushrooms. We used a Pleurotus pulmonarius (Fr.) Quél. sporeless strain to identify and characterize the single recessive gene controlling the mutation. The 3,853-bp stpp1 gene encodes a protein of 854 amino acids and belongs to the MutS homolog (MSH) family associated with mismatch repair in DNA synthesis or recombination in meiosis. Gene expression analysis of the fruiting body showed that this gene is strongly expressed in the gills. Phenotypic analysis of disruptants formed by gene targeting suggested a reproducible sporeless phenotype. Mutants deficient in a functional copy of this gene have no unfavorable traits for sporeless cultivar breeding, so this gene will be an extremely useful target for efficient and versatile sporeless breeding in P. pulmonarius and various other cultivated mushrooms.
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Edelbrock MA, Kaliyaperumal S, Williams KJ. Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities. Mutat Res 2013; 743-744:53-66. [PMID: 23391514 DOI: 10.1016/j.mrfmmm.2012.12.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/28/2012] [Accepted: 12/31/2012] [Indexed: 11/18/2022]
Abstract
The field of DNA mismatch repair (MMR) has rapidly expanded after the discovery of the MutHLS repair system in bacteria. By the mid 1990s yeast and human homologues to bacterial MutL and MutS had been identified and their contribution to hereditary non-polyposis colorectal cancer (HNPCC; Lynch syndrome) was under intense investigation. The human MutS homologue 6 protein (hMSH6), was first reported in 1995 as a G:T binding partner (GTBP) of hMSH2, forming the hMutSα mismatch-binding complex. Signal transduction from each DNA-bound hMutSα complex is accomplished by the hMutLα heterodimer (hMLH1 and hPMS2). Molecular mechanisms and cellular regulation of individual MMR proteins are now areas of intensive research. This review will focus on molecular mechanisms associated with mismatch binding, as well as emerging evidence that MutSα, and in particular, MSH6, is a key protein in MMR-dependent DNA damage response and communication with other DNA repair pathways within the cell. MSH6 is unstable in the absence of MSH2, however it is the DNA lesion-binding partner of this heterodimer. MSH6, but not MSH2, has a conserved Phe-X-Glu motif that recognizes and binds several different DNA structural distortions, initiating different cellular responses. hMSH6 also contains the nuclear localization sequences required to shuttle hMutSα into the nucleus. For example, upon binding to O(6)meG:T, MSH6 triggers a DNA damage response that involves altered phosphorylation within the N-terminal disordered domain of this unique protein. While many investigations have focused on MMR as a post-replication DNA repair mechanism, MMR proteins are expressed and active in all phases of the cell cycle. There is much more to be discovered about regulatory cellular roles that require the presence of MutSα and, in particular, MSH6.
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Affiliation(s)
| | - Saravanan Kaliyaperumal
- Division of Comparative Medicine and Pathology, New England Primate Research Center, One Pine Hill Drive, Southborough, MA 01772, USA.
| | - Kandace J Williams
- University of Toledo College of Medicine and Life Sciences, Department of Biochemistry & Cancer Biology, 3000 Transverse Dr., Toledo, OH 43614, USA.
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Shamsi MH, Kraatz HB. Interactions of Metal Ions with DNA and Some Applications. J Inorg Organomet Polym Mater 2012. [DOI: 10.1007/s10904-012-9694-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chisholm KM, Aubert SD, Freese KP, Zakian VA, King MC, Welcsh PL. A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1. PLoS One 2012; 7:e30748. [PMID: 22347400 PMCID: PMC3276492 DOI: 10.1371/journal.pone.0030748] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/23/2011] [Indexed: 11/18/2022] Open
Abstract
Alu-mediated rearrangement of tumor suppressor genes occurs frequently during carcinogenesis. In breast cancer, this mechanism contributes to loss of the wild-type BRCA1 allele in inherited disease and to loss of heterozygosity in sporadic cancer. To identify genes required for suppression of Alu-mediated recombination we performed a genomewide screen of a collection of 4672 yeast gene deletion mutants using a direct repeat recombination assay. The primary screen and subsequent analysis identified 12 candidate genes including TSA, ELG1, and RRM3, which are known to play a significant role in maintaining genomic stability. Genetic analysis of the corresponding human homologs was performed in sporadic breast tumors and in inherited BRCA1-associated carcinomas. Sequencing of these genes in high risk breast cancer families revealed a potential role for the helicase PIF1 in cancer predisposition. PIF1 variant L319P was identified in three breast cancer families; importantly, this variant, which is predicted to be functionally damaging, was not identified in a large series of controls nor has it been reported in either dbSNP or the 1000 Genomes Project. In Schizosaccharomyces pombe, Pfh1 is required to maintain both mitochondrial and nuclear genomic integrity. Functional studies in yeast of human PIF1 L319P revealed that this variant cannot complement the essential functions of Pfh1 in either the nucleus or mitochondria. Our results provide a global view of nonessential genes involved in suppressing Alu-mediated recombination and implicate variation in PIF1 in breast cancer predisposition.
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Affiliation(s)
- Karen M Chisholm
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Hombauer H, Campbell CS, Smith CE, Desai A, Kolodner RD. Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell 2012; 147:1040-53. [PMID: 22118461 DOI: 10.1016/j.cell.2011.10.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/22/2011] [Accepted: 10/07/2011] [Indexed: 11/17/2022]
Abstract
DNA mismatch repair (MMR) increases replication fidelity by eliminating mispaired bases resulting from replication errors. In Saccharomyces cerevisiae, mispairs are primarily detected by the Msh2-Msh6 complex and corrected following recruitment of the Mlh1-Pms1 complex. Here, we visualized functional fluorescent versions of Msh2-Msh6 and Mlh1-Pms1 in living cells. We found that the Msh2-Msh6 complex is an S phase component of replication centers independent of mispaired bases; this localized pool accounted for 10%-15% of MMR in wild-type cells but was essential for MMR in the absence of Exo1. Unexpectedly, Mlh1-Pms1 formed nuclear foci that, although dependent on Msh2-Msh6 for formation, rarely colocalized with Msh2-Msh6 replication-associated foci. Mlh1-Pms1 foci increased when the number of mispaired bases was increased; in contrast, Msh2-Msh6 foci were unaffected. These findings suggest the presence of replication machinery-coupled and -independent pathways for mispair recognition by Msh2-Msh6, which direct formation of superstoichiometric Mlh1-Pms1 foci that represent sites of active MMR.
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Affiliation(s)
- Hans Hombauer
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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Amunugama R, Fishel R. Homologous Recombination in Eukaryotes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:155-206. [DOI: 10.1016/b978-0-12-387665-2.00007-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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