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Xiao Y, Ni M, Zheng Z, Liu Y, Yin M, Mao S, Zhao Y, Tian B, Wang L, Xu H, Hua Y. POLM variant G312R promotes ovarian tumorigenesis through genomic instability and COL11A1-NF-κB axis. Am J Physiol Cell Physiol 2024; 327:C168-C183. [PMID: 38826139 DOI: 10.1152/ajpcell.00025.2024] [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: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
In ovarian cancer (OC), identifying key molecular players in disease escalation and chemoresistance remains critical. Our investigation elucidates the role of the DNA polymerase mu (POLM), especially G312R mutation, in propelling oncogenesis through dual pathways. POLMG312R markedly augments the ribonucleotide insertion capability of POLM, precipitating genomic instability. In addition, our research reveals that POLMG312R perturbs collagen alpha-1 (XI) chain (COL11A1) expression-a gene that plays a key role in oncogenesis-and modulates the NF-κB signaling pathway, alters the secretion of downstream inflammatory cytokines, and promotes tumor-macrophage interactions. We illustrate a bidirectional regulatory interaction between POLM, particularly its G312R variant, and COL11A1. This interaction regulates NF-κB signaling, culminating in heightened malignancy and resistance to chemotherapy in OC cells. These insights position the POLM as a potential molecular target for OC therapy, shedding light on the intricate pathways underpinning POLM variant disease progression.NEW & NOTEWORTHY Our research reveals that POLM plays an important role in ovarian cancer development, especially the mutation G312R. We uncover the POLMG312R mutation as a driver of genomic instability in ovarian cancer via aberrant ribonucleotide incorporation. We reveal that POLMG312R upregulates COL11A1 and activates NF-κB signaling, contributing to tumor progression and chemoresistance. This study identifies the POLM-COL11A1-NF-κB axis as a novel oncogenic pathway.
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Affiliation(s)
- Yue Xiao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Yufeng Liu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Mingyu Yin
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
| | - Shuyu Mao
- Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, People's Republic of China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Bing Tian
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Liangyan Wang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Hong Xu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Hangzhou, People's Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People's Republic of China
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2
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Verma I, Chhatlani K, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae. iScience 2024; 27:110012. [PMID: 38868188 PMCID: PMC11166700 DOI: 10.1016/j.isci.2024.110012] [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: 10/02/2023] [Revised: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.
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Affiliation(s)
- Deepali L. Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L. Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ishika Verma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kirti Chhatlani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zeel H. Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Yang J, Sun M, Ran Z, Yang T, Kundnani DL, Storici F, Xu P. rNMPID: a database for riboNucleoside MonoPhosphates in DNA. BIOINFORMATICS ADVANCES 2024; 4:vbae063. [PMID: 38736683 PMCID: PMC11088741 DOI: 10.1093/bioadv/vbae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/27/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Motivation Ribonucleoside monophosphates (rNMPs) are the most abundant non-standard nucleotides embedded in genomic DNA. If the presence of rNMP in DNA cannot be controlled, it can lead to genome instability. The actual regulatory functions of rNMPs in DNA remain mainly unknown. Considering the association between rNMP embedment and various diseases and cancer, the phenomenon of rNMP embedment in DNA has become a prominent area of research in recent years. Results We introduce the rNMPID database, which is the first database revealing rNMP-embedment characteristics, strand bias, and preferred incorporation patterns in the genomic DNA of samples from bacterial to human cells of different genetic backgrounds. The rNMPID database uses datasets generated by different rNMP-mapping techniques. It provides the researchers with a solid foundation to explore the features of rNMP embedded in the genomic DNA of multiple sources, and their association with cellular functions, and, in future, disease. It also significantly benefits researchers in the fields of genetics and genomics who aim to integrate their studies with the rNMP-embedment data. Availability and implementation rNMPID is freely accessible on the web at https://www.rnmpid.org.
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Affiliation(s)
- Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai 200438, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong 511462, China
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Zihan Ran
- Department of Research, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
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4
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Kundnani DL, Yang T, Gombolay AL, Mukherjee K, Newnam G, Meers C, Mehta ZH, Mouawad C, Storici F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560505. [PMID: 37873120 PMCID: PMC10592897 DOI: 10.1101/2023.10.02.560505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations in Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome of rnh201-G42S than in wild-type and rnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.
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Affiliation(s)
- Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Zeel H Mehta
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Celine Mouawad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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5
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Nischwitz E, Schoonenberg VA, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F, Scheibe M. DNA damage repair proteins across the Tree of Life. iScience 2023; 26:106778. [PMID: 37250769 PMCID: PMC10220248 DOI: 10.1016/j.isci.2023.106778] [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: 10/31/2022] [Revised: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Genome maintenance is orchestrated by a highly regulated DNA damage response with specific DNA repair pathways. Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by base excision repair (BER) and ribonucleotide excision repair (RER): (1) 8-oxoguanine, (2) abasic site, and (3) incorporated ribonucleotide in DNA in 11 species: Escherichia coli, Bacillus subtilis, Halobacterium salinarum, Trypanosoma brucei, Tetrahymena thermophila, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Zea mays. Using quantitative mass spectrometry, we identified 337 binding proteins across these species. Of these proteins, 99 were previously characterized to be involved in DNA repair. Through orthology, network, and domain analysis, we linked 44 previously unconnected proteins to DNA repair. Our study presents a resource for future study of the crosstalk and evolutionary conservation of DNA damage repair across all domains of life.
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Affiliation(s)
| | | | | | - Mario Dejung
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Olga Vydzhak
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Marion Scheibe
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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6
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Development of an RNase H2 Activity Assay for Clinical Screening. J Clin Med 2023; 12:jcm12041598. [PMID: 36836134 PMCID: PMC9961991 DOI: 10.3390/jcm12041598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
As the key enzyme mediating ribonucleotide excision repair, RNase H2 is essential for the removal of single ribonucleotides from DNA in order to prevent genome damage. Loss of RNase H2 activity directly contributes to the pathogenesis of autoinflammatory and autoimmune diseases and might further play a role in ageing and neurodegeneration. Moreover, RNase H2 activity is a potential diagnostic and prognostic marker in several types of cancer. Until today, no method for quantification of RNase H2 activity has been validated for the clinical setting. Herein, validation and benchmarks of a FRET-based whole-cell lysate RNase H2 activity assay are presented, including standard conditions and procedures to calculate standardized RNase H2 activity. Spanning a wide working range, the assay is applicable to various human cell or tissue samples with overall methodological assay variability from 8.6% to 16%. Using our assay, we found RNase H2 activity was reduced in lymphocytes of two patients with systemic lupus erythematosus and one with systemic sclerosis carrying heterozygous mutations in one of the RNASEH2 genes. Implementation of larger control groups will help to assess the diagnostic and prognostic value of clinical screening for RNase H2 activity in the future.
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7
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Wei ZT, Wu SY, Shen GQ, Yan L, Chen XH. Density Functional Study on the Hydrogenation of Phosphorus Oxides: Structural, Electronic, and Spectral Properties. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422130283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Fugger K, Hewitt G, West SC, Boulton SJ. Tackling PARP inhibitor resistance. Trends Cancer 2021; 7:1102-1118. [PMID: 34563478 DOI: 10.1016/j.trecan.2021.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022]
Abstract
Homologous recombination-deficient (HRD) tumours, including those harbouring mutations in the BRCA genes, are hypersensitive to treatment with inhibitors of poly(ADP-ribose) polymerase (PARPis). Despite high response rates, most HRD cancers ultimately develop resistance to PARPi treatment through reversion mutations or genetic/epigenetic alterations to DNA repair pathways. Counteracting these resistance pathways, thereby increasing the potency of PARPi therapy, represents a potential strategy to improve the treatment of HRD cancers. In this review, we discuss recent insights derived from genetic screens that have identified a number of novel genes that can be targeted to improve PARPi treatment of HRD cancers and may provide a means to overcome PARPi resistance.
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Affiliation(s)
- Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Artios Pharma Ltd. B940, Babraham Research Campus, Cambridge, CB22 3FH, UK.
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9
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Vaisman A, Łazowski K, Reijns MAM, Walsh E, McDonald JP, Moreno KC, Quiros DR, Schmidt M, Kranz H, Yang W, Makiela-Dzbenska K, Woodgate R. Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity. Mol Microbiol 2021; 116:909-925. [PMID: 34181784 PMCID: PMC8485763 DOI: 10.1111/mmi.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/26/2022]
Abstract
The Escherichia coli dnaE gene encodes the α‐catalytic subunit (pol IIIα) of DNA polymerase III, the cell’s main replicase. Like all high‐fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so‐called “steric gate” residue in the active site of the polymerase that physically clashes with the 2′‐OH of an incoming ribonucleotide. Our structural modeling data suggest that H760 is the steric gate residue in E.coli pol IIIα. To understand how H760 and the adjacent S759 residue help maintain genome stability, we generated DNA fragments in which the codons for H760 or S759 were systematically changed to the other nineteen naturally occurring amino acids and attempted to clone them into a plasmid expressing pol III core (α‐θ‐ε subunits). Of the possible 38 mutants, only nine were successfully sub‐cloned: three with substitutions at H760 and 6 with substitutions at S759. Three of the plasmid‐encoded alleles, S759C, S759N, and S759T, exhibited mild to moderate mutator activity and were moved onto the chromosome for further characterization. These studies revealed altered phenotypes regarding deoxyribonucleotide base selectivity and ribonucleotide discrimination. We believe that these are the first dnaE mutants with such phenotypes to be reported in the literature.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Martin A M Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Erin Walsh
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kristiniana C Moreno
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dominic R Quiros
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marlen Schmidt
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Harald Kranz
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karolina Makiela-Dzbenska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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10
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Sassa A, Odagiri M. Understanding the sequence and structural context effects in oxidative DNA damage repair. DNA Repair (Amst) 2021; 93:102906. [PMID: 33087272 DOI: 10.1016/j.dnarep.2020.102906] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
8-Oxo-7,8-dihydroguanine (8-oxoG) is the major base damage in the genomic DNA by exposure to reactive oxygen species. Organisms have evolved various DNA repair mechanisms, such as base excision repair (BER) and nucleotide excision repair (NER), to protect the cellular genome from these mutagenic DNA lesions. The efficiency and capacity of BER and NER mechanisms can be modulated by the local sequence and structural contexts in which 8-oxoG is located. This graphical review summarizes the biochemical and structural studies that have provided insights into the impact of the microenvironment around the site of the lesion on oxidative DNA damage repair.
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Affiliation(s)
- Akira Sassa
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| | - Mizuki Odagiri
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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11
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Takeishi A, Kogashi H, Odagiri M, Sasanuma H, Takeda S, Yasui M, Honma M, Suzuki T, Kamiya H, Sugasawa K, Ura K, Sassa A. Tyrosyl-DNA phosphodiesterases are involved in mutagenic events at a ribonucleotide embedded into DNA in human cells. PLoS One 2020; 15:e0244790. [PMID: 33382846 PMCID: PMC7775084 DOI: 10.1371/journal.pone.0244790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/23/2020] [Indexed: 01/26/2023] Open
Abstract
Ribonucleoside triphosphates are often incorporated into genomic DNA during DNA replication. The accumulation of unrepaired ribonucleotides is associated with genomic instability, which is mediated by DNA topoisomerase 1 (Top1) processing of embedded ribonucleotides. The cleavage initiated by Top1 at the site of a ribonucleotide leads to the formation of a Top1-DNA cleavage complex (Top1cc), occasionally resulting in a DNA double-strand break (DSB). In humans, tyrosyl-DNA phosphodiesterases (TDPs) are essential repair enzymes that resolve the trapped Top1cc followed by downstream repair factors. However, there is limited cellular evidence of the involvement of TDPs in the processing of incorporated ribonucleotides in mammals. We assessed the role of TDPs in mutagenesis induced by a single ribonucleotide embedded into DNA. A supF shuttle vector site-specifically containing a single riboguanosine (rG) was introduced into the human lymphoblastoid TK6 cell line and its TDP1-, TDP2-, and TDP1/TDP2-deficient derivatives. TDP1 and TDP2 insufficiency remarkably decreased the mutant frequency caused by an embedded rG. The ratio of large deletion mutations induced by rG was also substantially lower in TDP1/TDP2-deficient cells than wild-type cells. Furthermore, the disruption of TDPs reduced the length of rG-mediated large deletion mutations. The recovery ratio of the propagated plasmid was also increased in TDP1/TDP2-deficient cells after the transfection of the shuttle vector containing rG. The results suggest that TDPs-mediated ribonucleotide processing cascade leads to unfavorable consequences, whereas in the absence of these repair factors, a more error-free processing pathway might function to suppress the ribonucleotide-induced mutagenesis. Furthermore, base substitution mutations at sites outside the position of rG were detected in the supF gene via a TDPs-independent mechanism. Overall, we provide new insights into the mechanism of mutagenesis induced by an embedded ribonucleotide in mammalian cells, which may lead to the fatal phenotype in the ribonucleotide excision repair deficiency.
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Affiliation(s)
- Ayuna Takeishi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiroyuki Kogashi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Mizuki Odagiri
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto, Japan
| | - Manabu Yasui
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan
| | - Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University; Minami-ku, Hiroshima, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University; Minami-ku, Hiroshima, Japan
| | | | - Kiyoe Ura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Akira Sassa
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
- * E-mail:
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12
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Zhao L, Sumberaz P. Mitochondrial DNA Damage: Prevalence, Biological Consequence, and Emerging Pathways. Chem Res Toxicol 2020; 33:2491-2502. [PMID: 32486637 DOI: 10.1021/acs.chemrestox.0c00083] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria have a plethora of functions within a eukaryotic cell, ranging from energy production, cell signaling, and protein cofactor synthesis to various aspects of metabolism. Mitochondrial dysfunction is known to cause over 200 named disorders and has been implicated in many human diseases and aging. Mitochondria have their own genetic material, mitochondrial DNA (mtDNA), which encodes 13 protein subunits in the oxidative phosphorylation system and a full set of transfer and rRNAs. Although more than 99% of the proteins in mitochondria are nuclear DNA (nDNA)-encoded, the integrity of mtDNA is critical for mitochondrial functions, as evidenced by mitochondrial diseases sourced from mtDNA mutations and depletions and the vital role of fragmented mtDNA molecules in cell signaling pathways. Previous research has shown that mtDNA is an important target of genotoxic assaults by a variety of chemical and physical factors. This Perspective discusses the prevalence of mtDNA damage by comparing the abundance of lesions in mDNA and nDNA and summarizes current knowledge on the biological pathways to cope with mtDNA damage, including mtDNA repair, mtDNA degradation, and mitochondrial fission and fusion. Also, emerging roles of mtDNA damage in mutagenesis and immune responses are reviewed.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Philip Sumberaz
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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13
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Ghodke PP, Guengerich FP. Impact of 1, N 6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair. J Biol Chem 2020; 295:6092-6107. [PMID: 32213600 DOI: 10.1074/jbc.ra120.012829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N 6-ethenoadenosine (1,N 6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2-mediated incision. Mass spectral analysis revealed that 1,N 6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N 6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N 6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N 6-ϵrA. We also found that RNase H2 recognizes 1,N 6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N 6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N 6-ϵrA is incompletely incised by RNase H2.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37323-0146.
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Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB, Freudenthal BD. Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β. J Biol Chem 2020; 295:1613-1622. [PMID: 31892517 PMCID: PMC7008369 DOI: 10.1074/jbc.ra119.011569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/29/2019] [Indexed: 01/07/2023] Open
Abstract
During oxidative stress, inflammation, or environmental exposure, ribo- and deoxyribonucleotides are oxidatively modified. 8-Oxo-7,8-dihydro-2'-guanosine (8-oxo-G) is a common oxidized nucleobase whose deoxyribonucleotide form, 8-oxo-dGTP, has been widely studied and demonstrated to be a mutagenic substrate for DNA polymerases. Guanine ribonucleotides are analogously oxidized to r8-oxo-GTP, which can constitute up to 5% of the rGTP pool. Because ribonucleotides are commonly misinserted into DNA, and 8-oxo-G causes replication errors, we were motivated to investigate how the oxidized ribonucleotide is utilized by DNA polymerases. To do this, here we employed human DNA polymerase β (pol β) and characterized r8-oxo-GTP insertion with DNA substrates containing either a templating cytosine (nonmutagenic) or adenine (mutagenic). Our results show that pol β has a diminished catalytic efficiency for r8-oxo-GTP compared with canonical deoxyribonucleotides but that r8-oxo-GTP is inserted mutagenically at a rate similar to those of other common DNA replication errors (i.e. ribonucleotide and mismatch insertions). Using FRET assays to monitor conformational changes of pol β with r8-oxo-GTP, we demonstrate impaired pol β closure that correlates with a reduced insertion efficiency. X-ray crystallographic analyses revealed that, similar to 8-oxo-dGTP, r8-oxo-GTP adopts an anti conformation opposite a templating cytosine and a syn conformation opposite adenine. However, unlike 8-oxo-dGTP, r8-oxo-GTP did not form a planar base pair with either templating base. These results suggest that r8-oxo-GTP is a potential mutagenic substrate for DNA polymerases and provide structural insights into how r8-oxo-GTP is processed by DNA polymerases.
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Affiliation(s)
- Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Khadijeh S Alnajjar
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona 85724
| | - Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, Arizona 85724
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160.
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15
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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Pol μ ribonucleotide insertion opposite 8-oxodG facilitates the ligation of premutagenic DNA repair intermediate. Sci Rep 2020; 10:940. [PMID: 31969622 PMCID: PMC6976671 DOI: 10.1038/s41598-020-57886-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/07/2020] [Indexed: 01/05/2023] Open
Abstract
DNA polymerase (pol) μ primarily inserts ribonucleotides into a single-nucleotide gapped DNA intermediate, and the ligation step plays a critical role in the joining of noncomplementary DNA ends during nonhomologous end joining (NHEJ) for the repair of double-strand breaks (DSBs) caused by reactive oxygen species. Here, we report that the pol μ insertion products of ribonucleotides (rATP or rCTP), instead of deoxyribonucleotides, opposite 8-oxo-2′-deoxyguanosine (8-oxodG) are efficiently ligated and the presence of Mn2+ stimulates this coupled reaction in vitro. Moreover, our results point to a role of pol μ in mediating ligation during the mutagenic bypass of 8-oxodG, while 3′-preinserted noncanonical base pairs (3′-rA or 3′-rC) on NHEJ repair intermediates compromise the end joining by DNA ligase I or the DNA ligase IV/XRCC4 complex.
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Lietard J, Damha MJ, Somoza MM. Large-Scale Photolithographic Synthesis of Chimeric DNA/RNA Hairpin Microarrays To Explore Sequence Specificity Landscapes of RNase HII Cleavage. Biochemistry 2019; 58:4389-4397. [PMID: 31631649 PMCID: PMC6838787 DOI: 10.1021/acs.biochem.9b00806] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ribonuclease HII (RNase HII) is an essential endoribonuclease that binds to double-stranded DNA with RNA nucleotide incorporations and cleaves 5' of the ribonucleotide at RNA-DNA junctions. Thought to be present in all domains of life, RNase HII protects genomic integrity by initiating excision repair pathways that protect the encoded information from rapid degradation. There is sparse evidence that the enzyme cleaves some substrates better than others, but a large-scale study is missing. Such large-scale studies can be carried out on microarrays, and we employ chemical photolithography to synthesize very large combinatorial libraries of fluorescently labeled DNA/RNA chimeric sequences that self-anneal to form hairpin structures that are substrates for Escherichia coli RNase HII. The relative activity is determined by the loss of fluorescence upon cleavage. Each substrate includes a double-stranded 5 bp variable region with one to five consecutive ribonucleotide substitutions. We also examined the effect of all possible single and double mismatches, for a total of >9500 unique structures. Differences in cleavage efficiency indicate some level of substrate preference, and we identified the 5'-dC/rC-rA-dX-3' motif in well-cleaved substrates. The results significantly extend known patterns of RNase HII sequence specificity and serve as a template using large-scale photolithographic synthesis to comprehensively map landscapes of substrate specificity of nucleic acid-processing enzymes.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry , University of Vienna , Althanstraße 14 (UZA II) , 1090 Vienna , Austria
| | - Masad J Damha
- Department of Chemistry , McGill University , 801 Rue Sherbrooke Ouest , Montreal , QC H3A 0B8 , Canada
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry , University of Vienna , Althanstraße 14 (UZA II) , 1090 Vienna , Austria
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Tsegay PS, Lai Y, Liu Y. Replication Stress and Consequential Instability of the Genome and Epigenome. Molecules 2019; 24:molecules24213870. [PMID: 31717862 PMCID: PMC6864812 DOI: 10.3390/molecules24213870] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Cells must faithfully duplicate their DNA in the genome to pass their genetic information to the daughter cells. To maintain genomic stability and integrity, double-strand DNA has to be replicated in a strictly regulated manner, ensuring the accuracy of its copy number, integrity and epigenetic modifications. However, DNA is constantly under the attack of DNA damage, among which oxidative DNA damage is the one that most frequently occurs, and can alter the accuracy of DNA replication, integrity and epigenetic features, resulting in DNA replication stress and subsequent genome and epigenome instability. In this review, we summarize DNA damage-induced replication stress, the formation of DNA secondary structures, peculiar epigenetic modifications and cellular responses to the stress and their impact on the instability of the genome and epigenome mainly in eukaryotic cells.
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Affiliation(s)
- Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η. Sci Rep 2019; 9:13910. [PMID: 31558768 PMCID: PMC6763444 DOI: 10.1038/s41598-019-50421-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022] Open
Abstract
DNA polymerases often incorporate non-canonical nucleotide, i.e., ribonucleoside triphosphates into the genomic DNA. Aberrant accumulation of ribonucleotides in the genome causes various cellular abnormalities. Here, we show the possible role of human nucleotide excision repair (NER) and DNA polymerase η (Pol η) in processing of a single ribonucleotide embedded into DNA. We found that the reconstituted NER system can excise the oxidized ribonucleotide on the plasmid DNA. Taken together with the evidence that Pol η accurately bypasses a ribonucleotide, i.e., riboguanosine (rG) or its oxidized derivative (8-oxo-rG) in vitro, we further assessed the mutagenic potential of the embedded ribonucleotide in human cells lacking NER or Pol η. A single rG on the supF reporter gene predominantly induced large deletion mutations. An embedded 8-oxo-rG caused base substitution mutations at the 3′-neighboring base rather than large deletions in wild-type cells. The disruption of XPA, an essential factor for NER, or Pol η leads to the increased mutant frequency of 8-oxo-rG. Furthermore, the frequency of 8-oxo-rG-mediated large deletions was increased by the loss of Pol η, but not XPA. Collectively, our results suggest that base oxidation of the embedded ribonucleotide enables processing of the ribonucleotide via alternative DNA repair and damage tolerance pathways.
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Malfatti MC, Henneke G, Balachander S, Koh KD, Newnam G, Uehara R, Crouch RJ, Storici F, Tell G. Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA. J Biol Chem 2019; 294:13061-13072. [PMID: 31300556 DOI: 10.1074/jbc.ra119.009493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 RNase H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damage, that is, ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus abyssi and the bacterium Escherichia coli, examining their ability to process damaged rNMPs embedded in DNA in vitro We found that E. coli RNase HII cleaves both rAP and oxidized rNMP sites. In contrast, like the eukaryotic RNase H2, P. abyssi RNase HII did not display any rAP or oxidized rNMP incision activities, even though it recognized them. Notably, the archaeal enzyme was also inactive on a mismatched rNMP, whereas the E. coli enzyme displayed a strong preference for the mispaired rNMP over the paired rNMP in DNA. On the basis of our biochemical findings and also structural modeling analyses of RNase HII/2 proteins from organisms belonging to all three domains of life, we propose that RNases HII/2's dual roles in ribonucleotide excision repair and RNA/DNA hydrolysis result in limited acceptance of modified rNMPs embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Ryo Uehara
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy.
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