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Martin S, Katainen R, Taira A, Välimäki N, Ristimäki A, Seppälä T, Renkonen-Sinisalo L, Lepistö A, Tahkola K, Mattila A, Koskensalo S, Mecklin JP, Rajamäki K, Palin K, Aaltonen LA. Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours. Hum Mol Genet 2024:ddae124. [PMID: 39180486 DOI: 10.1093/hmg/ddae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
Microsatellite unstable colorectal cancer (MSI-CRC) can arise through germline mutations in mismatch repair (MMR) genes in individuals with Lynch syndrome (LS), or sporadically through promoter methylation of the MMR gene MLH1. Despite the different origins of hereditary and sporadic MSI tumours, their genomic features have not been extensively compared. A prominent feature of MMR-deficient genomes is the occurrence of many indels in short repeat sequences, an understudied mutation type due to the technical challenges of variant calling in these regions. In this study, we performed whole genome sequencing and RNA-sequencing on 29 sporadic and 14 hereditary MSI-CRCs. We compared the tumour groups by analysing genome-wide mutation densities, microsatellite repeat indels, recurrent protein-coding variants, signatures of single base, doublet base, and indel mutations, and changes in gene expression. We show that the mutational landscapes of hereditary and sporadic MSI-CRCs, including mutational signatures and mutation densities genome-wide and in microsatellites, are highly similar. Only a low number of differentially expressed genes were found, enriched to interferon-γ regulated immune response pathways. Analysis of the variance in allelic fractions of somatic variants in each tumour group revealed higher clonal heterogeneity in sporadic MSI-CRCs. Our results suggest that the differing molecular origins of MMR deficiency in hereditary and sporadic MSI-CRCs do not result in substantial differences in the mutational landscapes of these tumours. The divergent patterns of clonal evolution between the tumour groups may have clinical implications, as high clonal heterogeneity has been associated with decreased tumour immunosurveillance and reduced responsiveness to immunotherapy.
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Affiliation(s)
- Samantha Martin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Riku Katainen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Aurora Taira
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Niko Välimäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, 00290 Helsinki, Finland
| | - Toni Seppälä
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital and TAYS Cancer Centre, Kuntokatu 2, 33520 Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, 33100 Tampere, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Anna Lepistö
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Central Hospital, Hospital District of Helsinki and Uusimaa, Haartmaninkatu 4, 00290 Helsinki, Finland
| | - Kyösti Tahkola
- Faculty of Medicine and Health Technology, Tampere University, Kalevantie 4, 33100 Tampere, Finland
- Department of Surgery, Central Finland Health Care District, Keskussairaalantie 19, 40620 Jyväskylä, Finland
| | - Anne Mattila
- Department of Surgery, Central Finland Health Care District, Keskussairaalantie 19, 40620 Jyväskylä, Finland
| | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, Helsinki University Central Hospital, Stenbäckinkatu 9A, 00029 Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Research, The Wellbeing Services of Central Finland, Hoitajatie 1, 40620 Jyväskylä, Finland
- Department of Sport and Health Sciences, University of Jyväskylä, Seminaarinkatu 15, 40014 Jyväskylä, Finland
| | - Kristiina Rajamäki
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Kimmo Palin
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Medicum/Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
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2
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Liu CC, Capart MMM, Lin JJ. Mismatch repair enzymes regulate telomere recombination in Saccharomycescerevisiae. Biochem Biophys Res Commun 2024; 707:149768. [PMID: 38489874 DOI: 10.1016/j.bbrc.2024.149768] [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: 02/20/2024] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
DNA mismatch repair (MMR) is a crucial mechanism that ensures chromosome stability and prevents the development of various human cancers. Apart from its role in correcting mismatches during DNA replication, MMR also plays a significant role in regulating recombination between non-identical sequences, a process known as homeologous recombination. Telomeres, the protective ends of eukaryotic chromosomes, possess sequences that are not perfectly homologous. While telomerase primarily maintains telomere length in the yeast Saccharomyces cerevisiae, recombination between telomeres becomes a major pathway for length maintenance in cells lacking telomerase. This study investigates the participation of MMR in telomere recombination. Our findings reveal that mutations in MMR genes activate type I recombination. Notably, among the MMR proteins, MutSα (Msh2 and Msh6) and MutLα (Mlh1 and Pms1) exerted the most pronounced effects on telomere recombination. We also found that yeast cells containing simple human telomeric TTAGGG DNA sequences preferentially utilize type II recombination to maintain their telomeres, highlighting the influence of the heterogeneous nature of yeast telomeric sequences on type II recombination. Furthermore, our observations indicate that MMR activity is indispensable for its impact on telomere recombination. Collectively, these results contribute to a more comprehensive understanding of the role of MMR in telomere recombination.
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Affiliation(s)
- Chia-Chun Liu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mathilde M M Capart
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan.
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3
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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4
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Dash S, Joshi S, Pankajam AV, Shinohara A, Nishant KT. Heterozygosity alters Msh5 binding to meiotic chromosomes in the baker's yeast. Genetics 2024; 226:iyad214. [PMID: 38124392 DOI: 10.1093/genetics/iyad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Meiotic crossovers are initiated from programmed DNA double-strand breaks. The Msh4-Msh5 heterodimer is an evolutionarily conserved mismatch repair-related protein complex that promotes meiotic crossovers by stabilizing strand invasion intermediates and joint molecule structures such as Holliday junctions. In vivo studies using homozygous strains of the baker's yeast Saccharomyces cerevisiae (SK1) show that the Msh4-Msh5 complex associates with double-strand break hotspots, chromosome axes, and centromeres. Many organisms have heterozygous genomes that can affect the stability of strand invasion intermediates through heteroduplex rejection of mismatch-containing sequences. To examine Msh4-Msh5 function in a heterozygous context, we performed chromatin immunoprecipitation and sequencing (ChIP-seq) analysis in a rapidly sporulating hybrid S. cerevisiae strain (S288c-sp/YJM789, containing sporulation-enhancing QTLs from SK1), using SNP information to distinguish reads from homologous chromosomes. Overall, Msh5 localization in this hybrid strain was similar to that determined in the homozygous strain (SK1). However, relative Msh5 levels were reduced in regions of high heterozygosity, suggesting that high mismatch densities reduce levels of recombination intermediates to which Msh4-Msh5 binds. Msh5 peaks were also wider in the hybrid background compared to the homozygous strain (SK1). We determined regions containing heteroduplex DNA by detecting chimeric sequence reads with SNPs from both parents. Msh5-bound double-strand break hotspots overlap with regions that have chimeric DNA, consistent with Msh5 binding to heteroduplex-containing recombination intermediates.
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Affiliation(s)
- Suman Dash
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Sameer Joshi
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Ajith V Pankajam
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
- Center for High-Performance Computing, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
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5
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Denu RA, Dann AM, Keung EZ, Nakazawa MS, Nassif Haddad EF. The Future of Targeted Therapy for Leiomyosarcoma. Cancers (Basel) 2024; 16:938. [PMID: 38473300 PMCID: PMC10930698 DOI: 10.3390/cancers16050938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Leiomyosarcoma (LMS) is an aggressive subtype of soft tissue sarcoma that arises from smooth muscle cells, most commonly in the uterus and retroperitoneum. LMS is a heterogeneous disease with diverse clinical and molecular characteristics that have yet to be fully understood. Molecular profiling has uncovered possible targets amenable to treatment, though this has yet to translate into approved targeted therapies in LMS. This review will explore historic and recent findings from molecular profiling, highlight promising avenues of current investigation, and suggest possible future strategies to move toward the goal of molecularly matched treatment of LMS. We focus on targeting the DNA damage response, the macrophage-rich micro-environment, the PI3K/mTOR pathway, epigenetic regulators, and telomere biology.
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Affiliation(s)
- Ryan A. Denu
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Amanda M. Dann
- Division of Surgical Oncology, Department of Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Emily Z. Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Michael S. Nakazawa
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elise F. Nassif Haddad
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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6
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Kim-Yip RP, McNulty R, Joyce B, Mollica A, Chen PJ, Ravisankar P, Law BK, Liu DR, Toettcher JE, Ivakine EA, Posfai E, Adamson B. Efficient prime editing in two-cell mouse embryos using PEmbryo. Nat Biotechnol 2024:10.1038/s41587-023-02106-x. [PMID: 38321114 DOI: 10.1038/s41587-023-02106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
Using transient inhibition of DNA mismatch repair during a permissive stage of development, we demonstrate highly efficient prime editing of mouse embryos with few unwanted, local byproducts (average 58% precise edit frequency, 0.5% on-target error frequency across 13 substitution edits at 8 sites), enabling same-generation phenotyping of founders. Whole-genome sequencing reveals that mismatch repair inhibition increases off-target indels at low-complexity regions in the genome without any obvious phenotype in mice.
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Affiliation(s)
- Rebecca P Kim-Yip
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ryan McNulty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Bradley Joyce
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Antonio Mollica
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Prime Medicine, Inc., Cambridge, MA, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Benjamin K Law
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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7
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Marple T, Son MY, Cheng X, Ko JH, Sung P, Hasty P. TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis. Cell Rep 2024; 43:113637. [PMID: 38175749 PMCID: PMC10883656 DOI: 10.1016/j.celrep.2023.113637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/15/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
TREX2, a 3'-5' exonuclease, is a part of the DNA damage tolerance (DDT) pathway that stabilizes replication forks (RFs) by ubiquitinating PCNA along with the ubiquitin E3 ligase RAD18 and other DDT factors. Mismatch repair (MMR) corrects DNA polymerase errors, including base mismatches and slippage. Here we demonstrate that TREX2 deletion reduces mutations in cells upon exposure to genotoxins, including those that cause base lesions and DNA polymerase slippage. Importantly, we show that TREX2 generates most of the spontaneous mutations in MMR-mutant cells derived from mice and people. TREX2-induced mutagenesis is dependent on the nuclease and DNA-binding attributes of TREX2. RAD18 deletion also reduces spontaneous mutations in MMR-mutant cells, albeit to a lesser degree. Inactivation of both MMR and TREX2 additively increases RF stalls, while it decreases DNA breaks, consistent with a synthetic phenotype.
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Affiliation(s)
- Teresa Marple
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mi Young Son
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Xiaodong Cheng
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Jun Ho Ko
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Hasty
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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8
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Chen J, Potlapalli R, Quan H, Chen L, Xie Y, Pouriyeh S, Sakib N, Liu L, Xie Y. Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights. BIOTECH 2024; 13:3. [PMID: 38247733 PMCID: PMC10801582 DOI: 10.3390/biotech13010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/21/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair.
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Affiliation(s)
- Jiawei Chen
- College of Letter and Science, University of California, Berkeley, CA 94720, USA;
| | - Ravi Potlapalli
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Heng Quan
- Department of Civil and Urban Engineering, New York University, New York, NY 11201, USA;
| | - Lingtao Chen
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Ying Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Seyedamin Pouriyeh
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Nazmus Sakib
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA;
| | - Yixin Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
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9
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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. eLife 2023; 12:RP86721. [PMID: 37769127 PMCID: PMC10538959 DOI: 10.7554/elife.86721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Isabel E Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
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10
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Han B, He J, Chen Q, Yuan M, Zeng X, Li Y, Zeng Y, He M, Feng D, Ma D. Identifying the role of NUDCD1 in human tumors from clinical and molecular mechanisms: a study based on comprehensive bioinformatics and experimental validation. Aging (Albany NY) 2023; 15:5611-5649. [PMID: 37338527 PMCID: PMC10333089 DOI: 10.18632/aging.204813] [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: 04/21/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
NUDCD1 (NudC domain-containing 1) is abnormally activated in multiple tumors and has been identified as a cancer antigen. But there is still no pan-cancer analysis available for NUDCD1 in human cancers. The role of NUDCD1 across multiple tumors was explored using data from the public databases including HPA, TCGA, GEO, GTEx, TIMER2, TISIDB, UALCAN, GEPIA2, cBioPortal, GSCA and so on. Molecular experiments (e.g., quantitative real-time PCR, immunohistochemistry and western blot) were conducted to validate the expression and biological function of NUDCD1 in STAD. Results showed that NUDCD1 was highly expressed in most tumors and its levels were associated with the prognosis. Multiple genetic and epigenetic features of NUDCD1 exist in different cancers. NUDCD1 was associated with expression levels of recognized immune checkpoints (anti-CTLA-4) and immune infiltrates (e.g., CD4+ and CD8+ T cells) in some cancers. Moreover, NUDCD1 correlated with the CTRP and GDSC drug sensitivity and acted as a link between chemicals and cancers. Importantly, NUDCD1-related genes were enriched in several tumors (e.g., COAD, STAD and ESCA) and affected apoptosis, cell cycle and DNA damage cancer-related pathways. Furthermore, expression, mutation and copy number variations for the gene sets were also associated with prognosis. At last, the overexpression and contribution of NUDCD1 in STAD were experimentally validated in vitro and in vivo. NUDCD1 was involved in diverse biological processes and it influenced the occurrence and development of cancers. This first pan-cancer analysis for NUDCD1 provides a comprehensive understanding about its roles across various cancer types, especially in STAD.
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Affiliation(s)
- Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Jinsong He
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Qing Chen
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Min Yuan
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Xi Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yuanting Li
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yan Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Meibo He
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Dan Feng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Daiyuan Ma
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
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11
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Li X, Xue X, Jia J, Zou X, Guan Y, Zhu L, Wang Z. Nonsteroidal anti-inflammatory drug diclofenac accelerates the emergence of antibiotic resistance via mutagenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121457. [PMID: 36958653 DOI: 10.1016/j.envpol.2023.121457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Overuse of antimicrobial agents are generally considered to be a key factor in the occurrence of antibiotic resistance bacteria (ARB). Nevertheless, it is unclear whether ARB can be induced by non-antibiotic chemicals such as nonsteroidal anti-inflammatory drug (NSAID). Thus, the objective of this study is to investigate whether NSAID diclofenac (DCF) promote the emergence of antibiotic resistance in Escherichia coli K12 MG1655. Our results suggested that DCF induced the occurrence of ARB which showed hereditary stability of resistance. Meanwhile, gene variation was identified on chromosome of the ARB, and DCF can cause bacterial oxidative stress and SOS response. Subsequently, transcriptional levels of antioxidant (soxS, sodA, sodC, gor, katG, ahpF) and SOS (recA, lexA, uvrA, uvrB, ruvA, ruvB, dinB, umuC, polB) system-related genes were enhanced. However, the expression of related genes cannot be increased in high-dosage treatment compared with low-dosage samples because of cytotoxicity and cellular damage. Simultaneously, high-dosage DCF decreased the mutation frequency but enhanced the resistance of mutants. Our findings expand our knowledge of the promoting effect on the emergence of ARB caused by DCF. More attention and regulations should be given to these potential ecological and health risks for widespread DCF.
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Affiliation(s)
- Xiangju Li
- Department of Aquaculture, College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, Yangling, Shaanxi, 712100, China
| | - Xue Xue
- Department of Aquaculture, College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, Yangling, Shaanxi, 712100, China
| | - Jia Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaocui Zou
- Department of Aquaculture, College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Zhu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, China
| | - Zaizhao Wang
- Department of Aquaculture, College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, Yangling, Shaanxi, 712100, China.
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12
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Thomason LC, Costantino N, Li X, Court DL. Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination. Curr Protoc 2023; 3:e656. [PMID: 36779782 PMCID: PMC10037674 DOI: 10.1002/cpz1.656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double-stranded DNA (dsDNA) or single-stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: Making electrocompetent cells and transforming with linear DNA Support Protocol 1: Selection/counter-selections for genome engineering Support Protocol 2: Creating and screening for oligo recombinants by PCR Support Protocol 3: Other methods of screening for unselected recombinants Support Protocol 4: Curing recombineering plasmids containing a temperature-sensitive replication function Support Protocol 5: Removal of the prophage by recombineering Alternate Protocol 1: Using CRISPR/Cas9 as a counter-selection following recombineering Alternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmids Alternate Protocol 3: Retrieval of alleles onto a plasmid by gap repair Alternate Protocol 4: Modifying multicopy plasmids with recombineering Support Protocol 6: Screening for unselected plasmid recombinants Alternate Protocol 5: Recombineering with an intact λ prophage Alternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains.
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Affiliation(s)
- Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- formerly with Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Armata Pharmaceuticals, 4503 Glencoe Avenue, Marina del Rey, CA 90292
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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13
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Bruekner SR, Pieters W, Fish A, Liaci AM, Scheffers S, Rayner E, Kaldenbach D, Drost L, Dekker M, van Hees-Stuivenberg S, Delzenne-Goette E, de Konink C, Houlleberghs H, Dubbink H, AlSaegh A, de Wind N, Förster F, te Riele H, Sixma T. Unexpected moves: a conformational change in MutSα enables high-affinity DNA mismatch binding. Nucleic Acids Res 2023; 51:1173-1188. [PMID: 36715327 PMCID: PMC9943660 DOI: 10.1093/nar/gkad015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
The DNA mismatch repair protein MutSα recognizes wrongly incorporated DNA bases and initiates their correction during DNA replication. Dysfunctions in mismatch repair lead to a predisposition to cancer. Here, we study the homozygous mutation V63E in MSH2 that was found in the germline of a patient with suspected constitutional mismatch repair deficiency syndrome who developed colorectal cancer before the age of 30. Characterization of the mutant in mouse models, as well as slippage and repair assays, shows a mildly pathogenic phenotype. Using cryogenic electron microscopy and surface plasmon resonance, we explored the mechanistic effect of this mutation on MutSα function. We discovered that V63E disrupts a previously unappreciated interface between the mismatch binding domains (MBDs) of MSH2 and MSH6 and leads to reduced DNA binding. Our research identifies this interface as a 'safety lock' that ensures high-affinity DNA binding to increase replication fidelity. Our mechanistic model explains the hypomorphic phenotype of the V63E patient mutation and other variants in the MBD interface.
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Affiliation(s)
| | | | - Alexander Fish
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, 1066 CX Amsterdam, The Netherlands
| | - A Manuel Liaci
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Serge Scheffers
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, 1066 CX Amsterdam, The Netherlands
| | - Emily Rayner
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600 2300RC Leiden, The Netherlands
| | - Daphne Kaldenbach
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Lisa Drost
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Marleen Dekker
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | | | - Elly Delzenne-Goette
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Charlotte de Konink
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Hellen Houlleberghs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Hendrikus Jan Dubbink
- Department of Pathology, Erasmus Medical Center, PO Box 2040 3000CA Rotterdam, The Netherlands
| | - Abeer AlSaegh
- Sultan Qaboos Comprehensive Cancer Care and Research Center, PO Box 787, 117 Muscat, Oman
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600 2300RC Leiden, The Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Hein te Riele
- Correspondence may also be addressed to Hein te Riele. Tel: +31 20 512 2084;
| | - Titia K Sixma
- To whom correspondence should be addressed: Tel: +31 20 512 1959;
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14
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Zheng WJ, Li WQ, Peng Y, Shao Y, Tang L, Liu CT, Zhang D, Zhang LJ, Li JH, Luo WZ, Yuan ZC, Zhao BR, Mao BG. E2Fs co-participate in cadmium stress response through activation of MSHs during the cell cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:1068769. [PMID: 36531377 PMCID: PMC9749859 DOI: 10.3389/fpls.2022.1068769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Cadmium is one of the most common heavy metal contaminants found in agricultural fields. MutSα, MutSβ, and MutSγ are three different MutS-associated protein heterodimer complexes consisting of MSH2/MSH6, MSH2/MSH3, and MSH2/MSH7, respectively. These complexes have different mismatch recognition properties and abilities to support MMR. However, changes in mismatch repair genes (OsMSH2, OsMSH3, OsMSH6, and OsMSH7) of the MutS system in rice, one of the most important food crops, under cadmium stress and their association with E2Fs, the key transcription factors affecting cell cycles, are poorly evaluated. In this study, we systematically categorized six rice E2Fs and confirmed that OsMSHs were the downstream target genes of E2F using dual-luciferase reporter assays. In addition, we constructed four msh mutant rice varieties (msh2, msh3, msh6, and msh7) using the CRISPR-Cas9 technology, exposed these mutant rice seedlings to different concentrations of cadmium (0, 2, and 4 mg/L) and observed changes in their phenotype and transcriptomic profiles using RNA-Seq and qRT-PCR. We found that the difference in plant height before and after cadmium stress was more significant in mutant rice seedlings than in wild-type rice seedlings. Transcriptomic profiling and qRT-PCR quantification showed that cadmium stress specifically mobilized cell cycle-related genes ATR, CDKB2;1, MAD2, CycD5;2, CDKA;1, and OsRBR1. Furthermore, we expressed OsE2Fs in yeasts and found that heterologous E2F expression in yeast strains regulated cadmium tolerance by regulating MSHs expression. Further exploration of the underlying mechanisms revealed that cadmium stress may activate the CDKA/CYCD complex, which phosphorylates RBR proteins to release E2F, to regulate downstream MSHs expression and subsequent DNA damage repairment, thereby enhancing the response to cadmium stress.
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Affiliation(s)
- Wen-Jie Zheng
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Wang-Qing Li
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Yan Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Ci-Tao Liu
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Dan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Lan-Jing Zhang
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Ji-Huan Li
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Wu-Zhong Luo
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Zhi-Cheng Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Bing-Ran Zhao
- Longping Branch, College of Biology, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Bi-Gang Mao
- Longping Branch, College of Biology, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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15
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G-Quadruplex Formed by the Promoter Region of the hTERT Gene: Structure-Driven Effects on DNA Mismatch Repair Functions. Biomedicines 2022; 10:biomedicines10081871. [PMID: 36009419 PMCID: PMC9405553 DOI: 10.3390/biomedicines10081871] [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: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
G-quadruplexes (G4s) are a unique class of noncanonical DNAs that play a key role in cellular processes and neoplastic transformation. Herein, we focused on the promoter region of human TERT oncogene, whose product is responsible for the immortality of cancer cells. It has been shown by chemical probing and spectroscopic methods that synthetic 96-nt DNAs modeling the wild-type G-rich strand of the hTERT promoter and its variants with G>A point substitutions corresponding to somatic driver mutations fold into three stacked parallel G4s with sites of local G4 destabilization caused by G>A substitutions in the G4 motif. These models were used to elucidate how the hTERT multiG4 affects the binding affinity and functional responses of two key proteins, MutS and MutL, involved in the initial stage of DNA mismatch repair (MMR) in Escherichiacoli and Neisseriagonorrhoeae with different MMR mechanisms. We have shown for the first time that (i) point substitutions do not affect the effective binding of these proteins to the hTERT G4 structure, and (ii) the endonuclease activity of MutL from N. gonorrhoeae is significantly suppressed by the stable G4 scaffold. It is likely that some of the genomic instability associated with G4 may be related to the blockage of human intrinsic methyl-independent MMR attempting to operate near G4 structures.
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16
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Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
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Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
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17
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Monakhova MV, Kubareva EA, Kolesnikov KK, Anashkin VA, Kosaretskiy EM, Zvereva MI, Romanova EA, Friedhoff P, Oretskaya TS, Zatsepin TS. Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model. Molecules 2022; 27:molecules27082438. [PMID: 35458636 PMCID: PMC9031232 DOI: 10.3390/molecules27082438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Covalent protein capture (cross-linking) by reactive DNA derivatives makes it possible to investigate structural features by fixing complexes at different stages of DNA–protein recognition. The most common cross-linking methods are based on reactive groups that interact with native or engineered cysteine residues. Nonetheless, high reactivity of most of such groups leads to preferential fixation of early-stage complexes or even non-selective cross-linking. We synthesised a set of DNA reagents carrying an acrylamide group attached to the C5 atom of a 2′-deoxyuridine moiety via various linkers and studied cross-linking with MutS as a model protein. MutS scans DNA for mismatches and damaged nucleobases and can form multiple non-specific complexes with DNA that may cause non-selective cross-linking. By varying the length of the linker between DNA and the acrylamide group and by changing the distance between the reactive nucleotide and a mismatch in the duplex, we showed that cross-linking occurs only if the distance between the acrylamide group and cysteine is optimal within the DNA–protein complex. Thus, acrylamide-modified DNA duplexes are excellent tools for studying DNA–protein interactions because of high selectivity of cysteine trapping.
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Affiliation(s)
- Mayya V. Monakhova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
- Correspondence: ; Tel.: +7-(903)-593-8905
| | - Elena A. Kubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Kirill K. Kolesnikov
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Viktor A. Anashkin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Egor M. Kosaretskiy
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia;
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
| | - Elena A. Romanova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany;
| | - Tatiana S. Oretskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (E.A.K.); (V.A.A.); (E.A.R.); (T.S.O.)
| | - Timofei S. Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, 119991 Moscow, Russia; (K.K.K.); (M.I.Z.); (T.S.Z.)
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18
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BK Polyomavirus Requires the Mismatch Repair Pathway for DNA Damage Response Activation. J Virol 2022; 96:e0202821. [PMID: 35389233 DOI: 10.1128/jvi.02028-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BK polyomavirus (PyV) infects the genitourinary tract of >90% of the adult population. Immunosuppression increases the risk of viral reactivation, making BKPyV a leading cause of graft failure in kidney transplant recipients. Polyomaviruses have a small double-stranded DNA (dsDNA) genome that requires host replication machinery to amplify the viral genome. Specifically, polyomaviruses promote S phase entry and delay S phase exit by activating the DNA damage response (DDR) pathway via an uncharacterized mechanism requiring viral replication. BKPyV infection elevates expression of MutSα, a mismatch repair (MMR) pathway protein complex that senses and repairs DNA mismatches and can activate the DDR. Thus, we investigated the role of the MMR pathway by silencing the MutSα component, Msh6, in BKPyV-infected primary cells. This resulted in severe DNA damage that correlated with weak DNA damage response activation and a failure to arrest the cell cycle to prevent mitotic entry during infection. Furthermore, silencing Msh6 expression resulted in significantly fewer infectious viral particles due to significantly lower levels of VP2, a minor capsid protein important for trafficking during subsequent infections. Since viral assembly occurs in the nucleus, our findings are consistent with a model in which entry into mitosis disrupts viral assembly due to nuclear envelope breakdown, which disperses VP2 throughout the cell, reducing its availability for encapsidation into viral particles. Thus, the MMR pathway may be required to activate the ATR (ATM-Rad3-related) pathway during infection to maintain a favorable environment for both viral replication and assembly. IMPORTANCE Since there are no therapeutics that target BKPyV reactivation in organ transplant patients, it is currently treated by decreasing immunosuppression to allow the natural immune system to fight the viral infection. Antivirals would significantly improve patient outcomes since reducing immunosuppression carries the risk of graft failure. PyVs activate the DDR, for which there are several promising inhibitors. However, a better understanding of how PyVs activate the DDR and what role the DDR plays during infection is needed. Here, we show that a component of the mismatch repair pathway is required for DDR activation during PyV infection. These findings show that the mismatch repair pathway is important for DDR activation during PyV infection and that inhibiting the DDR reduces viral titers by generating less infectious virions that lack the minor capsid protein VP2, which is important for viral trafficking.
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19
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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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20
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CNOT6: A Novel Regulator of DNA Mismatch Repair. Cells 2022; 11:cells11030521. [PMID: 35159331 PMCID: PMC8833972 DOI: 10.3390/cells11030521] [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: 12/28/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mismatch repair (MMR) is a highly conserved pathway that corrects both base–base mispairs and insertion-deletion loops (IDLs) generated during DNA replication. Defects in MMR have been linked to carcinogenesis and drug resistance. However, the regulation of MMR is poorly understood. Interestingly, CNOT6 is one of four deadenylase subunits in the conserved CCR4-NOT complex and it targets poly(A) tails of mRNAs for degradation. CNOT6 is overexpressed in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and androgen-independent prostate cancer cells, which suggests that an altered expression of CNOT6 may play a role in tumorigenesis. Here, we report that a depletion of CNOT6 sensitizes human U2OS cells to N-methyl-N′nitro-N-nitrosoguanidine (MNNG) and leads to enhanced apoptosis. We also demonstrate that the depletion of CNOT6 upregulates MMR and decreases the mutation frequency in MMR-proficient cells. Furthermore, the depletion of CNOT6 increases the stability of mRNA transcripts from MMR genes, leading to the increased expression of MMR proteins. Our work provides insight into a novel CNOT6-dependent mechanism for regulating MMR.
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On YY, Welch M. The methylation-independent mismatch repair machinery in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34882086 PMCID: PMC8744996 DOI: 10.1099/mic.0.001120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last 70 years, we've all gotten used to an Escherichia coli-centric view of the microbial world. However, genomics, as well as the development of improved tools for genetic manipulation in other species, is showing us that other bugs do things differently, and that we cannot simply extrapolate from E. coli to everything else. A particularly good example of this is encountered when considering the mechanism(s) involved in DNA mismatch repair by the opportunistic human pathogen, Pseudomonas aeruginosa (PA). This is a particularly relevant phenotype to examine in PA, since defects in the mismatch repair (MMR) machinery often give rise to the property of hypermutability. This, in turn, is linked with the vertical acquisition of important pathoadaptive traits in the organism, such as antimicrobial resistance. But it turns out that PA lacks some key genes associated with MMR in E. coli, and a closer inspection of what is known (or can be inferred) about the MMR enzymology reveals profound differences compared with other, well-characterized organisms. Here, we review these differences and comment on their biological implications.
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Affiliation(s)
- Yue Yuan On
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Downing Site, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Martin Welch
- Department of Biochemistry, Hopkins Building, Tennis Court Road, Downing Site, University of Cambridge, Cambridge, CB2 1QW, UK
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22
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Phillips MA, Steenwyk JL, Shen XX, Rokas A. Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. Genome Biol Evol 2021; 13:evab219. [PMID: 34554246 PMCID: PMC8597960 DOI: 10.1093/gbe/evab219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The DNA mismatch repair (MMR) pathway corrects mismatched bases produced during DNA replication and is highly conserved across the tree of life, reflecting its fundamental importance for genome integrity. Loss of function in one or a few MMR genes can lead to increased mutation rates and microsatellite instability, as seen in some human cancers. Although loss of MMR genes has been documented in the context of human disease and in hypermutant strains of pathogens, examples of entire species and species lineages that have experienced substantial MMR gene loss are lacking. We examined the genomes of 1,107 species in the fungal phylum Ascomycota for the presence of 52 genes known to be involved in the MMR pathway of fungi. We found that the median ascomycete genome contained 49/52 MMR genes. In contrast, four closely related species of obligate plant parasites from the powdery mildew genera Erysiphe and Blumeria, have lost between five and 21 MMR genes, including MLH3, EXO1, and DPB11. The lost genes span MMR functions, include genes that are conserved in all other ascomycetes, and loss of function of any of these genes alone has been previously linked to increased mutation rate. Consistent with the hypothesis that loss of these genes impairs MMR pathway function, we found that powdery mildew genomes with higher levels of MMR gene loss exhibit increased numbers of mononucleotide runs, longer microsatellites, accelerated sequence evolution, elevated mutational bias in the A|T direction, and decreased GC content. These results identify a striking example of macroevolutionary loss of multiple MMR pathway genes in a eukaryotic lineage, even though the mutational outcomes of these losses appear to resemble those associated with detrimental MMR dysfunction in other organisms.
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Affiliation(s)
| | | | - Xing-Xing Shen
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, USA
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23
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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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24
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Control of Genome Stability by EndoMS/NucS-Mediated Non-Canonical Mismatch Repair. Cells 2021; 10:cells10061314. [PMID: 34070467 PMCID: PMC8228993 DOI: 10.3390/cells10061314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
The DNA repair endonuclease EndoMS/NucS is highly conserved in Archaea and Actinobacteria. This enzyme is able to recognize and cleave dsDNA carrying a mismatched base pair, and its activity is enhanced by the interaction with the sliding clamp of the replisome. Today, EndoMS/NucS has been established as the key protein of a non-canonical mismatch repair (MMR) pathway, acting specifically in the repair of transitions and being essential for maintaining genome stability. Despite having some particularities, such as its lower activity on transversions and the inability to correct indels, EndoMS/NucS meets the main hallmarks of a MMR. Its absence leads to a hypermutator phenotype, a transition-biased mutational spectrum and an increase in homeologous recombination. Interestingly, polymorphic EndoMS/NucS variants with a possible effect in mutation rate have been detected in clinical isolates of the relevant actinobacterial pathogen Mycobacterium tuberculosis. Considering that MMR defects are often associated with the emergence of resistant bacteria, the existence of EndoMS/NucS-defective mutators could have an important role in the acquisition of antibiotic resistance in M. tuberculosis. Therefore, a further understanding of the EndoMS/NucS-mediated non-canonical MMR pathway may reveal new strategies to predict and fight drug resistance. This review is focused on the recent progress in NucS, with special emphasis on its effect on genome stability and evolvability in Actinobacteria.
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25
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Yuan Y, Xiao WW, Xie WH, Li RZ, Gao YH. Prognostic value of ubiquitin E2 UBE2W and its correlation with tumor-infiltrating immune cells in breast cancer. BMC Cancer 2021; 21:479. [PMID: 33931024 PMCID: PMC8086329 DOI: 10.1186/s12885-021-08234-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ubiquitin-conjugating enzyme E2W (UBE2W) is a protein-coding gene that has an important role in ubiquitination and may be vital in the repair of DNA damage. However, studies on the prognostic value of UBE2W and its correlation with tumor-infiltrating immune cells in multiple cancers have not been addressed. Methods We investigated UBE2W expression in the Oncomine database, the Tumor Immune Estimation Resource (TIMER), TNMplot database. Then, the clinical prognostic value of UBE2W was analyzed via online public databases. Meanwhile, we explored the correlation between UBE2W and DNA repair associate genes expression and DNA methyltransferase expression by TIMER and Gene Expression Profiling Interactive Analysis (GEPIA). By using the same method, the correlation between UBE2W and tumor-infiltrating immune cells was explored. Genomic Profiles of UBE2W in breast cancer (BRCA) were accessed in cBioPortal (v3.5.0). Functional proteins associated network was analyzed by STRING database (v11.0). Results UBE2W was abnormally expressed and significantly correlated with mismatch repair (MMR) gene mutation levels, DNA methyltransferase, and BRCA1/2 expression in breast cancer. High expression of UBE2W may promote the tumor immunosuppression and metastasis, induce endocrine therapy resistance and deteriorate outcomes of patients with breast cancer. These findings suggest that UBE2W could be a potential biomarker of prognosis and tumor-infiltrating immune cells. Besides, RBX1 may be a new E3 that was regulated by UBE2W. Conclusions Ubiquitin E2 UBE2W is a potential prognostic biomarker and is correlated with immune infiltration in BRCA. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08234-4.
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Affiliation(s)
- Yan Yuan
- State Key laboratory of Oncology in South China, Collaborative innovation Center for cancer Medicine, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei-Wei Xiao
- State Key laboratory of Oncology in South China, Collaborative innovation Center for cancer Medicine, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei-Hao Xie
- State Key laboratory of Oncology in South China, Collaborative innovation Center for cancer Medicine, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Rong-Zhen Li
- State Key laboratory of Oncology in South China, Collaborative innovation Center for cancer Medicine, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yuan-Hong Gao
- State Key laboratory of Oncology in South China, Collaborative innovation Center for cancer Medicine, Guangzhou, P. R. China. .,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
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26
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V K, Chandrashekar BK, K K, Ag S, Makarla U, Ramu VS. Disruption in the DNA Mismatch Repair Gene MSH2 by CRISPR- Cas9 in Indica Rice Can Create Genetic Variability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4144-4152. [PMID: 33789420 DOI: 10.1021/acs.jafc.1c00328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genetic variation is crucial for crop improvement. We adopted a gene editing approach to create variations in the rice genome by targeting the mutator locus homolog 2 (MSH2), a DNA mismatch repair gene. The hypothesis is that disruption of the MSH2 gene leads to a reduced DNA mismatch repair that creates INDELs, resulting in altered phenotypes. The Indica rice (IR-64) genotype was transformed with a guide RNA targeted to the MSH2 gene using an Agrobacterium-mediated in planta method. Many plants showed integration of Cas9 and gRNA constructs in rice plants. One of the msh2 mutants showed a superior phenotype due to editing and possible INDELs in the whole genome. The stable integration of the transgene and its flanking sequence analysis confirms no disruption of any gene, and the observed phenotype is due to the mutations in the MSH2 gene. Few transgenic plants showed disruption of genes due to T-DNA integration that led to altered phenotypes. The plants with altered phenotypes having more tiller number, early flowering, and robust growth with a high biomass were identified. These genetically reprogrammed rice plants could be a potential resource to create more segregating population or act as donor lines to stabilize the important agronomic traits that may help in a speed breeding process.
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Affiliation(s)
- Karthika V
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Babitha K Chandrashekar
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad 121001, India
| | - Kiranmai K
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Shankar Ag
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Udayakumar Makarla
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India
| | - Vemanna S Ramu
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad 121001, India
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27
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Nardi T, Olivieri E, Kariuki E, Sassera D, Castelli M. Sequence of a Coxiella Endosymbiont of the Tick Amblyomma nuttalli Suggests a Pattern of Convergent Genome Reduction in the Coxiella Genus. Genome Biol Evol 2021; 13:evaa253. [PMID: 33275132 PMCID: PMC7851586 DOI: 10.1093/gbe/evaa253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to the Coxiella genus, which also includes the human pathogen Coxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete cocladogenesis with the tick hosts. Here, we report the genome sequence of a novel Coxiella, endosymbiont of the African tick Amblyomma nuttalli, and the ensuing comparative analyses. Its size (∼1 Mb) is intermediate between symbionts of Rhipicephalus species and other Amblyomma species. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent of C. burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous among Coxiella endosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities among Coxiella endosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects.
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Affiliation(s)
- Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia, Italy
| | | | - Edward Kariuki
- Veterinary and Capture Service Department, Kenya Wildlife Service, Kenya
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Italy
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28
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Zhao N, Li Z, Zhang L, Yang X, Mackenzie SA, Hu Z, Zhang M, Yang J. MutS HOMOLOG1 mediates fertility reversion from cytoplasmic male sterile Brassica juncea in response to environment. PLANT, CELL & ENVIRONMENT 2021; 44:234-246. [PMID: 32978825 DOI: 10.1111/pce.13895] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/14/2020] [Indexed: 05/15/2023]
Abstract
Spontaneous fertility reversion has been documented in cytoplasmic male sterile (CMS) plants of several species, influenced in frequency by nuclear genetic background. In this study, we found that MutS HOMOLOG1 (MSH1) mediates fertility reversion via substoichiometric shifting (SSS) of the CMS-associated mitochondrial Open Reading Frame 220 (ORF220), a process that may be regulated by pollination signalling in Brassica juncea. We show that plants adjust their growth and development in response to unsuccessful pollination. Measurable decrease in MSH1 transcript levels and evidence of ORF220 SSS under non-pollination conditions suggest that this nuclear-mitochondrial interplay influences fertility reversion in CMS plants in response to physiological signals. Suppression of MSH1 expression induced higher frequency SSS in CMS plants than occurs normally. Transcriptional analysis of floral buds under pollination and non-pollination conditions, and the response of MSH1 expression to different sugars, supports the hypothesis that carbon flux is involved in the pollination signalling of fertility reversion in CMS plants. Our findings suggest that facultative gynodioecy as a reproductive strategy may incorporate environmentally responsive genes like MSH1 as an "on-off" switch for sterility-fertility transition under ecological conditions of reproductive isolation.
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Affiliation(s)
- Na Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Lili Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xiaodong Yang
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, China
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Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nat Commun 2020; 11:3105. [PMID: 32561723 PMCID: PMC7305214 DOI: 10.1038/s41467-020-16932-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics. The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.
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30
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Probing the DNA-binding center of the MutL protein from the Escherichia coli mismatch repair system via crosslinking and Förster resonance energy transfer. Biochimie 2020; 171-172:43-54. [PMID: 32061805 DOI: 10.1016/j.biochi.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/11/2020] [Indexed: 11/23/2022]
Abstract
As no crystal structure of full-size MutL bound to DNA has been obtained up to date, in the present work we used crosslinking and Förster resonance energy transfer (FRET) assays for probing the putative DNA-binding center of MutL from Escherichia coli. Several single-cysteine MutL variants (scMutL) were used for site-specific crosslinking or fluorophore modification. The crosslinking efficiency between scMutL proteins and mismatched DNA modified with thiol-reactive probes correlated with the distances from the Cys residues to the DNA calculated from a model of MutS-MutL-DNA complex. FRET-based investigation of DNA binding with different scMutL variants clearly showed that the highest signals were detected for the variants MutL(T218C) and MutL(A251C) indicating closeness of the positions 218 and 251 to DNA in the MutL-DNA complex. Indeed, the Cys218 and Cys251 of scMutL were crosslinked to the reactive DNA with the highest yield demonstrating their proximity to DNA in the MutL-DNA complex. The presence of MutS increased the yield of conjugate formation between the MutL variants and the modified DNA due to tighter MutL-DNA interactions caused by MutS binding to MutL.
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31
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Waterworth SC, Flórez LV, Rees ER, Hertweck C, Kaltenpoth M, Kwan JC. Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome. mBio 2020; 11:e02430-19. [PMID: 32098813 PMCID: PMC7042692 DOI: 10.1128/mbio.02430-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 12/20/2022] Open
Abstract
Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.
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Affiliation(s)
- Samantha C Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Laura V Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenburg University, Mainz, Germany
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, Jena, Germany
- Department of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenburg University, Mainz, Germany
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Khand FM, Yao DW, Hao P, Wu XQ, Kamboh AA, Yang DJ. Microsatellite Instability and MMR Genes Abnormalities in Canine Mammary Gland Tumors. Diagnostics (Basel) 2020; 10:diagnostics10020104. [PMID: 32075116 PMCID: PMC7169452 DOI: 10.3390/diagnostics10020104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/03/2023] Open
Abstract
Early diagnosis of mammary gland tumors is a challenging task in animals, especially in unspayed dogs. Hence, this study investigated the role of microsatellite instability (MSI), MMR gene mRNA transcript levels and SNPs of MMR genes in canine mammary gland tumors (CMT). A total of 77 microsatellite (MS) markers in 23 primary CMT were selected from four breeds of dogs. The results revealed that 11 out of 77 MS markers were unstable and showed MSI in all the tumors (at least at one locus), while the other markers were stable. Compared to the other markers, the ABC9TETRA, MEPIA, 9A5, SCNA11 and FJL25 markers showed higher frequencies of instability. All CMT demonstrated MSI, with eight tumors presenting MSI-H. The RT-qPCR results revealed significant upregulation of the mRNA levels of cMSH3, cMLH1, and cPMSI, but downregulation of cMSH2 compared to the levels in the control group. Moreover, single nucleotide polymorphisms (SNPs) were observed in the cMSH2 gene in four exons, i.e., 2, 6, 15, and 16. In conclusion, MSI, overexpression of MMR genes and SNPs in the MMR gene are associated with CMT and could be served as diagnostic biomarkers for CMT in the future.
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Affiliation(s)
- Faiz Muhammad Khand
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
| | - Da-Wei Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
| | - Pan Hao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
| | - Xin-Qi Wu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
| | - Asghar Ali Kamboh
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
| | - De-Ji Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; (F.M.K.); (D.-W.Y.); (P.H.); (X.-Q.W.); (A.A.K.)
- Correspondence: ; Tel.: +86-025-843-95505
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33
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Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
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Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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35
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Fujimori H, Hyodo M, Matsuno Y, Shimizu A, Minakawa Y, Atsumi Y, Nakatsu Y, Tsuzuki T, Murakami Y, Yoshioka KI. Mismatch repair dependence of replication stress-associated DSB recognition and repair. Heliyon 2019; 5:e03057. [PMID: 32083205 PMCID: PMC7019108 DOI: 10.1016/j.heliyon.2019.e03057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/21/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022] Open
Abstract
Most cancers develop with one of two types of genomic instability, namely, chromosomal instability (CIN) or microsatellite instability (MSI). Both are induced by replication stress-associated DNA double-strand breaks (DSBs). The type of genomic instability that arises is dependent on the choice of DNA repair pathway. Specifically, MSI is induced via a PolQ-dependent repair pathway called microhomology-mediated end joining (MMEJ) in a mismatch repair (MMR)-deficient background. However, it is unclear how the MMR status determines the choice of DSB repair pathway. Here, we show that replication stress-associated DSBs initially targeted by the homologous recombination (HR) system were subsequently hijacked by PolQ-dependent MMEJ in MMR-deficient cells, but persisted as HR intermediates in MMR-proficient cells. PolQ interacting with MMR factors was effectively loaded onto damaged chromatin in an MMR-deficient background, in which merged MRE11/γH2AX foci also effectively formed. Thus, the choice of DNA repair pathway according to the MMR status determines whether CIN or MSI is induced.
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Affiliation(s)
- Haruka Fujimori
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mai Hyodo
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yusuke Matsuno
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Atsuhiro Shimizu
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yusuke Minakawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yuko Atsumi
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasufumi Murakami
- Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
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Płaczkiewicz J, Adamczyk-Popławska M, Lasek R, Bącal P, Kwiatek A. Inactivation of Genes Encoding MutL and MutS Proteins Influences Adhesion and Biofilm Formation by Neisseria gonorrhoeae. Microorganisms 2019; 7:microorganisms7120647. [PMID: 31817122 PMCID: PMC6955733 DOI: 10.3390/microorganisms7120647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/16/2022] Open
Abstract
Neisseria gonorrhoeae is an etiological agent of gonorrhea, which remains a global health problem. This bacterium possesses MutL and MutS DNA repair proteins encoded by mutL and mutS genes, whose inactivation causes a mutator phenotype. We have demonstrated the differential gene expression in N. gonorrhoeae mutL and mutS mutants using DNA microarrays. A subset of differentially expressed genes encodes proteins that can influence adhesion and biofilm formation. Compared to the wild-type strain, N. gonorrhoeae mutL and mutS mutants formed denser biofilms with increased biofilm-associated biomass on the abiotic surface. The N. gonorrhoeae mutS::km, but not the mutL mutant, was also more adherent and invasive to human epithelial cells. Further, during infection of epithelial cells with N. gonorrhoeae mutS::km, the expression of some bacterial genes encoding proteins that can influence gonococcal adhesion was changed compared with their expression in cells infected with the wild-type gonococcus, as well as of human genes' encoding receptors utilized by N. gonorrhoeae (CD46, CEACAM 1, HSPG 2). Thus, deficiency in the mutS gene resulting in increased mutation frequency in singular organisms can be beneficial in populations because these mutants can be a source of features linked to microbial fitness.
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Affiliation(s)
- Jagoda Płaczkiewicz
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.); (R.L.)
| | - Monika Adamczyk-Popławska
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.); (R.L.)
| | - Robert Lasek
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.); (R.L.)
| | - Pawel Bącal
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, 02-109 Warsaw, Poland
| | - Agnieszka Kwiatek
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.); (R.L.)
- Correspondence: ; Tel.: +48-22-554-14-21
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37
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Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida. DNA Repair (Amst) 2019; 85:102745. [PMID: 31715424 DOI: 10.1016/j.dnarep.2019.102745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022]
Abstract
Nucleoid-associated proteins (NAPs) such as IHF, HU, Fis, and H-NS alter the topology of bound DNA and may thereby affect accessibility of DNA to repair and recombination processes. To examine this possibility, we investigated the effect of IHF on the frequency of homologous recombination (HR) and point mutations in soil bacterium Pseudomonas putida by using plasmidial and chromosomal assays. We observed positive effect of IHF on the frequency of HR, whereas this effect varied depending both on the chromosomal location of the HR target and the type of plasmid used in the assay. The occurrence of point mutations in plasmid was also facilitated by IHF, whereas in the chromosome the positive effect of IHF appeared only at certain DNA sequences and/or chromosomal positions. We did not observe any significant effects of IHF on the spectrum of mutations. However, despite of the presence or absence of IHF, different mutational hot spots appeared both in plasmid and in chromosome. Additionally, the frequency of frameshift mutations in the chromosome was also strongly affected by the location of the mutational target sequence. Taking together, our results indicate that IHF facilitates the occurrence of genetic changes in P. putida, whereas the location of the target sequence affects both the IHF-dependent and IHF-independent mechanisms.
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38
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Matsuno Y, Atsumi Y, Shimizu A, Katayama K, Fujimori H, Hyodo M, Minakawa Y, Nakatsu Y, Kaneko S, Hamamoto R, Shimamura T, Miyano S, Tsuzuki T, Hanaoka F, Yoshioka KI. Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro. Nat Commun 2019; 10:3925. [PMID: 31477700 PMCID: PMC6718401 DOI: 10.1038/s41467-019-11760-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. However, it remains unclear how MSI and hypermutation arise and contribute to cancer development. Here, we show that MSI and hypermutation are triggered by replication stress in an MMR-deficient background, enabling clonal expansion of cells harboring ARF/p53-module mutations and cells that are resistant to the anti-cancer drug camptothecin. While replication stress-associated DNA double-strand breaks (DSBs) caused chromosomal instability (CIN) in an MMR-proficient background, they induced MSI with concomitant suppression of CIN via a PARP-mediated repair pathway in an MMR-deficient background. This was associated with the induction of mutations, including cancer-driver mutations in the ARF/p53 module, via chromosomal deletions and base substitutions. Immortalization of MMR-deficient mouse embryonic fibroblasts (MEFs) in association with ARF/p53-module mutations was ~60-fold more efficient than that of wild-type MEFs. Thus, replication stress-triggered MSI and hypermutation efficiently lead to clonal expansion of cells with abrogated defense systems. Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. Here authors reveal a mechanism by which replication stress induces MSI and associated induction of mutations in vitro.
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Affiliation(s)
- Yusuke Matsuno
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Yuko Atsumi
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Atsuhiro Shimizu
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kotoe Katayama
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Haruka Fujimori
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mai Hyodo
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yusuke Minakawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, 103-0027, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Tsurumai-cho, Syouwa-ku, Nagoya, 466-8550, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.,National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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39
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LeBlanc SJ, Gauer JW, Hao P, Case BC, Hingorani MM, Weninger KR, Erie DA. Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS. Nucleic Acids Res 2019; 46:10782-10795. [PMID: 30272207 PMCID: PMC6237781 DOI: 10.1093/nar/gky865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein–DNA and DNA–DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jacob W Gauer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Brandon C Case
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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40
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Wang J, Liu F, Su T, Chang Y, Guo Q, Wang Q, Liang Q, Qi Q. The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis. Microb Cell Fact 2019; 18:107. [PMID: 31196093 PMCID: PMC6567493 DOI: 10.1186/s12934-019-1160-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/09/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Microbial mutagenesis is an important avenue to acquire microbial strains with desirable traits for industry application. However, mutagens either chemical or physical used often leads narrow library pool due to high lethal rate. The T4 DNA ligase is one of the most widely utilized enzymes in modern molecular biology. Its contribution to repair chromosomal DNA damages, therefore cell survival during mutagenesis will be discussed. RESULTS Expression of T4 DNA ligase in vivo could substantially increase cell survival to ionizing radiation in multiple species. A T4 mediated survival-coupled mutagenesis approach was proposed. When polyhydroxybutyrate (PHB)-producing E. coli with T4 DNA ligase expressed in vivo was subjected to ionizing radiation, mutants with improved PHB production were acquired quickly owing to a large viable mutant library generated. Draft genome sequence analysis showed that the mutants obtained possess not only single nucleotide variation (SNV) but also DNA fragment deletion, indicating that T4 DNA ligase in vivo may contribute to the repair of DNA double strand breaks. CONCLUSIONS Expression of T4 DNA ligase in vivo could notably enhance microbial survival to excess chromosomal damages caused by various mutagens. Potential application of T4 DNA ligase in microbial mutagenesis was explored by mutating and screening PHB producing E. coli XLPHB strain. When applied to atmospheric and room temperature plasma (ARTP) microbial mutagenesis, large survival pool was obtained. Mutants available for subsequent screening for desirable features. The use of T4 DNA ligase we were able to quickly improve the PHB production by generating a larger viable mutants pool. This method is a universal strategy can be employed in wide range of bacteria. It indicated that traditional random mutagenesis became more powerful in combine with modern genetic molecular biology and has exciting prospect.
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Affiliation(s)
- Junshu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Fapeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yizhao Chang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qi Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
- National Glycoengineering Center, Shandong University, Qingdao, 266237 China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 2566101 China
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41
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Alexander LM, Oh JH, Stapleton DS, Schueler KL, Keller MP, Attie AD, van Pijkeren JP. Exploiting Prophage-Mediated Lysis for Biotherapeutic Release by Lactobacillus reuteri. Appl Environ Microbiol 2019; 85:e02335-18. [PMID: 30683744 PMCID: PMC6498169 DOI: 10.1128/aem.02335-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Lactobacillus reuteri has the potential to be developed as a microbial therapeutic delivery platform because of an established safety profile, health-promoting properties, and available genome editing tools. Here, we show that L. reuteri VPL1014 exhibits a low mutation rate compared to other Gram-positive bacteria, which we expect will contribute to the stability of genetically modified strains. VPL1014 encodes two biologically active prophages, which are induced during gastrointestinal transit. We hypothesized that intracellularly accumulated recombinant protein can be released following bacteriophage-mediated lysis. To test this, we engineered VPL1014 to accumulate leptin, our model protein, inside the cell. In vitro prophage induction of recombinant VPL1014 released leptin into the extracellular milieu, which corresponded to bacteriophage production. We also employed a plasmid system that does not require antibiotic in the growth medium for plasmid maintenance. Collectively, these data provide new avenues to exploit native prophages to deliver therapeutic molecules.IMPORTANCE Lactic acid bacteria (LAB) have been explored as potential biotherapeutic vehicles for the past 20 years. To secrete a therapeutic in the extracellular milieu, one typically relies on the bacterial secretion pathway, i.e., the Sec pathway. Overexpression of a secreted protein can overload the secretory pathway and impact the organism's fitness, and optimization of the signal peptide is also required to maximize the efficiency of the release of mature protein. Here, we describe a previously unexplored approach to release therapeutics from the probiotic Lactobacillus reuteri We demonstrate that an intracellularly accumulated recombinant protein is released following prophage activation. Since we recently demonstrated that prophages are activated during gastrointestinal transit, we propose that this method will provide a straightforward and efficient approach to deliver therapeutics in vivo.
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Affiliation(s)
- Laura M Alexander
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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42
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Aberrations in DNA repair pathways in cancer and therapeutic significances. Semin Cancer Biol 2019; 58:29-46. [PMID: 30922960 DOI: 10.1016/j.semcancer.2019.02.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 01/16/2023]
Abstract
Cancer cells show various types of mutations and aberrant expression in genes involved in DNA repair responses. These alterations induce genome instability and promote carcinogenesis steps and cancer progression processes. These defects in DNA repair have also been considered as suitable targets for cancer therapies. A most effective target so far clinically demonstrated is "homologous recombination repair defect", such as BRCA1/2 mutations, shown to cause synthetic lethality with inhibitors of poly(ADP-ribose) polymerase (PARP), which in turn is involved in DNA repair as well as multiple physiological processes. Different approaches targeting genomic instability, including immune therapy targeting mismatch-repair deficiency, have also recently been demonstrated to be promising strategies. In these DNA repair targeting-strategies, common issues could be how to optimize treatment and suppress/conquer the development of drug resistance. In this article, we review the extending framework of DNA repair response pathways and the potential impact of exploiting those defects on cancer treatments, including chemotherapy, radiation therapy and immune therapy.
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43
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A Novel, Drug Resistance-Independent, Fluorescence-Based Approach To Measure Mutation Rates in Microbial Pathogens. mBio 2019; 10:mBio.00120-19. [PMID: 30808701 PMCID: PMC6391916 DOI: 10.1128/mbio.00120-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Measurements of mutation rates—i.e., how often proliferating cells acquire mutations in their DNA—are essential for understanding cellular processes that maintain genome stability. Many traditional mutation rate measurement assays are based on detecting mutations that cause resistance to a particular drug. Such assays typically work well for laboratory strains but have significant limitations when comparing clinical or environmental isolates that have various intrinsic levels of drug tolerance, which confounds the interpretation of results. Here we report the development and validation of a novel method of measuring mutation rates, which detects mutations that cause loss of fluorescence rather than acquisition of drug resistance. Using this method, we measured the mutation rates of clinical isolates of fungal pathogen Candida glabrata. This assay can be adapted to other organisms and used to compare mutation rates in contexts where unequal drug sensitivity is anticipated. All evolutionary processes are underpinned by a cellular capacity to mutate DNA. To identify factors affecting mutagenesis, it is necessary to compare mutation rates between different strains and conditions. Drug resistance-based mutation reporters are used extensively to measure mutation rates, but they are suitable only when the compared strains have identical drug tolerance levels—a condition that is not satisfied under many “real-world” circumstances, e.g., when comparing mutation rates among a series of environmental or clinical isolates. Candida glabrata is a fungal pathogen that shows a high degree of genetic diversity and fast emergence of antifungal drug resistance. To enable meaningful comparisons of mutation rates among C. glabrata clinical isolates, we developed a novel fluorescence-activated cell sorting-based approach to measure the mutation rate of a chromosomally integrated GFP gene. We found that in Saccharomyces cerevisiae this approach recapitulated the reported mutation rate of a wild-type strain and the mutator phenotype of a shu1Δ mutant. In C. glabrata, the GFP reporter captured the mutation rate increases caused either by a genotoxic agent or by deletion of DNA mismatch repair gene MSH2, as well as the specific mutational signature associated with msh2Δ. Finally, the reporter was used to measure the mutation rates of C. glabrata clinical isolates carrying different alleles of MSH2. Together, these results show that fluorescence-based mutation reporters can be used to measure mutation rates in microbes under conditions of unequal drug susceptibility to reveal new insights about drivers of mutagenesis.
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Rakosy-Tican E, Lörincz-Besenyei E, Molnár I, Thieme R, Hartung F, Sprink T, Antonova O, Famelaer I, Angenon G, Aurori A. New Phenotypes of Potato Co-induced by Mismatch Repair Deficiency and Somatic Hybridization. FRONTIERS IN PLANT SCIENCE 2019; 10:3. [PMID: 30723483 PMCID: PMC6349821 DOI: 10.3389/fpls.2019.00003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/04/2019] [Indexed: 06/01/2023]
Abstract
As plants are sessile they need a very efficient system for repairing damage done by external or internal mutagens to their DNA. Mismatch repair (MMR) is one of the systems that maintain genome integrity and prevent homeologous recombination. In all eukaryotes mismatches are recognized by evolutionary conserved MSH proteins often acting as heterodimers, the constant component of which is MSH2. Changes affecting the function of MSH2 gene may induce a 'mutator' phenotype and microsatellite instability (MSI), as is demonstrated in MSH2 knock-out and silenced lines of Arabidopsis thaliana. The goal of this study was to screen for 'mutator' phenotypes in somatic hybrids between potato cvs. 'Delikat' and 'Désirée' and MMR deficient Solanum chacoense transformed using antisense (AS) or dominant negative mutant (DN) AtMSH2 genes. The results demonstrate that first generation fusion hybrids have a range of morphological abnormalities caused by uniparental MMR deficiency; these mutant phenotypes include: dwarf or gigantic plants; bushiness; curled, small, large or abnormal leaves; a deterioration in chloroplast structure; small deep-purple tubers and early dehiscent flowers. Forty percent of the viable somatic hybrids planted in a greenhouse, (10 out of 25 genotypes) had mutant phenotypes accompanied by MSI. The majority of the hybrids with 'mutator' phenotypes cultured on media containing kanamycin developed roots so sustaining the presence of selectable marker gene nptII, from the initial constructs. Here for the first time, MMR deficiency combined with somatic hybridization, are used to induce new phenotypes in plants, which supports the role of MMR deficiency in increasing introgressions between two related species.
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Affiliation(s)
- Elena Rakosy-Tican
- Plant Genetic Engineering Group, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Enikö Lörincz-Besenyei
- Plant Genetic Engineering Group, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Imola Molnár
- Plant Genetic Engineering Group, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Ramona Thieme
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| | - Frank Hartung
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg, Germany
| | - Olga Antonova
- Department of Plant Biotechnology, N.I. Vavilov Institute of Plant Industry, St. Petersburg, Russia
| | - Ivan Famelaer
- Laboratory of Plant Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Geert Angenon
- Laboratory of Plant Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adriana Aurori
- Plant Genetic Engineering Group, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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45
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Li S, Wehrenberg B, Waldman BC, Waldman AS. Mismatch tolerance during homologous recombination in mammalian cells. DNA Repair (Amst) 2018; 70:25-36. [PMID: 30103093 DOI: 10.1016/j.dnarep.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site. Recombination events were recoverable by selection for tk-positive clones. Three different donors were used containing 16, 25, or 33 mismatches relative to the recipient. The mismatches were clustered, forming an interval of "homeology" relative to the recipient sequences. We show that when homeologous sequences were surrounded by high homology, mismatches were frequently included in gene conversion events. Notably, conversion tracts from spontaneous recombination included either all or none of the mismatches, suggesting that recombination must begin and end in high homology. This requirement was relaxed for events that occurred near an induced DSB, as a significant number of these latter conversion tracts had one end positioned within homeology. Knock-down of mismatch repair showed that incorporation of mismatches into gene conversion tracts can involve repair of mismatched heteroduplex intermediates, indicating that mismatch repair does not necessarily impede homeologous genetic exchange. Our results illustrate (1) genetic exchange between homeologous sequences in a mammalian genome is enabled by nearby homology, (2) proximity to a DSB impacts the homology requirements for where genetic exchange may begin and end, and (3) mismatch correction and previously documented anti-recombination activity are separable functions of the mismatch repair machinery in mammalian cells.
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Affiliation(s)
- Shen Li
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Bryan Wehrenberg
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA.
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46
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Bubnov DM, Yuzbashev TV, Vybornaya TV, Netrusov AI, Sineoky SP. Development of new versatile plasmid-based systems for λRed-mediated Escherichia coli genome engineering. J Microbiol Methods 2018; 151:48-56. [PMID: 29885886 DOI: 10.1016/j.mimet.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/06/2018] [Accepted: 06/06/2018] [Indexed: 10/14/2022]
Abstract
Plasmid-based systems are the most appropriate for multistep lambda Red (λRed)-mediated recombineering, such as the assembly of strains for biotechnological applications. Currently, the widely used λRed-expressing plasmids use a temperature-sensitive origin of replication or temperature shift control of λRed expression. In this work, we have constructed a new, conditionally replicating vector that can be efficiently eliminated from the host strain through passaging in medium containing isopropyl-β-d-thiogalactopyranoside. Using the new vector, we have developed two improved helper plasmids (viz., pDL17 and pDL14) for dsDNA and oligonucleotide-mediated recombineering, respectively. The plasmid pDL14 contains a dominant negative mutSK622A allele that suppresses methyl-directed mismatch repair (MMR). The coexpression of λRed and mutSK622A provides efficient oligonucleotide-mediated recombineering in the presence of active host MMR. The expression of λRed was placed under the control of the tightly regulated PrhaB promoter. Because of their low expression level under uninduced conditions, both plasmids could be maintained without elimination for multiple recombineering steps. The temperature-independent replication of the plasmids and control of λRed expression by l-rhamnose allow for all procedures to be performed at 37 °C. Thus, the new plasmids are robust, convenient, and versatile tools for Escherichia coli genome editing.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia; Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills, 1-12, Moscow 119234, Russia.
| | - Tigran V Yuzbashev
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia.
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Alexander I Netrusov
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills, 1-12, Moscow 119234, Russia
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia.
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47
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Sarma S, Pandey AK, Sharma K, Ravi M, Sreelakshmi Y, Sharma R. MutS-Homolog2 silencing generates tetraploid meiocytes in tomato ( Solanum lycopersicum). PLANT DIRECT 2018; 2:e00017. [PMID: 31245679 PMCID: PMC6508528 DOI: 10.1002/pld3.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/07/2017] [Accepted: 09/12/2017] [Indexed: 05/16/2023]
Abstract
MSH2 is the core protein of MutS-homolog family involved in recognition and repair of the errors in the DNA. While other members of MutS-homolog family reportedly regulate mitochondrial stability, meiosis, and fertility, MSH2 is believed to participate mainly in mismatch repair. The search for polymorphism in MSH2 sequence in tomato accessions revealed both synonymous and nonsynonymous SNPs; however, SIFT algorithm predicted that none of the SNPs influenced MSH2 protein function. The silencing of MSH2 gene expression by RNAi led to phenotypic abnormalities in highly silenced lines, particularly in the stamens with highly reduced pollen formation. MSH2 silencing exacerbated formation of UV-B-induced thymine dimers and blocked light-induced repair of the dimers. The MSH2 silencing also affected the progression of male meiosis to a varying degree with either halt of meiosis at zygotene stage or formation of diploid tetrads. The immunostaining of male meiocytes with centromere localized CENPC (centromere protein C) antibody showed the presence of 48 univalent along with 24 bivalent chromosomes suggesting abnormal tetraploid meiosis. The mitotic cells of root tips of silenced lines showed diploid nuclei but lacked intervening cell plates leading to cells with syncytial nuclei. Thus, we speculate that tetraploid pollen mother cells may have arisen due to the fusion of syncytial nuclei before the onset of meiosis. It is likely that in addition to mismatch repair (MMR), MSH2 may have an additional role in regulating ploidy stability.
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Affiliation(s)
- Supriya Sarma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
- Present address:
Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Arun Kumar Pandey
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
- Present address:
International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kapil Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
| | - Maruthachalam Ravi
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKeralaIndia
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
| | - Rameshwar Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
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48
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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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49
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High homology is not required at the site of strand invasion during recombinational double-strand break repair in mammalian chromosomes. DNA Repair (Amst) 2017; 60:1-8. [PMID: 29055804 DOI: 10.1016/j.dnarep.2017.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/22/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022]
Abstract
We investigated the impact of sequence divergence on DNA double-strand break (DSB) repair occurring via recombination in cultured thymidine kinase deficient mouse fibroblasts. We stably transfected cells with a DNA construct harboring a herpes thymidine kinase (tk) gene (the "recipient") rendered nonfunctional by insertion of an oligonucleotide containing the recognition site for endonuclease I-SceI. The construct also contained a closely linked truncated "donor" tk sequence. The donor could potentially restore function to the recipient gene via recombination provoked by induction of a DSB at the I-SceI site in the recipient. Repair events were recoverable by selection for tk-positive clones. The donor contained 33 mismatches relative to the recipient. The mismatches were clustered, forming a localized segment of DNA sequence displaying about 20% divergence relative to the recipient, and the mismatched segment was surrounded by regions of high homology. When the donor was aligned with the recipient, the DSB site in the recipient aligned opposite the mismatched segment, allowing us to potentially capture recombinational repair events initiating between diverged sequences. Previous work demonstrated that mammalian cells effectively avoid recombination between 20% diverged sequences. In the current study we asked whether flanking regions of high homology would enable genetic exchange between highly diverged sequences or, instead, would rejection of exchange between diverged sequences remain unchanged. We found that by surrounding mismatches with high homology, suppression of recombination between diverged sequences was overcome. Strikingly, we recovered a high frequency of gene conversion tracts positioned entirely within the mismatched sequences. We infer that such events were enabled by homologous pairing interactions between sequences surrounding the site of strand invasion. Our results suggest a search for high homology prior to recombination that is not mediated by an invading DNA terminus.
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50
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Shweta H, Singh MK, Yadav K, Verma SD, Pal N, Sen S. Effect of T·T Mismatch on DNA Dynamics Probed by Minor Groove Binders: Comparison of Dynamic Stokes Shifts of Hoechst and DAPI. J Phys Chem B 2017; 121:10735-10748. [PMID: 28922599 DOI: 10.1021/acs.jpcb.7b06937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recognition of DNA base mismatches and their subsequent repair by enzymes is vital for genomic stability. However, it is difficult to comprehend such a process in which enzymes sense and repair different types of mismatches with different ability. It has been suggested that the differential structural changes of mismatched bases act as cues to the repair enzymes, although the effect of such DNA structural changes on surrounding water and ion dynamics is inevitable due to strong electrostatic coupling among them. Thus, collective dynamics of DNA, water, and ions near the mismatch site is believed to be important for mismatch recognition and repair mechanism. Here we show that introduction of a T·T mismatch in the minor groove of DNA induces dispersed (collective) power-law solvation dynamics (of exponent ∼0.24), measured by monitoring the time-resolved fluorescence Stokes shifts (TRFSS) of two popular minor groove binders (Hoechst 33258 and DAPI) over five decades of time from 100 fs to 10 ns. The same ligands however sense different dynamics (power-law of exponent ∼0.15 or power-law multiplied with biexponential relaxation) in the minor groove of normal-DNA. The similar fluorescence anisotropy decays of ligands measured in normal- and T·T-DNA suggest that Stokes shift dynamics and their changes in T·T-DNA purely originate from the solvation process, and not from any internal rotational motion of probe-ligands. The dispersed power-law solvation dynamics seen in T·T-DNA indicate that the ligands do not sense any particular (exponential) relaxation specific to T·T wobbling and/or other conformational changes. This could be the reason why T·T mismatch is recognized by enzymes with lower efficiency compared to purine-pyrimidine and purine-purine mismatches.
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Affiliation(s)
- Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Sachin Dev Verma
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Nibedita Pal
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India
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