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Maslowska KH, Makiela‐Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:368-384. [PMID: 30447030 PMCID: PMC6590174 DOI: 10.1002/em.22267] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Katarzyna H. Maslowska
- Cancer Research Center of Marseille, CNRS, UMR7258Inserm, U1068; Institut Paoli‐Calmettes, Aix‐Marseille UniversityMarseilleFrance
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | | | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
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102
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Roles of Bacillus subtilis RecA, Nucleotide Excision Repair, and Translesion Synthesis Polymerases in Counteracting Cr(VI)-Promoted DNA Damage. J Bacteriol 2019; 201:JB.00073-19. [PMID: 30745368 DOI: 10.1128/jb.00073-19] [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: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 11/20/2022] Open
Abstract
Bacteria deploy global programs of gene expression, including components of the SOS response, to counteract the cytotoxic and genotoxic effects of environmental DNA-damaging factors. Here we report that genetic damage promoted by hexavalent chromium elicited the SOS response in Bacillus subtilis, as evidenced by the induction of transcriptional uvrA-lacZ, recA-lacZ, and P recA-gfp fusions. Accordingly, B. subtilis strains deficient in homologous recombination (RecA) and nucleotide excision repair (NER) (UvrA), components of the SOS response, were significantly more sensitive to Cr(VI) treatment than were cells of the wild-type strain. These results strongly suggest that Cr(VI) induces the formation in growing B. subtilis cells of cytotoxic and genotoxic bulky DNA lesions that are processed by RecA and/or the NER pathways. In agreement with this notion, Cr(VI) significantly increased the formation of DNA-protein cross-links (DPCs) and induced mutagenesis in recA- and uvrA-deficient B. subtilis strains, through a pathway that required YqjH/YqjW-mediated translesion synthesis. We conclude that Cr(VI) promotes mutagenesis and cell death in B. subtilis by a mechanism that involves the formation of DPCs and that such deleterious effects are counteracted by both the NER and homologous recombination pathways, belonging to the RecA-dependent SOS system.IMPORTANCE It has been shown that, following permeation of cell barriers, Cr(VI) kills B. subtilis cells following a mechanism of reactive oxygen species-promoted DNA damage, which is counteracted by the guanine oxidized repair system. Here we report a distinct mechanism of Cr(VI)-promoted DNA damage that involves production of DPCs capable of eliciting the bacterial SOS response. We also report that the NER and homologous recombination (RecA) repair pathways, as well as low-fidelity DNA polymerases, counteract this metal-induced mechanism of killing in B. subtilis Hence, our results contribute to an understanding of how environmental pollutants activate global programs of gene expression that allow bacteria to contend with the cytotoxic and genotoxic effects of heavy metals.
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103
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Romero H, Torres R, Hernández-Tamayo R, Carrasco B, Ayora S, Graumann PL, Alonso JC. Bacillus subtilis RarA acts at the interplay between replication and repair-by-recombination. DNA Repair (Amst) 2019; 78:27-36. [PMID: 30954900 DOI: 10.1016/j.dnarep.2019.03.010] [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: 04/19/2018] [Revised: 02/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Bacterial RarA is thought to play crucial roles in the cellular response to blocked replication forks. We show that lack of Bacillus subtilis RarA renders cells very sensitive to H2O2, but not to methyl methane sulfonate or 4-nitroquinoline-1-oxide. RarA is epistatic to RecA in response to DNA damage. Inactivation of rarA partially suppressed the DNA repair defect of mutants lacking translesion synthesis polymerases. RarA may contribute to error-prone DNA repair as judged by the reduced frequency of rifampicin-resistant mutants in ΔrarA and in ΔpolY1 ΔrarA cells. The absence of RarA strongly reduced the viability of dnaD23ts and dnaB37ts cells upon partial thermal inactivation, suggesting that ΔrarA cells are deficient in replication fork assembly. A ΔrarA mutation also partially reduced the viability of dnaC30ts and dnaX51ts cells and slightly improved the viability of dnaG40ts cells at semi-permissive temperature. These results suggest that RarA links re-initiation of DNA replication with repair-by-recombination by controlling the access of the replication machinery to a collapsed replication fork.
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Affiliation(s)
- Hector Romero
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain; SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain.
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104
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McIntyre J, Sobolewska A, Fedorowicz M, McLenigan MP, Macias M, Woodgate R, Sledziewska-Gojska E. DNA polymerase ι is acetylated in response to S N2 alkylating agents. Sci Rep 2019; 9:4789. [PMID: 30886224 PMCID: PMC6423139 DOI: 10.1038/s41598-019-41249-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/04/2019] [Indexed: 02/07/2023] Open
Abstract
DNA polymerase iota (Polι) belongs to the Y-family of DNA polymerases that are involved in DNA damage tolerance through their role in translesion DNA synthesis. Like all other Y-family polymerases, Polι interacts with proliferating cell nuclear antigen (PCNA), Rev1, ubiquitin and ubiquitinated-PCNA and is also ubiquitinated itself. Here, we report that Polι also interacts with the p300 acetyltransferase and is acetylated. The primary acetylation site is K550, located in the Rev1-interacting region. However, K550 amino acid substitutions have no effect on Polι's ability to interact with Rev1. Interestingly, we find that acetylation of Polι significantly and specifically increases in response to SN2 alkylating agents and to a lower extent to SN1 alkylating and oxidative agents. As we have not observed acetylation of Polι's closest paralogue, DNA polymerase eta (Polη), with which Polι shares many functional similarities, we believe that this modification might exclusively regulate yet to be determined, and separate function(s) of Polι.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Aleksandra Sobolewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Mikolaj Fedorowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Mary P McLenigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892-3371, USA
| | - Matylda Macias
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892-3371, USA
| | - Ewa Sledziewska-Gojska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106, Warsaw, Poland
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105
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Su Y, Ghodke PP, Egli M, Li L, Wang Y, Guengerich FP. Human DNA polymerase η has reverse transcriptase activity in cellular environments. J Biol Chem 2019; 294:6073-6081. [PMID: 30842261 DOI: 10.1074/jbc.ra119.007925] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Indexed: 12/24/2022] Open
Abstract
Classical DNA and RNA polymerase (pol) enzymes have defined roles with their respective substrates, but several pols have been found to have multiple functions. We reported previously that purified human DNA pol η (hpol η) can incorporate both deoxyribonucleoside triphosphates (dNTPs) and ribonucleoside triphosphates (rNTPs) and can use both DNA and RNA as substrates. X-ray crystal structures revealed that two pol η residues, Phe-18 and Tyr-92, behave as steric gates to influence sugar selectivity. However, the physiological relevance of these phenomena has not been established. Here, we show that purified hpol η adds rNTPs to DNA primers at physiological rNTP concentrations and in the presence of competing dNTPs. When two rATPs were inserted opposite a cyclobutane pyrimidine dimer, the substrate was less efficiently cleaved by human RNase H2. Human XP-V fibroblast extracts, devoid of hpol η, could not add rNTPs to a DNA primer, but the expression of transfected hpol η in the cells restored this ability. XP-V cell extracts did not add dNTPs to DNA primers hybridized to RNA, but could when hpol η was expressed in the cells. HEK293T cell extracts could add dNTPs to DNA primers hybridized to RNA, but lost this ability if hpol η was deleted. Interestingly, a similar phenomenon was not observed when other translesion synthesis (TLS) DNA polymerases-hpol ι, κ, or ζ-were individually deleted. These results suggest that hpol η is one of the major reverse transcriptases involved in physiological processes in human cells.
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Affiliation(s)
- Yan Su
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Pratibha P Ghodke
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Lin Li
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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106
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Wu B, Wang H, Zhang L, Sun C, Li H, Jiang C, Liu X. High expression of RAD18 in glioma induces radiotherapy resistance via down-regulating P53 expression. Biomed Pharmacother 2019; 112:108555. [PMID: 30798132 DOI: 10.1016/j.biopha.2019.01.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 01/04/2019] [Accepted: 01/06/2019] [Indexed: 12/14/2022] Open
Abstract
As a key regulator of DNA translesion synthesis (TLS) pathway, RAD18 is reported to be abnormally expressed in many kinds of cancers. In glioma, RAD18 was overexpressed in the primary and recurrent glioblastoma multiforme specimens, and its overexpression weakened ionizing radiation-induced apoptosis in glioma A172 cells. Moreover, A172 cells with mutational P53 also showed enhanced radiation resistance. And RAD18 activation induced by cyclin-dependent kinase 2 (CDK2) was repressed by P53. However, whether P53 involves in RAD18-induced radiation resistance remains unknown. Therefore, this study was conducted to explore the effects and mechanism of RAD18 in the radiation resistance of glioma and study P53 role in this process. Results showed that, RAD18 expression was obviously elevated in glioma tissues and cell lines such as U251, SHG-44, A172, U-87 MG and U-118 MG as compared with the normal brain tissues and neuroglia cells. Up-regulation of RAD18 in U-118 MG and A172 cells with lentivirus infection significantly increased cell growth and inhibited cell apoptosis, determined by CCK-8 and flow cytometry technologies. Besides, RAD18 overexpression enhanced cell growth and inhibited cell apoptosis after U-118 MG or A172 cells were irradiated at a dose of 4 Gy. On the contrary, silencing of endogenous RAD18 sensitized U-118 MG and A172 cells to radiation. Moreover, RAD18 and P53 proteins were co-located in the nucleus, and up-regulation of RAD18 decreased the expression of P53 protein and facilitated its nuclear export. Furthermore, cell growth promotion and cell apoptosis inhibition induced by RAD18 up-regulation were impaired when P53 expression was up-regulated under radiation condition. In a word, this study clarifies that RAD18 functions as a promoter in glioma progression and reduces glioma cells' sensibility to radiation through down-regulating P53, which provides new strategies to overcome the radiation resistance in glioma.
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Affiliation(s)
- Bing Wu
- NHC Key Lab of Radiobiology, Jilin University, Changchun, Jilin 130021, China; Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, China
| | - Heyuan Wang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, China; Department of Immunology in College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Lenign Zhang
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, China
| | - Chenglin Sun
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, China
| | - Hang Li
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, China
| | - Chunyan Jiang
- Key Laboratory of Hormones and Development (Ministry of Health), Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin 300070, China
| | - Xiaodong Liu
- NHC Key Lab of Radiobiology, Jilin University, Changchun, Jilin 130021, China; School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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107
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Muenter MM, Aiken A, Akanji JO, Baig S, Bellou S, Carlson A, Conway C, Cowell CM, DeLateur NA, Hester A, Joshi C, Kramer C, Leifer BS, Nash E, Qi MH, Travers M, Wong KC, Hu M, Gou N, Giese RW, Gu AZ, Beuning PJ. The response of Escherichia coli to the alkylating agents chloroacetaldehyde and styrene oxide. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 840:1-10. [PMID: 30857727 DOI: 10.1016/j.mrgentox.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
DNA damage is ubiquitous and can arise from endogenous or exogenous sources. DNA-damaging alkylating agents are present in environmental toxicants as well as in cancer chemotherapy drugs and are a constant threat, which can lead to mutations or cell death. All organisms have multiple DNA repair and DNA damage tolerance pathways to resist the potentially negative effects of exposure to alkylating agents. In bacteria, many of the genes in these pathways are regulated as part of the SOS reponse or the adaptive response. In this work, we probed the cellular responses to the alkylating agents chloroacetaldehyde (CAA), which is a metabolite of 1,2-dichloroethane used to produce polyvinyl chloride, and styrene oxide (SO), a major metabolite of styrene used in the production of polystyrene and other polymers. Vinyl chloride and styrene are produced on an industrial scale of billions of kilograms annually and thus have a high potential for environmental exposure. To identify stress response genes in E. coli that are responsible for tolerance to the reactive metabolites CAA and SO, we used libraries of transcriptional reporters and gene deletion strains. In response to both alkylating agents, genes associated with several different stress pathways were upregulated, including protein, membrane, and oxidative stress, as well as DNA damage. E. coli strains lacking genes involved in base excision repair and nucleotide excision repair were sensitive to SO, whereas strains lacking recA and the SOS gene ybfE were sensitive to both alkylating agents tested. This work indicates the varied systems involved in cellular responses to alkylating agents, and highlights the specific DNA repair genes involved in the responses.
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Affiliation(s)
- Mark M Muenter
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Ariel Aiken
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Jadesola O Akanji
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Samir Baig
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Sirine Bellou
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alyssa Carlson
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Charles Conway
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Courtney M Cowell
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Nicholas A DeLateur
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alexis Hester
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Christopher Joshi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Caitlin Kramer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Becky S Leifer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Emma Nash
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Macee H Qi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Meghan Travers
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Kelly C Wong
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Man Hu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA
| | - Na Gou
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115 USA
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Penny J Beuning
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA.
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108
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Jaszczur MM, Vo DD, Stanciauskas R, Bertram JG, Sikand A, Cox MM, Woodgate R, Mak CH, Pinaud F, Goodman MF. Conformational regulation of Escherichia coli DNA polymerase V by RecA and ATP. PLoS Genet 2019; 15:e1007956. [PMID: 30716079 PMCID: PMC6375631 DOI: 10.1371/journal.pgen.1007956] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 02/14/2019] [Accepted: 01/11/2019] [Indexed: 12/27/2022] Open
Abstract
Mutagenic translesion DNA polymerase V (UmuD'2C) is induced as part of the DNA damage-induced SOS response in Escherichia coli, and is subjected to multiple levels of regulation. The UmuC subunit is sequestered on the cell membrane (spatial regulation) and enters the cytosol after forming a UmuD'2C complex, ~ 45 min post-SOS induction (temporal regulation). However, DNA binding and synthesis cannot occur until pol V interacts with a RecA nucleoprotein filament (RecA*) and ATP to form a mutasome complex, pol V Mut = UmuD'2C-RecA-ATP. The location of RecA relative to UmuC determines whether pol V Mut is catalytically on or off (conformational regulation). Here, we present three interrelated experiments to address the biochemical basis of conformational regulation. We first investigate dynamic deactivation during DNA synthesis and static deactivation in the absence of DNA synthesis. Single-molecule (sm) TIRF-FRET microscopy is then used to explore multiple aspects of pol V Mut dynamics. Binding of ATP/ATPγS triggers a conformational switch that reorients RecA relative to UmuC to activate pol V Mut. This process is required for polymerase-DNA binding and synthesis. Both dynamic and static deactivation processes are governed by temperature and time, in which on → off switching is "rapid" at 37°C (~ 1 to 1.5 h), "slow" at 30°C (~ 3 to 4 h) and does not require ATP hydrolysis. Pol V Mut retains RecA in activated and deactivated states, but binding to primer-template (p/t) DNA occurs only when activated. Studies are performed with two forms of the polymerase, pol V Mut-RecA wt, and the constitutively induced and hypermutagenic pol V Mut-RecA E38K/ΔC17. We discuss conformational regulation of pol V Mut, determined from biochemical analysis in vitro, in relation to the properties of pol V Mut in RecA wild-type and SOS constitutive genetic backgrounds in vivo.
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Affiliation(s)
- Malgorzata M. Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Dan D. Vo
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Ramunas Stanciauskas
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Jeffrey G. Bertram
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Adhirath Sikand
- Department of Chemistry, University of Southern California, Los Angeles, California, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi H. Mak
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Chemistry, University of Southern California, Los Angeles, California, United States of America
- Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Fabien Pinaud
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Chemistry, University of Southern California, Los Angeles, California, United States of America
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Chemistry, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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109
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Yatagai F, Honma M, Dohmae N, Ishioka N. Biological effects of space environmental factors: A possible interaction between space radiation and microgravity. LIFE SCIENCES IN SPACE RESEARCH 2019; 20:113-123. [PMID: 30797428 DOI: 10.1016/j.lssr.2018.10.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/27/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
In the mid-1980s, space experiments began to examine if microgravity could alter the biological effects of space radiation. In the late 1990s, repair of DNA strand breaks was reported to not be influenced by microgravity using the pre-irradiated cells, because the exposure doses of space radiation were few due to the short spaceflight. There were, however, conflicting reports depending on the biological endpoints used in various systems. While almost no attempts were made to assess the possibility that the microgravity effects could be altered by space radiation. This was probably due to the general understanding that microgravity plays a major role in space and works independently from space radiation. Recent ground-based simulation studies focusing on DNA oxidative damage and signal transduction suggested that combined effects of microgravity and space radiation might exist. These studies also implicated the importance of research focusing not only on chromosomal DNA but also on cytoplasm, especially mitochondria. Therefore, we propose a new model which accounts for the combined-effects through the window of cellular responses. In this model, the interactions between microgravity and space radiation might occur during the following cellular-responses; (A) damaging and signaling by ROS, (B) damage responses on DNA (repair, replication, transcription, etc.), and (C) expression of gene and protein (regulation by chromatin, epigenetic control, etc.).
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Affiliation(s)
- Fumio Yatagai
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Center for Sustainable Resource Science, The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
| | - Masamitsu Honma
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Naoshi Dohmae
- Center for Sustainable Resource Science, The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Noriaki Ishioka
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Department of Space and Astronautical Science, The Graduate University for Advanced Studies, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan
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110
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Suan Lim K, Li H, Roberts EA, Gaudiano EF, Clairmont C, Sambel L, Ponnienselvan K, Liu JC, Yang C, Kozono D, Parmar K, Yusufzai T, Zheng N, D’Andrea AD. USP1 Is Required for Replication Fork Protection in BRCA1-Deficient Tumors. Mol Cell 2018; 72:925-941.e4. [PMID: 30576655 PMCID: PMC6390489 DOI: 10.1016/j.molcel.2018.10.045] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/23/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
BRCA1-deficient tumor cells have defects in homologous-recombination repair and replication fork stability, resulting in PARP inhibitor sensitivity. Here, we demonstrate that a deubiquitinase, USP1, is upregulated in tumors with mutations in BRCA1. Knockdown or inhibition of USP1 resulted in replication fork destabilization and decreased viability of BRCA1-deficient cells, revealing a synthetic lethal relationship. USP1 binds to and is stimulated by fork DNA. A truncated form of USP1, lacking its DNA-binding region, was not stimulated by DNA and failed to localize and protect replication forks. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of cell death in the absence of USP1. Taken together, USP1 exhibits DNA-mediated activation at the replication fork, protects the fork, and promotes survival in BRCA1-deficient cells. Inhibition of USP1 may be a useful treatment for a subset of PARP-inhibitor-resistant BRCA1-deficient tumors with acquired replication fork stabilization.
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Affiliation(s)
- Kah Suan Lim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Heng Li
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Emma A. Roberts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Emily F. Gaudiano
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Jessica C. Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Chunyu Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA,Howard Hughes Medical Institute, Box 357280, Seattle, WA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
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111
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Acharya N, Manohar K, Peroumal D, Khandagale P, Patel SK, Sahu SR, Kumari P. Multifaceted activities of DNA polymerase η: beyond translesion DNA synthesis. Curr Genet 2018; 65:649-656. [PMID: 30535880 DOI: 10.1007/s00294-018-0918-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
DNA polymerases are evolved to extend the 3'-OH of a growing primer annealed to a template DNA substrate. Since replicative DNA polymerases have a limited role while replicating structurally distorted template, translesion DNA polymerases mostly from Y-family come to the rescue of stalled replication fork and maintain genome stability. DNA polymerase eta is one such specialized enzyme whose function is directly associated with casual development of certain skin cancers and chemo-resistance. More than 20 years of extensive studies are available to support TLS activities of Polη in bypassing various DNA lesions, in addition, limited but crucial growing evidence also exist to suggest Polη possessing TLS-independent cellular functions. In this review, we have mostly focused on non-TLS activities of Polη from different organisms including our recent findings from pathogenic yeast Candida albicans.
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Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
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112
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Raychaudhury P, Marians KJ. The recombination mediator proteins RecFOR maintain RecA* levels for maximal DNA polymerase V Mut activity. J Biol Chem 2018; 294:852-860. [PMID: 30482842 DOI: 10.1074/jbc.ra118.005726] [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: 09/05/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
DNA template damage can potentially block DNA replication. Cells have therefore developed different strategies to repair template lesions. Activation of the bacterial lesion bypass DNA polymerase V (Pol V) requires both the cleavage of the UmuD subunit to UmuD' and the acquisition of a monomer of activated RecA recombinase, forming Pol V Mut. Both of these events are mediated by the generation of RecA* via the formation of a RecA-ssDNA filament during the SOS response. Formation of RecA* is itself modulated by competition with the ssDNA-binding protein (SSB) for binding to ssDNA. Previous observations have demonstrated that RecA filament formation on SSB-coated DNA can be favored in the presence of the recombination mediator proteins RecF, RecO, and RecR. We show here using purified proteins that in the presence of SSB and RecA, a stable RecA-ssDNA filament is not formed, although sufficient RecA* is generated to support some activation of Pol V. The presence of RecFOR increased RecA* generation and allowed Pol V to synthesize longer DNA products and to elongate from an unpaired primer terminus opposite template damage, also without the generation of a stable RecA-ssDNA filament.
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Affiliation(s)
- Paromita Raychaudhury
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kenneth J Marians
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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113
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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114
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Manic G, Sistigu A, Corradi F, Musella M, De Maria R, Vitale I. Replication stress response in cancer stem cells as a target for chemotherapy. Semin Cancer Biol 2018; 53:31-41. [PMID: 30081229 DOI: 10.1016/j.semcancer.2018.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 02/08/2023]
Abstract
Cancer stem cells (CSCs) are subpopulations of multipotent stem cells (SCs) responsible for the initiation, long-term clonal maintenance, growth and spreading of most human neoplasms. Reportedly, CSCs share a very robust DNA damage response (DDR) with embryonic and adult SCs, which allows them to survive endogenous and exogenous genotoxins. A range of experimental evidence indicates that CSCs have high but heterogeneous levels of replication stress (RS), arising from, and being boosted by, endogenous causes, such as specific genetic backgrounds (e.g., p53 deficiency) and/or aberrant karyotypes (e.g., supernumerary chromosomes). A multipronged RS response (RSR) is put in place by CSCs to limit and ensure tolerability to RS. The characteristics of such dedicated cascade have two opposite consequences, both relevant for cancer therapy. On the one hand, RSR efficiency often increases the reliance of CSCs on specific DDR components. On the other hand, the functional redundancy of pathways of the RSR can paradoxically promote the acquisition of resistance to RS- and/or DNA damage-inducing agents. Here, we provide an overview of the molecular mechanisms of the RSR in cancer cells and CSCs, focusing on the role of CHK1 and some emerging players, such as PARP1 and components of the homologous recombination repair, whose targeting can represent a long-term effective anti-CSC strategy.
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Affiliation(s)
- Gwenola Manic
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy.
| | - Antonella Sistigu
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Institute of General Pathology, Catholic University and Gemelli Polyclinic, Rome, Italy
| | - Francesca Corradi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Martina Musella
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Department of Molecular Medicine, University "La Sapienza", Rome, Italy
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University and Gemelli Polyclinic, Rome, Italy.
| | - Ilio Vitale
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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115
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Peddu C, Zhang S, Zhao H, Wong A, Lee EYC, Lee MYWT, Zhang Z. Phosphorylation Alters the Properties of Pol η: Implications for Translesion Synthesis. iScience 2018; 6:52-67. [PMID: 30240625 PMCID: PMC6137289 DOI: 10.1016/j.isci.2018.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/26/2018] [Accepted: 07/13/2018] [Indexed: 12/28/2022] Open
Abstract
There are significant ambiguities regarding how DNA polymerase η is recruited to DNA lesion sites in stressed cells while avoiding normal replication forks in non-stressed cells. Even less is known about the mechanisms responsible for Pol η-induced mutations in cancer genomes. We show that there are two safeguards to prevent Pol η from adventitious participation in normal DNA replication. These include sequestration by a partner protein and low basal activity. Upon cellular UV irradiation, phosphorylation enables Pol η to be released from sequestration by PDIP38 and activates its polymerase function through increased affinity toward monoubiquitinated proliferating cell nuclear antigen (Ub-PCNA). Moreover, the high-affinity binding of phosphorylated Pol η to Ub-PCNA limits its subsequent displacement by Pol δ. Consequently, activated Pol η replicates DNA beyond the lesion site and potentially introduces clusters of mutations due to its low fidelity. This mechanism could account for the prevalence of Pol η signatures in cancer genome. Pol η activation requires both ATR and PKC phosphorylation Phosphorylation directly enhances the affinity of Pol η toward Ub-PCNA PDIP38 sequesters Pol η away from normal replication fork Pol δ is not able to displace phosphorylated Pol η from Ub-PCNA complex
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Affiliation(s)
- Chandana Peddu
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Hong Zhao
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA
| | - Agnes Wong
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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116
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Abstract
Accurate transmission of the genetic information requires complete duplication of the chromosomal DNA each cell division cycle. However, the idea that replication forks would form at origins of DNA replication and proceed without impairment to copy the chromosomes has proven naive. It is now clear that replication forks stall frequently as a result of encounters between the replication machinery and template damage, slow-moving or paused transcription complexes, unrelieved positive superhelical tension, covalent protein-DNA complexes, and as a result of cellular stress responses. These stalled forks are a major source of genome instability. The cell has developed many strategies for ensuring that these obstructions to DNA replication do not result in loss of genetic information, including DNA damage tolerance mechanisms such as lesion skipping, whereby the replisome jumps the lesion and continues downstream; template switching both behind template damage and at the stalled fork; and the error-prone pathway of translesion synthesis.
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Affiliation(s)
- Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
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117
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Specialised DNA polymerases in Escherichia coli: roles within multiple pathways. Curr Genet 2018; 64:1189-1196. [PMID: 29700578 DOI: 10.1007/s00294-018-0840-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 01/15/2023]
Abstract
In many bacterial species, DNA damage triggers the SOS response; a pathway that regulates the production of DNA repair and damage tolerance proteins, including error-prone DNA polymerases. These specialised polymerases are capable of bypassing lesions in the template DNA, a process known as translesion synthesis (TLS). Specificity for lesion types varies considerably between the different types of TLS polymerases. TLS polymerases are mainly described as working in the context of replisomes that are stalled at lesions or in lesion-containing gaps left behind the replisome. Recently, a series of single-molecule fluorescence microscopy studies have revealed that two TLS polymerases, pol IV and pol V, rarely colocalise with replisomes in Escherichia coli cells, suggesting that most TLS activity happens in a non-replisomal context. In this review, we re-visit the evidence for the involvement of TLS polymerases in other pathways. A series of genetic and biochemical studies indicates that TLS polymerases could participate in nucleotide excision repair, homologous recombination and transcription. In addition, oxidation of the nucleotide pool, which is known to be induced by multiple stressors, including many antibiotics, appears to favour TLS polymerase activity and thus increases mutation rates. Ultimately, participation of TLS polymerases within non-replisomal pathways may represent a major source of mutations in bacterial cells and calls for more extensive investigation.
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118
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Genome instability syndromes caused by impaired DNA repair and aberrant DNA damage responses. Cell Biol Toxicol 2018; 34:337-350. [DOI: 10.1007/s10565-018-9429-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/25/2018] [Indexed: 11/25/2022]
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119
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High-accuracy lagging-strand DNA replication mediated by DNA polymerase dissociation. Proc Natl Acad Sci U S A 2018; 115:4212-4217. [PMID: 29610333 DOI: 10.1073/pnas.1720353115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The fidelity of DNA replication is a critical factor in the rate at which cells incur mutations. Due to the antiparallel orientation of the two chromosomal DNA strands, one strand (leading strand) is replicated in a mostly processive manner, while the other (lagging strand) is synthesized in short sections called Okazaki fragments. A fundamental question that remains to be answered is whether the two strands are copied with the same intrinsic fidelity. In most experimental systems, this question is difficult to answer, as the replication complex contains a different DNA polymerase for each strand, such as, for example, DNA polymerases δ and ε in eukaryotes. Here we have investigated this question in the bacterium Escherichia coli, in which the replicase (DNA polymerase III holoenzyme) contains two copies of the same polymerase (Pol III, the dnaE gene product), and hence the two strands are copied by the same polymerase. Our in vivo mutagenesis data indicate that the two DNA strands are not copied with the same accuracy, and that, remarkably, the lagging strand has the highest fidelity. We postulate that this effect results from the greater dissociative character of the lagging-strand polymerase, which provides additional options for error removal. Our conclusion is strongly supported by results with dnaE antimutator polymerases characterized by increased dissociation rates.
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120
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Coordinated Activity of Y Family TLS Polymerases and EXO1 Protects Non-S Phase Cells from UV-Induced Cytotoxic Lesions. Mol Cell 2018; 70:34-47.e4. [PMID: 29551515 DOI: 10.1016/j.molcel.2018.02.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/18/2017] [Accepted: 02/08/2018] [Indexed: 11/23/2022]
Abstract
UV-induced photoproducts are responsible for the pathological effects of sunlight. Mutations in nucleotide excision repair (NER) cause severe pathologies characterized by sunlight sensitivity, coupled to elevated predisposition to cancer and/or neurological dysfunctions. We have previously shown that in UV-irradiated non-cycling cells, only a particular subset of lesions activates the DNA damage response (DDR), and this requires NER and EXO1 activities. To define the molecular mechanism acting at these lesions, we demonstrate that Y family TLS polymerases are recruited at NER- and EXO1-positive lesion sites in non-S phase cells. The coordinated action of EXO1 and Y family TLS polymerases promotes checkpoint activation, leads to lesion repair, and is crucial to prevent cytotoxic double-strand break (DSB) formation.
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121
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Cortese F, Klokov D, Osipov A, Stefaniak J, Moskalev A, Schastnaya J, Cantor C, Aliper A, Mamoshina P, Ushakov I, Sapetsky A, Vanhaelen Q, Alchinova I, Karganov M, Kovalchuk O, Wilkins R, Shtemberg A, Moreels M, Baatout S, Izumchenko E, de Magalhães JP, Artemov AV, Costes SV, Beheshti A, Mao XW, Pecaut MJ, Kaminskiy D, Ozerov IV, Scheibye-Knudsen M, Zhavoronkov A. Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization. Oncotarget 2018; 9:14692-14722. [PMID: 29581875 PMCID: PMC5865701 DOI: 10.18632/oncotarget.24461] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/31/2018] [Indexed: 12/12/2022] Open
Abstract
While many efforts have been made to pave the way toward human space colonization, little consideration has been given to the methods of protecting spacefarers against harsh cosmic and local radioactive environments and the high costs associated with protection from the deleterious physiological effects of exposure to high-Linear energy transfer (high-LET) radiation. Herein, we lay the foundations of a roadmap toward enhancing human radioresistance for the purposes of deep space colonization and exploration. We outline future research directions toward the goal of enhancing human radioresistance, including upregulation of endogenous repair and radioprotective mechanisms, possible leeways into gene therapy in order to enhance radioresistance via the translation of exogenous and engineered DNA repair and radioprotective mechanisms, the substitution of organic molecules with fortified isoforms, and methods of slowing metabolic activity while preserving cognitive function. We conclude by presenting the known associations between radioresistance and longevity, and articulating the position that enhancing human radioresistance is likely to extend the healthspan of human spacefarers as well.
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Affiliation(s)
- Franco Cortese
- Biogerontology Research Foundation, London, UK
- Department of Biomedical and Molecular Sciences, Queen's University School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Dmitry Klokov
- Canadian Nuclear Laboratories, Chalk River, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andreyan Osipov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Jakub Stefaniak
- Biogerontology Research Foundation, London, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Alexey Moskalev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - Jane Schastnaya
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | - Charles Cantor
- Boston University, Department of Biomedical Engineering, Boston, MA, USA
| | - Alexander Aliper
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- Laboratory of Bioinformatics, D. Rogachev Federal Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Polina Mamoshina
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- Computer Science Department, University of Oxford, Oxford, UK
| | - Igor Ushakov
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - Alex Sapetsky
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - Quentin Vanhaelen
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | - Irina Alchinova
- Laboratory of Physicochemical and Ecological Pathophysiology, Institute of General Pathology and Pathophysiology, Moscow, Russia
- Research Institute for Space Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Mikhail Karganov
- Laboratory of Physicochemical and Ecological Pathophysiology, Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - Olga Kovalchuk
- Canada Cancer and Aging Research Laboratories, Ltd., Lethbridge, Alberta, Canada
- University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ruth Wilkins
- Environmental and Radiation and Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Andrey Shtemberg
- Laboratory of Extreme Physiology, Institute of Medical and Biological Problems RAS, Moscow, Russia
| | - Marjan Moreels
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre, (SCK·CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre, (SCK·CEN), Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Evgeny Izumchenko
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- The Johns Hopkins University, School of Medicine, Department of Otolaryngology, Head and Neck Cancer Research, Baltimore, MD, USA
| | - João Pedro de Magalhães
- Biogerontology Research Foundation, London, UK
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Artem V. Artemov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | | | - Afshin Beheshti
- Wyle Laboratories, Space Biosciences Division, NASA Ames Research Center, Mountain View, CA, USA
- Division of Hematology/Oncology, Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - Xiao Wen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, USA
| | - Michael J. Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, USA
| | - Dmitry Kaminskiy
- Biogerontology Research Foundation, London, UK
- Deep Knowledge Life Sciences, London, UK
| | - Ivan V. Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | | | - Alex Zhavoronkov
- Biogerontology Research Foundation, London, UK
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
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122
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Zou S, Yang J, Guo J, Su Y, He C, Wu J, Yu L, Ding WQ, Zhou J. RAD18 promotes the migration and invasion of esophageal squamous cell cancer via the JNK-MMPs pathway. Cancer Lett 2018; 417:65-74. [DOI: 10.1016/j.canlet.2017.12.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/04/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
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123
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Henrikus SS, Wood EA, McDonald JP, Cox MM, Woodgate R, Goodman MF, van Oijen AM, Robinson A. DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli. PLoS Genet 2018; 14:e1007161. [PMID: 29351274 PMCID: PMC5792023 DOI: 10.1371/journal.pgen.1007161] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/31/2018] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5–10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90–180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites. Translesion DNA polymerases play a critical role in DNA damage tolerance in all cells. In Escherichia coli, the translesion polymerases include DNA polymerases II, IV, and V. At stalled replication forks, DNA polymerase IV is thought to compete with, and perhaps displace the polymerizing subunits of DNA polymerase III to facilitate translesion replication. The results of the current fluorescence microscopy study challenge that view. The results indicate that DNA polymerase IV acts predominantly at sites away from the replisome. These sites may include recombination intermediates, stalled transcription complexes, and single-stranded gaps left in the wake of DNA polymerase III replisomes that re-initiate replication downstream of a lesion.
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Affiliation(s)
- Sarah S. Henrikus
- School of Chemistry, University of Wollongong, Wollongong, Australia
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John P. McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | | | - Andrew Robinson
- School of Chemistry, University of Wollongong, Wollongong, Australia
- * E-mail:
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Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage. Nat Commun 2017; 8:2170. [PMID: 29255195 PMCID: PMC5735139 DOI: 10.1038/s41467-017-02333-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023] Open
Abstract
Unrepaired DNA lesions are a potent block to replication, leading to replication fork collapse, double-strand DNA breaks, and cell death. Error-prone polymerases overcome this blockade by synthesizing past DNA lesions in a process called translesion synthesis (TLS), but how TLS polymerases gain access to the DNA template remains poorly understood. In this study, we use particle-tracking PALM to image live Escherichia coli cells containing a functional fusion of the endogenous copy of Pol IV to the photoactivatable fluorescent protein PAmCherry. We find that Pol IV is strongly enriched near sites of replication only upon DNA damage. Surprisingly, we find that the mechanism of Pol IV recruitment is dependent on the type of DNA lesion, and that interactions with proteins other than the processivity factor β play a role under certain conditions. Collectively, these results suggest that multiple interactions, influenced by lesion identity, recruit Pol IV to sites of DNA damage. Translesion synthesis (TLS) enables cells to tolerate damaged DNA encountered during replication. Here the authors use super-resolution photoactivation localization microscopy to reveal a lesion type dependent mechanism of recruitment of the TLS polymerase Pol IV following DNA damage.
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125
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Lada AG, Stepchenkova EI, Zhuk AS, Kliver SF, Rogozin IB, Polev DE, Dhar A, Pavlov YI. Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases. Front Genet 2017; 8:202. [PMID: 29312434 PMCID: PMC5733079 DOI: 10.3389/fgene.2017.00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
DNA editing deaminases (APOBECs) are implicated in generation of mutations in somatic cells during tumorigenesis. APOBEC-dependent mutagenesis is thought to occur during transient exposure of unprotected single-stranded DNA. Mutations frequently occur in clusters (kataegis). We investigated mechanisms of mutant generation in growing and resting diploid yeast expressing APOBEC from sea lamprey, PmCDA1, whose kataegistic effect was previously shown to be associated with transcription. We have found that the frequency of canavanine-resistant mutants kept raising after growth cessation, while the profile of transcription remained unchanged. Surprisingly, the overall number of mutations in the genomes did not elevate in resting cells. Thus, mutations were accumulated during vigorous growth stage with both intense replication and transcription. We found that the elevated recovery of can1 mutant clones in non-growing cells is the result of loss of heterozygosity (LOH) leading to clusters of homozygous mutations in the chromosomal regions distal to the reporter gene. We confirmed that recombination frequency in resting cells was elevated by orders of magnitude, suggesting that cells were transiently committed to meiotic levels of recombination, a process referred to in yeast genetics as return-to-growth. In its extreme, on day 6 of starvation, a few mutant clones were haploid, likely resulting from completed meiosis. Distribution of mutations along chromosomes indicated that PmCDA1 was active during ongoing recombination events and sometimes produced characteristic kataegis near initial breakpoints. AID and APOBEC1 behaved similar to PmCDA1. We conclude that replication, transcription, and mitotic recombination contribute to the recovered APOBEC-induced mutations in resting diploids. The mechanism is relevant to the initial stages of oncogenic transformation in terminally differentiated cells, when recombination may lead to the LOH exposing recessive mutations induced by APOBECs in cell's history and to acquisition of new mutations near original break.
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Affiliation(s)
- Artem G Lada
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Elena I Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Anna S Zhuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Sergei F Kliver
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.,Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitrii E Polev
- Research Resource Center "Biobank", Research Park, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Alok Dhar
- Department of Genetics, Cell Biology and Anatomy and Vice Chancellor of Research Core, University of Nebraska Medical Center, Omaha, NE, United States
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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126
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Zhao G, Gleave ES, Lamers MH. Single-molecule studies contrast ordered DNA replication with stochastic translesion synthesis. eLife 2017; 6:32177. [PMID: 29210356 PMCID: PMC5731819 DOI: 10.7554/elife.32177] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
High fidelity replicative DNA polymerases are unable to synthesize past DNA adducts that result from diverse chemicals, reactive oxygen species or UV light. To bypass these replication blocks, cells utilize specialized translesion DNA polymerases that are intrinsically error prone and associated with mutagenesis, drug resistance, and cancer. How untimely access of translesion polymerases to DNA is prevented is poorly understood. Here we use co-localization single-molecule spectroscopy (CoSMoS) to follow the exchange of the E. coli replicative DNA polymerase Pol IIIcore with the translesion polymerases Pol II and Pol IV. We find that in contrast to the toolbelt model, the replicative and translesion polymerases do not form a stable complex on one clamp but alternate their binding. Furthermore, while the loading of clamp and Pol IIIcore is highly organized, the exchange with the translesion polymerases is stochastic and is not determined by lesion-recognition but instead a concentration-dependent competition between the polymerases.
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Affiliation(s)
- Gengjing Zhao
- MRC laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Emma S Gleave
- MRC laboratory of Molecular Biology, Cambridge, United Kingdom
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127
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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128
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Minko IG, Rizzo CJ, Lloyd RS. Mutagenic potential of nitrogen mustard-induced formamidopyrimidine DNA adduct: Contribution of the non-canonical α-anomer. J Biol Chem 2017; 292:18790-18799. [PMID: 28972137 DOI: 10.1074/jbc.m117.802520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/15/2017] [Indexed: 12/14/2022] Open
Abstract
Nitrogen mustards (NMs) are DNA-alkylating compounds that represent the earliest anticancer drugs. However, clinical use of NMs is limited because of their own mutagenic properties. The mechanisms of NM-induced mutagenesis remain unclear. The major product of DNA alkylation by NMs is a cationic NM-N7-dG adduct that can yield the imidazole ring-fragmented lesion, N5-NM-substituted formamidopyrimidine (NM-Fapy-dG). Characterization of this adduct is complicated because it adopts different conformations, including both a canonical β- and an unnatural α-anomeric configuration. Although formation of NM-Fapy-dG in cellular DNA has been demonstrated, its potential role in NM-induced mutagenesis is unknown. Here, we created site-specifically modified single-stranded vectors for replication in primate (COS7) or Escherichia coli cells. In COS7 cells, NM-Fapy-dG caused targeted mutations, predominantly G → T transversions, with overall frequencies of ∼11-12%. These frequencies were ∼2-fold higher than that induced by 8-oxo-dG adduct. Replication in E. coli was essentially error-free. To elucidate the mechanisms of bypass of NM-Fapy-dG, we performed replication assays in vitro with a high-fidelity DNA polymerase, Saccharomyces cerevisiae polymerase (pol) δ. It was found that pol δ could catalyze high-fidelity synthesis past NM-Fapy-dG, but only on a template subpopulation, presumably containing the β-anomeric adduct. Consistent with the low mutagenic potential of the β-anomer in vitro, the mutation frequency was significantly reduced when conditions for vector preparation were modified to favor this configuration. Collectively, these data implicate the α-anomer as a major contributor to NM-Fapy-dG-induced mutagenesis in primate cells.
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Affiliation(s)
- Irina G Minko
- From the Oregon Institute of Occupational Health Sciences and
| | - Carmelo J Rizzo
- the Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - R Stephen Lloyd
- From the Oregon Institute of Occupational Health Sciences and .,the Departments of Molecular and Medical Genetics and Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon 97239 and
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129
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Raguse M, Torres R, Seco EM, Gándara C, Ayora S, Moeller R, Alonso JC. Bacillus subtilis DisA helps to circumvent replicative stress during spore revival. DNA Repair (Amst) 2017; 59:57-68. [PMID: 28961460 DOI: 10.1016/j.dnarep.2017.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
The mechanisms that allow to circumvent replicative stress, and to resume DNA synthesis are poorly understood in Bacillus subtilis. To study the role of the diadenylate cyclase DisA and branch migration translocase (BMT) RadA/Sms in restarting a stalled replication fork, we nicked and broke the circular chromosome of an inert mature haploid spore, damaged the bases, and measured survival of reviving spores. During undisturbed ripening, nicks and breaks should be repaired by pathways that do not invoke long-range end resection or genetic exchange by homologous recombination, after which DNA replication might be initiated. We found that DNA damage reduced the viability of spores that lacked DisA, BMT (RadA/Sms, RuvAB or RecG), the Holliday junction resolvase RecU, or the translesion synthesis DNA polymerases (PolY1 or PolY2). DisA and RadA/Sms, in concert with RuvAB, RecG, RecU, PolY1 or PolY2, are needed to bypass replication-blocking lesions. DisA, which binds to stalled or reversed forks, did not apparently affect initiation of PriA-dependent DNA replication in vitro. We propose that DisA is necessary to coordinate responses to replicative stress; it could help to circumvent damaged template bases that otherwise impede fork progression.
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Affiliation(s)
- Marina Raguse
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany
| | - Rubén Torres
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Elena M Seco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Carolina Gándara
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Ralf Moeller
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany.
| | - Juan C Alonso
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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130
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Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants. Appl Environ Microbiol 2017; 83:AEM.01013-17. [PMID: 28710267 DOI: 10.1128/aem.01013-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4. Furthermore, the A181D mutant showed lower fidelity and higher nucleotide incorporation efficiency (4.74 × 10-4 s-1 μM-1) than E63K and I248Y mutants. When tasked with bypassing damage, the A181D mutant exhibited a 3.81-fold and 2.62-fold higher catalytic efficiency (kcat/Km ) at incorporating dCTP and dATP, respectively, than wild-type Dpo4. It also showed a 55% and 91.5% higher catalytic efficiency when moving beyond the damaged 8-oxoG:C and 8-oxoG:A base pairs, respectively, compared to wild-type Dpo4. Protein engineering and bioinformatics methods can effectively increase the processivity and translesion synthesis ability of Dpo4.IMPORTANCE DNA polymerases with poor fidelity can be exploited to store data and record changes in response to the intracellular environment. Sulfolobus solfataricus Dpo4 is such an enzyme, although its use is hindered by its low processivity. In this work, we used a bioinformatics and protein engineering approach to generate Dpo4 mutants with improved processivity. We identified the Dpo4 thumb domain as the most relevant in controlling processivity.
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132
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A mitochondrial proteomics view of complex I deficiency in Candida albicans. Mitochondrion 2017; 38:48-57. [PMID: 28801230 DOI: 10.1016/j.mito.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/28/2022]
Abstract
Proteomic analyses were carried out on isolated mitochondrial samples of C. albicans from gene-deleted mutants (nuo1Δ, nuo2Δ and goa1Δ) as well as the parental strain in order to better understand the contribution of these three fungal-specific mitochondrial ETC complex I (CI) subunits to cellular activities. Herein, we identify 2333 putative proteins from four strains, in which a total of 663 proteins (28.5%) are putatively located in mitochondria. Comparison of protein abundances between mutants and the parental strain reveal 146 differentially-expressed proteins, of which 78 are decreased and 68 are increased in at least one mutant. The common changes across the three mutants include the down-regulation of nuclear-encoded CI subunit proteins as well as phospholipid, ergosterol and cell wall mannan synthesis, and up-regulated proteins in CIV and the alternative oxidase (AOX2). As for gene-specific functions, we find that NUO1 participates in nucleotide synthesis and ribosomal biogenesis; NUO2 is involved in vesicle trafficking; and GOA1 appears to regulate membrane transporter proteins, ROS removal, and substrates trafficking between peroxisomes and mitochondria. The proteomic view of general as well as mutant-specific proteins further extends our understanding of the functional roles of non-mammalian CI-specific subunit proteins in cell processes. Particularly intriguing is the confirmation of a regulatory role for GOA1 on ETC function, a protein found almost exclusively in Candida species. SIGNIFICANCE Fungal mitochondria are critical for fungal pathogenesis. The absence of any of the three fungal specific CI subunits in mitochondria causes an avirulence phenotype of C. albicans in a murine model of invasive disease. As model yeast (Saccharomyces cerevisiae) lacks a CI and is rarely a pathogen of humans, C. albicans is a better choice for establishing a link between mitochondrial CI and pathogenesis. Apart from the general effects of CI mutants on respiration, previous phenotyping of these mutants were quite similar to each other or to CI conservative subunit. By comparison to transcriptional data, the proteomic data obtained in this study indicate that biosynthetic events in each mutant such as cell wall and cell membrane phospholipids and ergosterol are generally decreased in both transcriptomal and translational levels. However, in the case of mitochondrial function, glycolysis/gluconeogenesis, and ROS scavengers, often gene changes are opposite that of proteomic data in mutants. We hypothesize that the loss of energy production in mutants is compensated by increases in protein levels of glycolysis, gluconeogenesis, and anti-ROS scavengers that at least extend mutant survival.
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133
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Polyzos AA, McMurray CT. Close encounters: Moving along bumps, breaks, and bubbles on expanded trinucleotide tracts. DNA Repair (Amst) 2017; 56:144-155. [PMID: 28690053 PMCID: PMC5558859 DOI: 10.1016/j.dnarep.2017.06.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expansion of simple triplet repeats (TNR) underlies more than 30 severe degenerative diseases. There is a good understanding of the major pathways generating an expansion, and the associated polymerases that operate during gap filling synthesis at these "difficult to copy" sequences. However, the mechanism by which a TNR is repaired depends on the type of lesion, the structural features imposed by the lesion, the assembled replication/repair complex, and the polymerase that encounters it. The relationships among these parameters are exceptionally complex and how they direct pathway choice is poorly understood. In this review, we consider the properties of polymerases, and how encounters with GC-rich or abnormal structures might influence polymerase choice and the success of replication and repair. Insights over the last three years have highlighted new mechanisms that provide interesting choices to consider in protecting genome stability.
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Affiliation(s)
- Aris A Polyzos
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States
| | - Cynthia T McMurray
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States.
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Genome-wide and protein kinase-focused RNAi screens reveal conserved and novel damage response pathways in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006477. [PMID: 28742144 PMCID: PMC5542689 DOI: 10.1371/journal.ppat.1006477] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/03/2017] [Accepted: 06/17/2017] [Indexed: 12/21/2022] Open
Abstract
All cells are subject to structural damage that must be addressed for continued growth. A wide range of damage affects the genome, meaning multiple pathways have evolved to repair or bypass the resulting DNA lesions. Though many repair pathways are conserved, their presence or function can reflect the life style of individual organisms. To identify genome maintenance pathways in a divergent eukaryote and important parasite, Trypanosoma brucei, we performed RNAi screens to identify genes important for survival following exposure to the alkylating agent methyl methanesulphonate. Amongst a cohort of broadly conserved and, therefore, early evolved repair pathways, we reveal multiple activities not so far examined functionally in T. brucei, including DNA polymerases, DNA helicases and chromatin factors. In addition, the screens reveal Trypanosoma- or kinetoplastid-specific repair-associated activities. We also provide focused analyses of repair-associated protein kinases and show that loss of at least nine, and potentially as many as 30 protein kinases, including a nuclear aurora kinase, sensitises T. brucei to alkylation damage. Our results demonstrate the potential for synthetic lethal genome-wide screening of gene function in T. brucei and provide an evolutionary perspective on the repair pathways that underpin effective responses to damage, with particular relevance for related kinetoplastid pathogens. By revealing that a large number of diverse T. brucei protein kinases act in the response to damage, we expand the range of eukaryotic signalling factors implicated in genome maintenance activities. Damage to the genome is a universal threat to life. Though the repair pathways used to tackle damage can be widely conserved, lineage-specific specialisations are found, reflecting the differing life styles of extant organisms. Using RNAi coupled with next generation sequencing we have screened for genes that are important for growth of Trypanosoma brucei, a diverged eukaryotic microbe and important parasite, in the presence of alkylation damage caused by methyl methanesulphonate. We reveal both repair pathway conservation relative to characterised eukaryotes and specialisation, including uncharacterised roles for translesion DNA polymerases, DNA helicases and chromatin factors. Furthermore, we demonstrate that loss of around 15% of T. brucei protein kinases sensitises the parasites to alkylation, indicating phosphorylation signalling plays widespread and under-investigated roles in the damage response pathways of eukaryotes.
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135
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Stefansson OA, Hermanowicz S, van der Horst J, Hilmarsdottir H, Staszczak Z, Jonasson JG, Tryggvadottir L, Gudjonsson T, Sigurdsson S. CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer. BMC Cancer 2017; 17:469. [PMID: 28679371 PMCID: PMC5498885 DOI: 10.1186/s12885-017-3453-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, the two E. coli AlkB homologs ALKBH2 and ALKBH3 have also been linked to direct reversal of alkylation damage. However, it is currently unknown whether ALKBH2 or ALKBH3 are found inactivated in cancer. METHODS Methylome datasets (GSE52865, GSE20713, GSE69914), available through Omnibus, were used to determine whether ALKBH2 or ALKBH3 are found inactivated by CpG promoter methylation. TCGA dataset enabled us to then assess the impact of CpG promoter methylation on mRNA expression for both ALKBH2 and ALKBH3. DNA methylation analysis for the ALKBH3 promoter region was carried out by pyrosequencing (PyroMark Q24) in 265 primary breast tumours and 30 proximal normal breast tissue samples along with 8 breast-derived cell lines. ALKBH3 mRNA and protein expression were analysed in cell lines using RT-PCR and Western blotting, respectively. DNA alkylation damage assay was carried out in cell lines based on immunofluorescence and confocal imaging. Data on clinical parameters and survival outcomes in patients were obtained and assessed in relation to ALKBH3 promoter methylation. RESULTS The ALKBH3 gene, but not ALKBH2, undergoes CpG promoter methylation and transcriptional silencing in breast cancer. We developed a quantitative alkylation DNA damage assay based on immunofluorescence and confocal imaging revealing higher levels of alkylation damage in association with epigenetic inactivation of the ALKBH3 gene (P = 0.029). In our cohort of 265 primary breast cancer, we found 72 cases showing aberrantly high CpG promoter methylation over the ALKBH3 promoter (27%; 72 out of 265). We further show that increasingly higher degree of ALKBH3 promoter methylation is associated with reduced breast-cancer specific survival times in patients. In this analysis, ALKBH3 promoter methylation at >20% CpG methylation was found to be statistically significantly associated with reduced survival (HR = 2.3; P = 0.012). By thresholding at the clinically relevant CpG methylation level (>20%), we find the incidence of ALKBH3 promoter methylation to be 5% (13 out of 265). CONCLUSIONS ALKBH3 is a novel addition to the catalogue of DNA repair genes found inactivated in breast cancer. Our results underscore a link between defective alkylation repair and breast cancer which, additionally, is found in association with poor disease outcome.
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Affiliation(s)
- Olafur Andri Stefansson
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Stefan Hermanowicz
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Jasper van der Horst
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Holmfridur Hilmarsdottir
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Zuzanna Staszczak
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Jon Gunnlaugur Jonasson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
| | - Thorkell Gudjonsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Stefan Sigurdsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
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136
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Nevin P, Gabbai CC, Marians KJ. Replisome-mediated translesion synthesis by a cellular replicase. J Biol Chem 2017. [PMID: 28642369 DOI: 10.1074/jbc.m117.800441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genome integrity relies on the ability of the replisome to navigate ubiquitous DNA damage during DNA replication. The Escherichia coli replisome transiently stalls at leading-strand template lesions and can either reinitiate replication downstream of the lesion or recruit specialized DNA polymerases that can bypass the lesion via translesion synthesis. Previous results had suggested that the E. coli replicase might play a role in lesion bypass, but this possibility has not been tested in reconstituted DNA replication systems. We report here that the DNA polymerase III holoenzyme in a stalled E. coli replisome can directly bypass a single cyclobutane pyrimidine dimer or abasic site by translesion synthesis in the absence of specialized translesion synthesis polymerases. Bypass efficiency was proportional to deoxynucleotide concentrations equivalent to those found in vivo and was dependent on the frequency of primer synthesis downstream of the lesion. Translesion synthesis came at the expense of lesion-skipping replication restart. Replication of a cyclobutane pyrimidine dimer was accurate, whereas replication of an abasic site resulted in mainly -1 frameshifts. Lesion bypass was accompanied by an increase in base substitution frequency for the base preceding the lesion. These findings suggest that DNA damage at the replication fork can be replicated directly by the replisome without the need to activate error-prone pathways.
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Affiliation(s)
- Philip Nevin
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Carolina C Gabbai
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kenneth J Marians
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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137
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Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene. Proc Natl Acad Sci U S A 2017; 114:6752-6757. [PMID: 28607059 DOI: 10.1073/pnas.1706021114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon, is the major cause of lung cancer. BaP forms covalent DNA adducts after metabolic activation and induces mutations. We have developed a method for capturing oligonucleotides carrying bulky base adducts, including UV-induced cyclobutane pyrimidine dimers (CPDs) and BaP diol epoxide-deoxyguanosine (BPDE-dG), which are removed from the genome by nucleotide excision repair. The isolated oligonucleotides are ligated to adaptors, and after damage-specific immunoprecipitation, the adaptor-ligated oligonucleotides are converted to dsDNA with an appropriate translesion DNA synthesis (TLS) polymerase, followed by PCR amplification and next-generation sequencing (NGS) to generate genome-wide repair maps. We have termed this method translesion excision repair-sequencing (tXR-seq). In contrast to our previously described XR-seq method, tXR-seq does not depend on repair/removal of the damage in the excised oligonucleotides, and thus it is applicable to essentially all DNA damages processed by nucleotide excision repair. Here we present the excision repair maps for CPDs and BPDE-dG adducts generated by tXR-Seq for the human genome. In addition, we report the sequence specificity of BPDE-dG excision repair using tXR-seq.
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138
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Abstract
Life as we know it, simply would not exist without DNA replication. All living organisms utilize a complex machinery to duplicate their genomes and the central role in this machinery belongs to replicative DNA polymerases, enzymes that are specifically designed to copy DNA. "Hassle-free" DNA duplication exists only in an ideal world, while in real life, it is constantly threatened by a myriad of diverse challenges. Among the most pressing obstacles that replicative polymerases often cannot overcome by themselves are lesions that distort the structure of DNA. Despite elaborate systems that cells utilize to cleanse their genomes of damaged DNA, repair is often incomplete. The persistence of DNA lesions obstructing the cellular replicases can have deleterious consequences. One of the mechanisms allowing cells to complete replication is "Translesion DNA Synthesis (TLS)". TLS is intrinsically error-prone, but apparently, the potential downside of increased mutagenesis is a healthier outcome for the cell than incomplete replication. Although most of the currently identified eukaryotic DNA polymerases have been implicated in TLS, the best characterized are those belonging to the "Y-family" of DNA polymerases (pols η, ι, κ and Rev1), which are thought to play major roles in the TLS of persisting DNA lesions in coordination with the B-family polymerase, pol ζ. In this review, we summarize the unique features of these DNA polymerases by mainly focusing on their biochemical and structural characteristics, as well as potential protein-protein interactions with other critical factors affecting TLS regulation.
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Affiliation(s)
- Alexandra Vaisman
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Roger Woodgate
- a Laboratory of Genomic Integrity , National Institute of Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
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139
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Tubbs A, Nussenzweig A. Endogenous DNA Damage as a Source of Genomic Instability in Cancer. Cell 2017; 168:644-656. [PMID: 28187286 DOI: 10.1016/j.cell.2017.01.002] [Citation(s) in RCA: 850] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/22/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022]
Abstract
Genome instability, defined as higher than normal rates of mutation, is a double-edged sword. As a source of genetic diversity and natural selection, mutations are beneficial for evolution. On the other hand, genomic instability can have catastrophic consequences for age-related diseases such as cancer. Mutations arise either from inactivation of DNA repair pathways or in a repair-competent background due to genotoxic stress from celluar processes such as transcription and replication that overwhelm high-fidelity DNA repair. Here, we review recent studies that shed light on endogenous sources of mutation and epigenomic features that promote genomic instability during cancer evolution.
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Affiliation(s)
- Anthony Tubbs
- Laboratory of Genome Integrity, NIH, Bethesda, MD 20892, USA
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140
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Sha Y, Minko IG, Malik CK, Rizzo CJ, Lloyd RS. Error-prone replication bypass of the imidazole ring-opened formamidopyrimidine deoxyguanosine adduct. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:182-189. [PMID: 28436537 PMCID: PMC5476229 DOI: 10.1002/em.22089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Addition of hydroxyl radicals to the C8 position of 2'-deoxyguanosine generates an 8-hydroxyguanyl radical that can be converted into either 8-oxo-7,8-dihydro-2'-deoxyguanosine or N-(2-deoxy-d-pentofuranosyl)-N-(2,6-diamino-4-hydroxy-5-formamidopyrimidine) (Fapy-dG). The Fapy-dG adduct can adopt different conformations and in particular, can exist in an unnatural α anomeric configuration in addition to canonical β configuration. Previous studies reported that in 5'-TGN-3' sequences, Fapy-dG predominantly induced G → T transversions in both mammalian cells and Escherichia coli, suggesting that mutations could be formed either via insertion of a dA opposite the 5' dT due to primer/template misalignment or as result of direct miscoding. To address this question, single-stranded vectors containing a site-specific Fapy-dG adduct were generated to vary the identity of the 5' nucleotide. Following vector replication in primate cells (COS7), complex mutation spectra were observed that included ∼3-5% G → T transversions and ∼14-21% G → A transitions. There was no correlation apparent between the identity of the 5' nucleotide and spectra of mutations. When conditions for vector preparation were modified to favor the β anomer, frequencies of both G → T and G → A substitutions were significantly reduced. Mutation frequencies in wild-type E. coli and a mutant deficient in damage-inducible DNA polymerases were significantly lower than detected in COS7 and spectra were dominated by deletions. Thus, mutagenic bypass of Fapy-dG can proceed via mechanisms that are different from the previously proposed primer/template misalignment or direct misinsertions of dA or dT opposite to the β anomer of Fapy-dG. Environ. Mol. Mutagen. 58:182-189, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yan Sha
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Chanchal K. Malik
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Carmelo J. Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, USA
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141
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McVey M, Khodaverdian VY, Meyer D, Cerqueira PG, Heyer WD. Eukaryotic DNA Polymerases in Homologous Recombination. Annu Rev Genet 2017; 50:393-421. [PMID: 27893960 DOI: 10.1146/annurev-genet-120215-035243] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.
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Affiliation(s)
- Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts 02155;
| | | | - Damon Meyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,College of Health Sciences, California Northstate University, Rancho Cordova, California 95670
| | - Paula Gonçalves Cerqueira
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616;
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, California 95616; .,Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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142
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Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E4442-E4451. [PMID: 28416670 DOI: 10.1073/pnas.1618714114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.
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143
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Translesion Synthesis DNA Polymerase Kappa Is Indispensable for DNA Repair Synthesis in Cisplatin Exposed Dorsal Root Ganglion Neurons. Mol Neurobiol 2017; 55:2506-2515. [PMID: 28391554 DOI: 10.1007/s12035-017-0507-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
In the peripheral nervous system (PNS) in the absence of tight blood barrier, neurons are at increased risk of DNA damage, yet the question of how effectively PNS neurons manage DNA damage remains largely unanswered. Genotoxins in systemic circulation include chemotherapeutic drugs that reach peripheral neurons and damage their DNA. Because neurotoxicity of platinum-based class of chemotherapeutic drugs has been implicated in PNS neuropathies, we utilized an in vitro model of Dorsal Root Ganglia (DRGs) to investigate how peripheral neurons respond to cisplatin that forms intra- and interstrand crosslinks with their DNA. Our data revealed strong transcriptional upregulation of the translesion synthesis DNA polymerase kappa (Pol κ), while expression of other DNA polymerases remained unchanged. DNA Pol κ is involved in bypass synthesis of diverse DNA lesions and considered a vital player in cellular survival under injurious conditions. To assess the impact of Pol κ deficiency on cisplatin-exposed DRG neurons, Pol κ levels were reduced using siRNA. Pol κ targeting siRNA diminished the cisplatin-induced nuclear Pol κ immunoreactivity in DRG neurons and decreased the extent of cisplatin-induced DNA repair synthesis, as reflected in reduced incorporation of thymidine analog into nuclear DNA. Moreover, Pol κ depletion exacerbated global transcriptional suppression induced by cisplatin in DRG neurons. Collectively, these findings provide the first evidence for critical role of Pol κ in DNA damage response in the nervous system and call attention to implications of polymorphisms that modify Pol κ activity, on maintenance of genomic integrity and neuronal function in exogenously challenged PNS.
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144
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Greene EC. Replication Protein A Blocks the Way. Biochemistry 2017; 56:1809-1810. [PMID: 28333436 DOI: 10.1021/acs.biochem.7b00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University , New York, New York 10032, United States
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145
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Fitzgerald DM, Hastings PJ, Rosenberg SM. Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance. ANNUAL REVIEW OF CANCER BIOLOGY 2017; 1:119-140. [PMID: 29399660 PMCID: PMC5794033 DOI: 10.1146/annurev-cancerbio-050216-121919] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genomic instability underlies many cancers and generates genetic variation that drives cancer initiation, progression, and therapy resistance. In contrast with classical assumptions that mutations occur purely stochastically at constant, gradual rates, microbes, plants, flies, and human cancer cells possess mechanisms of mutagenesis that are upregulated by stress responses. These generate transient, genetic-diversity bursts that can propel evolution, specifically when cells are poorly adapted to their environments-that is, when stressed. We review molecular mechanisms of stress-response-dependent (stress-induced) mutagenesis that occur from bacteria to cancer, and are activated by starvation, drugs, hypoxia, and other stressors. We discuss mutagenic DNA break repair in Escherichia coli as a model for mechanisms in cancers. The temporal regulation of mutagenesis by stress responses and spatial restriction in genomes are common themes across the tree of life. Both can accelerate evolution, including the evolution of cancers. We discuss possible anti-evolvability drugs, aimed at targeting mutagenesis and other variation generators, that could be used to delay the evolution of cancer progression and therapy resistance.
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Affiliation(s)
- Devon M Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston Texas 77030
- The Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
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146
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Tashjian TF, Lin I, Belt V, Cafarelli TM, Godoy VG. RNA Primer Extension Hinders DNA Synthesis by Escherichia coli Mutagenic DNA Polymerase IV. Front Microbiol 2017; 8:288. [PMID: 28298904 PMCID: PMC5331060 DOI: 10.3389/fmicb.2017.00288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
In Escherichia coli the highly conserved DNA damage regulated dinB gene encodes DNA Polymerase IV (DinB), an error prone specialized DNA polymerase with a central role in stress-induced mutagenesis. Since DinB is the DNA polymerase with the highest intracellular concentrations upon induction of the SOS response, further regulation must exist to maintain genomic stability. Remarkably, we find that DinB DNA synthesis is inherently poor when using an RNA primer compared to a DNA primer, while high fidelity DNA polymerases are known to have no primer preference. Moreover, we show that the poor DNA synthesis from an RNA primer is conserved in DNA polymerase Kappa, the human DinB homolog. The activity of DinB is modulated by interactions with several other proteins, one of which is the equally evolutionarily conserved recombinase RecA. This interaction is known to positively affect DinB's fidelity on damaged templates. We find that upon interaction with RecA, DinB shows a significant reduction in DNA synthesis when using an RNA primer. Furthermore, with DinB or DinB:RecA a robust pause, sequence and lesion independent, occurs only when RNA is used as a primer. The robust pause is likely to result in abortive DNA synthesis when RNA is the primer. These data suggest a novel mechanism to prevent DinB synthesis when it is not needed despite its high concentrations, thus protecting genome stability.
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Affiliation(s)
- Tommy F Tashjian
- Godoy Lab, Department of Biology, Northeastern University Boston, MA, USA
| | - Ida Lin
- Godoy Lab, Department of Biology, Northeastern University Boston, MA, USA
| | - Verena Belt
- Godoy Lab, Department of Biology, Northeastern University Boston, MA, USA
| | | | - Veronica G Godoy
- Godoy Lab, Department of Biology, Northeastern University Boston, MA, USA
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147
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Impact of Age and Insulin-Like Growth Factor-1 on DNA Damage Responses in UV-Irradiated Human Skin. Molecules 2017; 22:molecules22030356. [PMID: 28245638 PMCID: PMC5432641 DOI: 10.3390/molecules22030356] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 01/19/2023] Open
Abstract
The growing incidence of non-melanoma skin cancer (NMSC) necessitates a thorough understanding of its primary risk factors, which include exposure to ultraviolet (UV) wavelengths of sunlight and age. Whereas UV radiation (UVR) has long been known to generate photoproducts in genomic DNA that promote genetic mutations that drive skin carcinogenesis, the mechanism by which age contributes to disease pathogenesis is less understood and has not been sufficiently studied. In this review, we highlight studies that have considered age as a variable in examining DNA damage responses in UV-irradiated skin and then discuss emerging evidence that the reduced production of insulin-like growth factor-1 (IGF-1) by senescent fibroblasts in the dermis of geriatric skin creates an environment that negatively impacts how epidermal keratinocytes respond to UVR-induced DNA damage. In particular, recent data suggest that two principle components of the cellular response to DNA damage, including nucleotide excision repair and DNA damage checkpoint signaling, are both partially defective in keratinocytes with inactive IGF-1 receptors. Overcoming these tumor-promoting conditions in aged skin may therefore provide a way to lower aging-associated skin cancer risk, and thus we will consider how dermal wounding and related clinical interventions may work to rejuvenate the skin, re-activate IGF-1 signaling, and prevent the initiation of NMSC.
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148
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Abstract
Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.
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Affiliation(s)
- Michalis Fragkos
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
| | - Valeria Naim
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
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149
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Zhao L, Washington MT. Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases. Genes (Basel) 2017; 8:genes8010024. [PMID: 28075396 PMCID: PMC5295019 DOI: 10.3390/genes8010024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1) template switching and recombination-dependent DNA synthesis; and (2) translesion synthesis (TLS) using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis. An accepted model of translesion synthesis involves DNA polymerase switching steps between a replicative DNA polymerase and one or more TLS DNA polymerases. The mechanisms that govern the selection and exchange of specialized DNA polymerases for a given DNA lesion are not well understood. In this review, recent studies concerning the mechanisms of selection and switching of DNA polymerases in eukaryotic systems are summarized.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA.
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, MI 48859, USA.
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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150
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Guilliam TA, Doherty AJ. PrimPol-Prime Time to Reprime. Genes (Basel) 2017; 8:genes8010020. [PMID: 28067825 PMCID: PMC5295015 DOI: 10.3390/genes8010020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
The complex molecular machines responsible for genome replication encounter many obstacles during their progression along DNA. Tolerance of these obstructions is critical for efficient and timely genome duplication. In recent years, primase-polymerase (PrimPol) has emerged as a new player involved in maintaining eukaryotic replication fork progression. This versatile replicative enzyme, a member of the archaeo-eukaryotic primase (AEP) superfamily, has the capacity to perform a range of template-dependent and independent synthesis activities. Here, we discuss the emerging roles of PrimPol as a leading strand repriming enzyme and describe the mechanisms responsible for recruiting and regulating the enzyme during this process. This review provides an overview and update of the current PrimPol literature, as well as highlighting unanswered questions and potential future avenues of investigation.
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Affiliation(s)
- Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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