1
|
Carvajal-Garcia J, Samadpour AN, Hernandez Viera AJ, Merrikh H. Oxidative stress drives mutagenesis through transcription-coupled repair in bacteria. Proc Natl Acad Sci U S A 2023; 120:e2300761120. [PMID: 37364106 PMCID: PMC10318952 DOI: 10.1073/pnas.2300761120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In bacteria, mutations lead to the evolution of antibiotic resistance, which is one of the main public health problems of the twenty-first century. Therefore, determining which cellular processes most frequently contribute to mutagenesis, especially in cells that have not been exposed to exogenous DNA damage, is critical. Here, we show that endogenous oxidative stress is a key driver of mutagenesis and the subsequent development of antibiotic resistance. This is the case for all classes of antibiotics and highly divergent species tested, including patient-derived strains. We show that the transcription-coupled repair pathway, which uses the nucleotide excision repair proteins (TC-NER), is responsible for endogenous oxidative stress-dependent mutagenesis and subsequent evolution. This suggests that a majority of mutations arise through transcription-associated processes rather than the replication fork. In addition to determining that the NER proteins play a critical role in mutagenesis and evolution, we also identify the DNA polymerases responsible for this process. Our data strongly suggest that cooperation between three different mutagenic DNA polymerases, likely at the last step of TC-NER, is responsible for mutagenesis and evolution. Overall, our work identifies a highly conserved pathway that drives mutagenesis due to endogenous oxidative stress, which has broad implications for all diseases of evolution, including antibiotic resistance development.
Collapse
Affiliation(s)
- Juan Carvajal-Garcia
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| | | | | | - Houra Merrikh
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| |
Collapse
|
2
|
Sikand A, Jaszczur M, Bloom LB, Woodgate R, Cox MM, Goodman MF. The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis. Cells 2021; 10:cells10051083. [PMID: 34062858 PMCID: PMC8147279 DOI: 10.3390/cells10051083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
In the mid 1970s, Miroslav Radman and Evelyn Witkin proposed that Escherichia coli must encode a specialized error-prone DNA polymerase (pol) to account for the 100-fold increase in mutations accompanying induction of the SOS regulon. By the late 1980s, genetic studies showed that SOS mutagenesis required the presence of two “UV mutagenesis” genes, umuC and umuD, along with recA. Guided by the genetics, decades of biochemical studies have defined the predicted error-prone DNA polymerase as an activated complex of these three gene products, assembled as a mutasome, pol V Mut = UmuD’2C-RecA-ATP. Here, we explore the role of the β-sliding processivity clamp on the efficiency of pol V Mut-catalyzed DNA synthesis on undamaged DNA and during translesion DNA synthesis (TLS). Primer elongation efficiencies and TLS were strongly enhanced in the presence of β. The results suggest that β may have two stabilizing roles: its canonical role in tethering the pol at a primer-3’-terminus, and a possible second role in inhibiting pol V Mut’s ATPase to reduce the rate of mutasome-DNA dissociation. The identification of umuC, umuD, and recA homologs in numerous strains of pathogenic bacteria and plasmids will ensure the long and productive continuation of the genetic and biochemical journey initiated by Radman and Witkin.
Collapse
Affiliation(s)
- Adhirath Sikand
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA;
| | - Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Linda B. Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA;
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20814, USA;
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Myron F. Goodman
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA;
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
- Correspondence:
| |
Collapse
|
3
|
Thompson PS, Cortez D. New insights into abasic site repair and tolerance. DNA Repair (Amst) 2020; 90:102866. [PMID: 32417669 PMCID: PMC7299775 DOI: 10.1016/j.dnarep.2020.102866] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Thousands of apurinic/apyrimidinic (AP or abasic) sites form in each cell, each day. This simple DNA lesion can have profound consequences to cellular function, genome stability, and disease. As potent blocks to polymerases, they interfere with the reading and copying of the genome. Since they provide no coding information, they are potent sources of mutation. Due to their reactive chemistry, they are intermediates in the formation of lesions that are more challenging to repair including double-strand breaks, interstrand crosslinks, and DNA protein crosslinks. Given their prevalence and deleterious consequences, cells have multiple mechanisms of repairing and tolerating these lesions. While base excision repair of abasic sites in double-strand DNA has been studied for decades, new interest in abasic site processing has come from more recent insights into how they are processed in single-strand DNA. In this review, we discuss the source of abasic sites, their biological consequences, tolerance mechanisms, and how they are repaired in double and single-stranded DNA.
Collapse
Affiliation(s)
- Petria S Thompson
- Vanderbilt University School of Medicine, Department of Biochemistry, Nashville, TN, 37232, USA
| | - David Cortez
- Vanderbilt University School of Medicine, Department of Biochemistry, Nashville, TN, 37232, USA.
| |
Collapse
|
4
|
Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863. Genes (Basel) 2019; 10:genes10040282. [PMID: 30965610 PMCID: PMC6523755 DOI: 10.3390/genes10040282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 01/17/2023] Open
Abstract
Quorum sensing (QS) is a cell-to-cell communication system that uses autoinducers as signaling molecules to enable inter-species and intra-species interactions in response to external stimuli according to the population density. QS allows bacteria such as Acinetobacter baumannii to react rapidly in response to environmental changes and hence, increase the chances of survival. A. baumannii is one of the causative agents in hospital-acquired infections and the number of cases has increased remarkably in the past decade. In this study, A. baumannii strain 863, a multidrug-resistant pathogen, was found to exhibit QS activity by producing N-acyl homoserine lactone. We identified the autoinducer synthase gene, which we named abaI, by performing whole genome sequencing analysis of A. baumannii strain 863. Using high resolution tandem triple quadrupole mass spectrometry, we reported that abaI of A. baumannii strain 863 produced 3-hydroxy-dodecanoyl-homoserine lactone. A gene deletion mutant was constructed, which confirmed the functionality of abaI. A growth defect was observed in the QS-deficient mutant strain. Transcriptome profiling was performed to determine the possible genes regulated by QS. Four groups of genes that showed differential expression were discovered, namely those involved in carbon source metabolism, energy production, stress response and the translation process.
Collapse
|
5
|
Patlán AG, Corona SU, Ayala-García VM, Pedraza-Reyes M. Non-canonical processing of DNA photodimers with Bacillus subtilis UV-endonuclease YwjD, 5'→3' exonuclease YpcP and low-fidelity DNA polymerases YqjH and YqjW. DNA Repair (Amst) 2018; 70:1-9. [PMID: 30096406 DOI: 10.1016/j.dnarep.2018.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022]
Abstract
It has been shown that mutation frequency decline (Mfd) and nucleotide excision repair (NER) deficiencies promote UV-induced mutagenesis in B. subtilis sporangia. As replication is halted in sporulating B. subtilis cells, in this report, we investigated if this response may result from an error-prone repair event involving the UV-endonuclease YwjD and low fidelity (LF) DNA synthesis. Accordingly, disruption of YwjD generated B. subtilis sporangia that were more susceptible to UV-C radiation than sporangia of the WT strain and such susceptibility increased even more after the single or simultaneous inactivation of the LF DNA polymerases YqjH and YqjW. To further explore this concept, functional His6-tagged YwjD and Y-DNA polymerases YqjH and YqjW were produced and purified to homogeneity. In vitro repair assays showed that YwjD hydrolyzed the phosphodiester bond immediately located 5´-end of a ds-DNA substrate bearing either, cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PD) or Dewar isomers (DWI). Notably, the 6-4 PD and DWI but not the CPDs repair intermediaries of YwjD were efficiently processed by the LF polymerase YqjH suggesting that an additional 5'→3' exonuclease event was necessary to process PD. Accordingly, the LF polymerase YqjW efficiently processed the incision-excision repair products derived from YwjD and exonuclease YpcP attack over CPD-containing DNA. In summary, our results unveiled a novel non-canonical repair pathway that employs YwjD to incise PD-containing DNA and low fidelity synthesis contributing thus to mutagenesis, survival and spore morphogenesis in B. subtilis.
Collapse
Affiliation(s)
- Adriana G Patlán
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Saúl U Corona
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Víctor M Ayala-García
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico.
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
| |
Collapse
|
7
|
Prantl EM, Kramer M, Schmidt CK, Knauer M, Gartiser S, Shuliakevich A, Milas J, Glatt H, Meinl W, Hollert H. Comparison of in vitro test systems using bacterial and mammalian cells for genotoxicity assessment within the "health-related indication value (HRIV) concept. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:3996-4010. [PMID: 27928753 DOI: 10.1007/s11356-016-8166-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
In numerous cases, the German health-related indication value (HRIV) concept has proved its practicability for the assessment of drinking water relevant trace substances (Umweltbundesamt 2003). The HRIV is based on the toxicological profile of a substance. An open point of the HRIV concept has been the assignment of standardized test procedures to be used for the assessment. The level of the HRIV is at its lowest as soon as the genotoxicity of the substance is detected. As a single test on its own, it is not sufficient enough to assess the human toxicological relevance of a genotoxic effect or exclude it in the case of a negative result; a reasonable test battery was required, technically oriented towards the already harmonized international, hierarchical evaluation for toxicological assessment of chemicals. Therefore, an important aim of this project was to define a strategy for the genotoxicological assessment of anthropogenic trace substances. The basic test battery for genotoxicity of micropollutants in drinking water needs to fulfill several requirements. Although quick test results are needed for the determination of HRIV, a high degree of transferability to human genotoxicity should be ensured. Therefore, an in vitro genotoxicity test battery consisting of the Ames fluctuation test with two tester strains (ISO 11350), the umu test and the micronucleus test, or from the Ames test with five tester strains (OECD 471) and the micronucleus test is proposed. On the basis of selected test substances, it could be shown that the test battery leads to positive, indifferent, and negative results. Given indifferent results, the health authority and the water supplier must assume that it is a genotoxic substance. Genetically modified tester strains are being sensitive to different chemical classes by expression of selected mammalian key enzymes for example nitroreductase, acetyltransferase, and glutathione-S-transferase. These strains may provide valuable additional information and may give a first indication of the mechanism of action. To check this hypothesis, various additional strains expressing specific human-relevant enzymes were investigated. It could be shown that the additional use of genetically modified tester strains can enhance the detectable substance spectrum with the bacterial genotoxicological standard procedures or increase the sensitivity. The additional use provides orienting information at this level as a lot of data can be obtained quite quickly and with little effort. These indications of the mechanism of action should be however verified with a test system that uses mammalian cells, better human cells, to check their actual relevance. The selection of appropriate additional tester strains has to be defined from case to case depending on the molecular structure and also still requires some major expertise.
Collapse
Affiliation(s)
- Eva-Maria Prantl
- Water Laboratory, RheinEnergie AG, Parkgürtel 24, 50823, Köln, Germany.
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Meike Kramer
- Water Laboratory, RheinEnergie AG, Parkgürtel 24, 50823, Köln, Germany
| | - Carsten K Schmidt
- Water Laboratory, RheinEnergie AG, Parkgürtel 24, 50823, Köln, Germany
| | - Martina Knauer
- Hydrotox GmbH, Bötzinger Straße 29, 79111, Freiburg im Breisgau, Germany
| | - Stefan Gartiser
- Hydrotox GmbH, Bötzinger Straße 29, 79111, Freiburg im Breisgau, Germany
| | - Aliaksandra Shuliakevich
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Julia Milas
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Hansruedi Glatt
- Department of Nutritional Toxicology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Walter Meinl
- Department of Nutritional Toxicology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| |
Collapse
|
8
|
Zhang Q, Ma X, Dzakpasu M, Wang XC. Evaluation of ecotoxicological effects of benzophenone UV filters: Luminescent bacteria toxicity, genotoxicity and hormonal activity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:338-347. [PMID: 28437725 DOI: 10.1016/j.ecoenv.2017.04.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/08/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The widespread use of organic ultraviolet (UV) filters in personal care products raises concerns about their potentially hazardous effects on human and ecosystem health. In this study, the toxicities of four commonly used benzophenones (BPs) UV filters including benzophenone (BP), 2-Hydroxybenzophenone (2HB), 2-Hydroxy-4-methoxybenzophenone (BP3), and 2-Hydroxy-4-methoxybenzophenone-5-sulfonicacid (BP4) in water were assayed in vitro using Vibrio fischeri, SOS/umu assay, and yeast estrogen screen (YES) assay, as well as in vivo using zebrafish larvae. The results showed that the luminescent bacteria toxicity, expressed as logEC50, increased with the lipophilicity (logKow) of BPs UV filters. Especially, since 2HB, BP3 and BP4 had different substituent groups, namely -OH, -OCH3 and -SO3H, respectively, these substituent functional groups had a major contribution to the lipophilicity and acute toxicity of these BPs. Similar tendency was observed for the genotoxicity, expressed as the value of induction ratio=1.5. Moreover, all the target BPs UV filters showed estrogenic activity, but no significant influences of lipophilicity on the estrogenicity were observed, with BP3 having the weakest estrogenic efficiency in vitro. Although BP3 displayed no noticeable adverse effects in any in vitro assays, multiple hormonal activities were observed in zebrafish larvae including estrogenicity, anti-estrogenicity and anti-androgenicity by regulating the expression of target genes. The results indicated potential hazardous effects of BPs UV filters and the importance of the combination of toxicological evaluation methods including in vitro and in vivo assays.
Collapse
Affiliation(s)
- Qiuya Zhang
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Engineering Technology Research Center for Wastewater Treatment and Reuse, Xi'an 710055, PR China; Key Lab of Environmental Engineering, Shaanxi Province, Xi'an 710055, PR China
| | - Xiaoyan Ma
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Engineering Technology Research Center for Wastewater Treatment and Reuse, Xi'an 710055, PR China; Key Lab of Environmental Engineering, Shaanxi Province, Xi'an 710055, PR China
| | - Mawuli Dzakpasu
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Engineering Technology Research Center for Wastewater Treatment and Reuse, Xi'an 710055, PR China; Key Lab of Environmental Engineering, Shaanxi Province, Xi'an 710055, PR China
| | - Xiaochang C Wang
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Engineering Technology Research Center for Wastewater Treatment and Reuse, Xi'an 710055, PR China; Key Lab of Environmental Engineering, Shaanxi Province, Xi'an 710055, PR China.
| |
Collapse
|
9
|
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: 2.5] [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.
Collapse
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
| |
Collapse
|
10
|
Goodman MF. Better living with hyper-mutation. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:421-34. [PMID: 27273795 PMCID: PMC4945469 DOI: 10.1002/em.22023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/05/2016] [Indexed: 05/12/2023]
Abstract
The simplest forms of mutations, base substitutions, typically have negative consequences, aside from their existential role in evolution and fitness. Hypermutations, mutations on steroids, occurring at frequencies of 10(-2) -10(-4) per base pair, straddle a domain between fitness and death, depending on the presence or absence of regulatory constraints. Two facets of hypermutation, one in Escherichia coli involving DNA polymerase V (pol V), the other in humans, involving activation-induced deoxycytidine deaminase (AID) are portrayed. Pol V is induced as part of the DNA-damage-induced SOS regulon, and is responsible for generating the lion's share of mutations when catalyzing translesion DNA synthesis (TLS). Four regulatory mechanisms, temporal, internal, conformational, and spatial, activate pol V to copy damaged DNA and then deactivate it. On the flip side of the coin, SOS-induced pols V, IV, and II mutate undamaged DNA, thus providing genetic diversity heightening long-term survival and evolutionary fitness. Fitness in humans is principally the domain of a remarkably versatile immune system marked by somatic hypermutations (SHM) in immunoglobulin variable (IgV) regions that ensure antibody (Ab) diversity. AID initiates SHM by deaminating C → U, favoring hot WRC (W = A/T, R = A/G) motifs. Since there are large numbers of trinucleotide motif targets throughout IgV, AID must exercise considerable catalytic restraint to avoid attacking such sites repeatedly, which would otherwise compromise diversity. Processive, random, and inefficient AID-catalyzed dC deamination simulates salient features of SHM, yet generates B-cell lymphomas when working at the wrong time in the wrong place. Environ. Mol. Mutagen. 57:421-434, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Myron F. Goodman
- Correspondence to Myron F. Goodman, Department of Biological Sciences, Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA,
| |
Collapse
|
11
|
Jaszczur M, Bertram JG, Robinson A, van Oijen AM, Woodgate R, Cox MM, Goodman MF. Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword. Biochemistry 2016; 55:2309-18. [PMID: 27043933 DOI: 10.1021/acs.biochem.6b00117] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1953, the year of Watson and Crick, bore witness to a less acclaimed yet highly influential discovery. Jean Weigle demonstrated that upon infection of Escherichia coli, λ phage deactivated by UV radiation, and thus unable to form progeny, could be reactivated by irradiation of the bacterial host. Evelyn Witkin and Miroslav Radman later revealed the presence of the SOS regulon. The more than 40 regulon genes are repressed by LexA protein and induced by the coproteolytic cleavage of LexA, catalyzed by RecA protein bound to single-stranded DNA, the RecA* nucleoprotein filament. Several SOS-induced proteins are engaged in repairing both cellular and extracellular damaged DNA. There's no "free lunch", however, because error-free repair is accompanied by error-prone translesion DNA synthesis (TLS), involving E. coli DNA polymerase V (UmuD'2C) and RecA*. This review describes the biochemical mechanisms of pol V-mediated TLS. pol V is active only as a mutasomal complex, pol V Mut = UmuD'2C-RecA-ATP. RecA* donates a single RecA subunit to pol V. We highlight three recent insights. (1) pol V Mut has an intrinsic DNA-dependent ATPase activity that governs polymerase binding and dissociation from DNA. (2) Active and inactive states of pol V Mut are determined at least in part by the distinct interactions between RecA and UmuC. (3) pol V is activated by RecA*, not at a blocked replisome, but at the inner cell membrane.
Collapse
Affiliation(s)
- Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States
| | - Andrew Robinson
- School of Chemistry, University of Wollongong , Wollongong, Australia
| | | | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health , Rockville, Maryland 20850, United States
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California , Los Angeles, California 90089-0371, United States.,Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
| |
Collapse
|
12
|
Affiliation(s)
- Rebecca S. Shapiro
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Institute of Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
13
|
Goodman MF. The discovery of error-prone DNA polymerase V and its unique regulation by RecA and ATP. J Biol Chem 2014; 289:26772-26782. [PMID: 25160630 DOI: 10.1074/jbc.x114.607374] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
My career pathway has taken a circuitous route, beginning with a Ph.D. degree in electrical engineering from The Johns Hopkins University, followed by five postdoctoral years in biology at Hopkins and culminating in a faculty position in biological sciences at the University of Southern California. My startup package in 1973 consisted of $2,500, not to be spent all at once, plus an ancient Packard scintillation counter that had a series of rapidly flashing light bulbs to indicate a radioactive readout in counts/minute. My research pathway has been similarly circuitous. The discovery of Escherichia coli DNA polymerase V (pol V) began with an attempt to identify the mutagenic DNA polymerase responsible for copying damaged DNA as part of the well known SOS regulon. Although we succeeded in identifying a DNA polymerase, one that was induced as part of the SOS response, we actually rediscovered DNA polymerase II, albeit in a new role. A decade later, we discovered a new polymerase, pol V, whose activity turned out to be regulated by bound molecules of RecA protein and ATP. This Reflections article describes our research trajectory, includes a review of key features of DNA damage-induced SOS mutagenesis leading us to pol V, and reflects on some of the principal researchers who have made indispensable contributions to our efforts.
Collapse
Affiliation(s)
- Myron F Goodman
- Molecular and Computational Section, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089.
| |
Collapse
|
14
|
Ye Y, Weiwei J, Na L, Mei M, Donghong W, Zijian W, Kaifeng R. Assessing of genotoxicity of 16 centralized source-waters in China by means of the SOS/umu assay and the micronucleus test: Initial identification of the potential genotoxicants by use of a GC/MS method and the QSAR Toolbox 3.0. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 763:36-43. [DOI: 10.1016/j.mrgentox.2013.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 09/10/2013] [Accepted: 11/02/2013] [Indexed: 10/25/2022]
|
15
|
Abstract
Living cells are continually exposed to DNA-damaging agents that threaten their genomic integrity. Although DNA repair processes rapidly target the damaged DNA for repair, some lesions nevertheless persist and block genome duplication by the cell's replicase. To avoid the deleterious consequence of a stalled replication fork, cells use specialized polymerases to traverse the damage. This process, termed "translesion DNA synthesis" (TLS), affords the cell additional time to repair the damage before the replicase returns to complete genome duplication. In many cases, this damage-tolerance mechanism is error-prone, and cell survival is often associated with an increased risk of mutagenesis and carcinogenesis. Despite being tightly regulated by a variety of transcriptional and posttranslational controls, the low-fidelity TLS polymerases also gain access to undamaged DNA where their inaccurate synthesis may actually be beneficial for genetic diversity and evolutionary fitness.
Collapse
Affiliation(s)
- Myron F Goodman
- Department of Biological Sciences and Department of Chemistry, University of Southern California, University Park, Los Angeles, California 90089-2910
| | | |
Collapse
|
16
|
Chaurasiya KR, Ruslie C, Silva MC, Voortman L, Nevin P, Lone S, Beuning PJ, Williams MC. Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA. Nucleic Acids Res 2013; 41:8959-68. [PMID: 23901012 PMCID: PMC3799427 DOI: 10.1093/nar/gkt648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.
Collapse
Affiliation(s)
- Kathy R. Chaurasiya
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Clarissa Ruslie
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Michelle C. Silva
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Lukas Voortman
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Philip Nevin
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Samer Lone
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Penny J. Beuning
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
| |
Collapse
|
17
|
A single residue unique to DinB-like proteins limits formation of the polymerase IV multiprotein complex in Escherichia coli. J Bacteriol 2013; 195:1179-93. [PMID: 23292773 DOI: 10.1128/jb.01349-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The activity of DinB is governed by the formation of a multiprotein complex (MPC) with RecA and UmuD. We identified two highly conserved surface residues in DinB, cysteine 66 (C66) and proline 67 (P67). Mapping on the DinB tertiary structure suggests these are noncatalytic, and multiple-sequence alignments indicate that they are unique among DinB-like proteins. To investigate the role of the C66-containing surface in MPC formation, we constructed the dinB(C66A) derivative. We found that DinB(C66A) copurifies with its interacting partners, RecA and UmuD, to a greater extent than DinB. Notably, copurification of RecA with DinB is somewhat enhanced in the absence of UmuD and is further increased for DinB(C66A). In vitro pulldown assays also indicate that DinB(C66A) binds RecA and UmuD better than DinB. We note that the increased affinity of DinB(C66A) for UmuD is RecA dependent. Thus, the C66-containing binding surface appears to be critical to modulate interaction with UmuD, and particularly with RecA. Expression of dinB(C66A) from the chromosome resulted in detectable differences in dinB-dependent lesion bypass fidelity and homologous recombination. Study of this DinB derivative has revealed a key surface on DinB, which appears to modulate the strength of MPC binding, and has suggested a binding order of RecA and UmuD to DinB. These findings will ultimately permit the manipulation of these enzymes to deter bacterial antibiotic resistance acquisition and to gain insights into cancer development in humans.
Collapse
|
18
|
Multiple strategies for translesion synthesis in bacteria. Cells 2012; 1:799-831. [PMID: 24710531 PMCID: PMC3901139 DOI: 10.3390/cells1040799] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/29/2012] [Accepted: 09/30/2012] [Indexed: 12/16/2022] Open
Abstract
Damage to DNA is common and can arise from numerous environmental and endogenous sources. In response to ubiquitous DNA damage, Y-family DNA polymerases are induced by the SOS response and are capable of bypassing DNA lesions. In Escherichia coli, these Y-family polymerases are DinB and UmuC, whose activities are modulated by their interaction with the polymerase manager protein UmuD. Many, but not all, bacteria utilize DinB and UmuC homologs. Recently, a C-family polymerase named ImuC, which is similar in primary structure to the replicative DNA polymerase DnaE, was found to be able to copy damaged DNA and either carry out or suppress mutagenesis. ImuC is often found with proteins ImuA and ImuB, the latter of which is similar to Y‑family polymerases, but seems to lack the catalytic residues necessary for polymerase activity. This imuAimuBimuC mutagenesis cassette represents a widespread alternative strategy for translesion synthesis and mutagenesis in bacteria. Bacterial Y‑family and ImuC DNA polymerases contribute to replication past DNA damage and the acquisition of antibiotic resistance.
Collapse
|
19
|
Ollivierre JN, Fang J, Beuning PJ. The Roles of UmuD in Regulating Mutagenesis. J Nucleic Acids 2010; 2010. [PMID: 20936072 PMCID: PMC2948943 DOI: 10.4061/2010/947680] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 08/01/2010] [Indexed: 11/20/2022] Open
Abstract
All organisms are subject to DNA damage from both endogenous and environmental sources. DNA damage that is not fully repaired can lead to mutations. Mutagenesis is now understood to be an active process, in part facilitated by lower-fidelity DNA polymerases that replicate DNA in an error-prone manner. Y-family DNA polymerases, found throughout all domains of life, are characterized by their lower fidelity on undamaged DNA and their specialized ability to copy damaged DNA. Two E. coli Y-family DNA polymerases are responsible for copying damaged DNA as well as for mutagenesis. These DNA polymerases interact with different forms of UmuD, a dynamic protein that regulates mutagenesis. The UmuD gene products, regulated by the SOS response, exist in two principal forms: UmuD(2), which prevents mutagenesis, and UmuD(2)', which facilitates UV-induced mutagenesis. This paper focuses on the multiple conformations of the UmuD gene products and how their protein interactions regulate mutagenesis.
Collapse
Affiliation(s)
- Jaylene N Ollivierre
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
| | | | | |
Collapse
|
20
|
Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF. A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol 2010; 45:171-84. [PMID: 20441441 DOI: 10.3109/10409238.2010.480968] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In Escherichia coli, cell survival and genomic stability after UV radiation depends on repair mechanisms induced as part of the SOS response to DNA damage. The early phase of the SOS response is mostly dominated by accurate DNA repair, while the later phase is characterized with elevated mutation levels caused by error-prone DNA replication. SOS mutagenesis is largely the result of the action of DNA polymerase V (pol V), which has the ability to insert nucleotides opposite various DNA lesions in a process termed translesion DNA synthesis (TLS). Pol V is a low-fidelity polymerase that is composed of UmuD'(2)C and is encoded by the umuDC operon. Pol V is strictly regulated in the cell so as to avoid genomic mutation overload. RecA nucleoprotein filaments (RecA*), formed by RecA binding to single-stranded DNA with ATP, are essential for pol V-catalyzed TLS both in vivo and in vitro. This review focuses on recent studies addressing the protein composition of active DNA polymerase V, and the role of RecA protein in activating this enzyme. Based on unforeseen properties of RecA*, we describe a new model for pol V-catalyzed SOS-induced mutagenesis.
Collapse
Affiliation(s)
- Meghna Patel
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | |
Collapse
|
21
|
Kivisaar M. Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads. FEMS Microbiol Lett 2010; 312:1-14. [DOI: 10.1111/j.1574-6968.2010.02027.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
22
|
Abstract
UV-induced melanogenesis (tanning) and "premature aging" or photoaging result in large part from DNA damage. This article reviews data tying both phenomena to telomere-based DNA damage signaling and develops a conceptual framework in which both responses may be understood as cancer-avoidance protective mechanisms.Journal of Investigative Dermatology Symposium Proceedings (2009) 14, 25-31; doi:10.1038/jidsymp.2009.9.
Collapse
|
23
|
Schlacher K, Goodman MF. Lessons from 50 years of SOS DNA-damage-induced mutagenesis. Nat Rev Mol Cell Biol 2007; 8:587-94. [PMID: 17551516 DOI: 10.1038/nrm2198] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This historical perspective integrates 50 years of research on SOS mutagenesis in Escherichia coli with the proverbial '3R' functions--replication, repair and recombination--that feature DNA polymerase V. Genetic and biochemical data are assimilated to arrive at a current picture of UV-damage-induced mutagenesis. An unprecedented DNA polymerase V transactivation mechanism, which involves the RecA protein, sheds new light on unresolved issues that have persisted over time, prompting us to reflect on evolving molecular concepts regarding DNA structures and polymerase-switching mechanisms.
Collapse
Affiliation(s)
- Katharina Schlacher
- University of Southern California, 1050 Childs Way, RIH 201B, Los Angeles, California 90089-2910, USA
| | | |
Collapse
|
24
|
Neuwoehner J, Schofer A, Erlenkaemper B, Steinbach K, Hund-Rinke TK, Eisentraeger A. Toxicological characterization of 2,4,6-trinitrotoluene, its transformation products, and two nitramine explosives. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2007; 26:1090-9. [PMID: 17571672 DOI: 10.1897/06-471r.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The soil and groundwater of former ordnance plants and their dumping sites have often been highly contaminated with the explosive 2,4,6-trinitrotoluene (2,4,6-TNT) leading to a potential hazard for humans and the environment. Further hazards can arise from metabolites of transformation, by-products of the manufacturing process, or incomplete combustion. This work examines the toxicity of polar nitro compounds relative to their parent compound 2,4,6-TNT using four different ecotoxicological bioassays (algae growth inhibition test, daphnids immobilization test, luminescence inhibition test, and cell growth inhibition test), three genotoxicological assays (umu test, NM2009 test, and SOS Chromotest), and the Ames fluctuation test for detection of mutagenicity. For this study, substances typical for certain steps of degradation/transformation of 2,4,6-TNT were chosen for investigation. This work determines that the parent compounds 2,4,6-TNT and 1,3,5-trinitrobenzene are the most toxic substances followed by 3,5-dinitrophenol, 3,5-dinitroaniline and 4-amino-2-nitrotoluene. Less toxic are the direct degradation products of 2,4,6-TNT like 2,4-dinitrotoluene, 2,6-dinitrotoluene, 2-amino-4,6-dinitrotoluene, and 4-amino-2,6-dinitrotoluene. A weak toxic potential was observed for 2,4,6-trinitrobenzoic acid, 2,4-diamino-6-nitrotoluene, 2,4-dinitrotoluene-5-sulfonic acid, and 2,6-diamino-4-nitrotoluene. Octahydro-l,3,5,7-tetranitro-l,3,5,7-tetrazocine and hexahydro-1,3,5-trinitro-l,3,5-triazine show no hint of acute toxicity. Based on the results of this study, we recommend expanding future monitoring programs of not only the parent substances but also potential metabolites based on conditions at the contaminated sites and to use bioassays as tools for estimating the toxicological potential directly by testing environmental samples. Site-specific protocols should be developed. If hazardous substances are found in relevant concentrations, action should be taken to prevent potential risks for humans and the environment. Analyses can then be used to prioritise reliable estimates of risk.
Collapse
Affiliation(s)
- Judith Neuwoehner
- Aachen University of Technology, Institute of Hygiene and Environmental Medicine, Pauwelsstrasse 30, 52074 Aachen, Germany
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
The identification and partial purification by Arthur Kornberg and his colleagues in 1956 of an enzyme - DNA polymerase I of Escherichia coli - that catalysed the stable incorporation of deoxyribonucleotides into DNA in vitro came as a surprise. At the time, most scientists in the field believed that DNA synthesis was too complicated to be accurately reflected outside the living cell.
Collapse
Affiliation(s)
- Errol C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 79503-9072, USA.
| |
Collapse
|
26
|
Abstract
When cells that are actively replicating DNA encounter sites of base damage or strand breaks, replication might stall or arrest. In this situation, cells rely on DNA-damage-tolerance mechanisms to bypass the damage effectively. One of these mechanisms, known as translesion DNA synthesis, is supported by specialized DNA polymerases that are able to catalyse nucleotide incorporation opposite lesions that cannot be negotiated by high-fidelity replicative polymerases. A second category of tolerance mechanism involves alternative replication strategies that obviate the need to replicate directly across sites of template-strand damage.
Collapse
Affiliation(s)
- Errol C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9072, USA.
| |
Collapse
|
27
|
Reifferscheid G, Arndt C, Schmid C. Further development of the beta-lactamase MutaGen assay and evaluation by comparison with Ames fluctuation tests and the umu test. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2005; 46:126-39. [PMID: 15880735 DOI: 10.1002/em.20140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A rapid, high-throughput bacterial mutagenicity test system has been developed (MutaGen test) that detects reversions of inactivating base-pair substitutions and frameshifts in a TEM-1 class A beta-lactamase (ampicillinase) gene. To quickly and sensitively detect mutagens, the system utilises a series of plasmids that contain the mutated ampicillinase gene and the mucAB operon. Inactivating mutations in the ampicillinase gene include frameshifts integrated into repetitive GC-sequences and G-runs known to be mutagenic hot-spots, and base-pair substitutions inserted in or around the beta-lactamase active site. Frameshift mutations completely inactivated the enzyme only when located downstream of the active-site serine (Ser68). Previous (reporter gene based) assays with this system have detected reversion to ampicillin resistance by luminescence driven by induction of the tet-promotor controlled lacZ gene. In the present study, we describe the construction and evaluation of 19 additional potential tester strains. We also developed conditions for detecting reversions by pH shift using bromocresol purple and by directly detecting the enzymatic activity of beta-lactamase using nitrocefin. A 384-well format version of the pH shift MutaGen test was used to assay more than 20 chemicals. The responses in the assay were compared with responses for the same chemicals in the umu test and Ames fluctuation assays. The results indicate that the MutaGen test has high specificity for detecting specific mutations and, in some instances, better sensitivity than the other tests. Since the test is easy to conduct, sterile working conditions are not necessary, and the mutagenicity results are available either within one working day or overnight, the assay shows promise for the rapid screening of potentially genotoxic substances.
Collapse
Affiliation(s)
- Georg Reifferscheid
- Department of Environmental and Molecular Genotoxicity (AMMUG), University of Mainz, Germany.
| | | | | |
Collapse
|
28
|
Fujii S, Gasser V, Fuchs RP. The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. J Mol Biol 2004; 341:405-17. [PMID: 15276832 DOI: 10.1016/j.jmb.2004.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 06/04/2004] [Accepted: 06/08/2004] [Indexed: 11/29/2022]
Abstract
In addition to replicative DNA polymerases, cells contain specialized DNA polymerases involved in processes such as lesion tolerance, mutagenesis and immunoglobulin diversity. In Escherichia coli, DNA polymerase V (Pol V), encoded by the umuDC locus, is involved in translesion synthesis (TLS) and mutagenesis. Genetic studies have established that mutagenesis requires both UmuC and a proteolytic product of UmuD (UmuD'). In addition, RecA protein and the replication processivity factor, the beta-clamp, were genetically found to be essential co-factors for mutagenesis. Here, we have reconstituted Pol V-mediated bypass of three common replication-blocking lesions, namely the two major UV-induced lesions and a guanine adduct formed by a chemical carcinogen (G-AAF) under conditions that fulfil these in vivo requirements. Two co-factors are essential for efficient Pol V-mediated lesion bypass: (i) a DNA substrate onto which the beta-clamp is stably loaded; and (ii) an extended single-stranded RecA/ATP filament assembled downstream from the lesion site. For efficient bypass, Pol V needs to interact simultaneously with the beta-clamp and the 3' tip of the RecA filament. Formation of an extended RecA/ATP filament and stable loading of the beta-clamp are best achieved on long single-stranded circular DNA templates. In contrast to previously published data, the single-stranded DNA-binding protein (SSB) is not absolutely required for Pol V-mediated lesion bypass provided ATP, instead of ATPgammaS, activates the RecA filament. Further discrepancies with the existing literature are explainable by the use of either inadequate DNA substrates or a UmuC fusion protein instead of native Pol V.
Collapse
Affiliation(s)
- Shingo Fujii
- UPR 9003 du CNRS, Cancerogenese et Mutagenese Moleculaire et Structurale, 67400 Strasbourg, France
| | | | | |
Collapse
|
29
|
Sommer S, Becherel OJ, Coste G, Bailone A, Fuchs RPP. Altered translesion synthesis in E. coli Pol V mutants selected for increased recombination inhibition. DNA Repair (Amst) 2004; 2:1361-9. [PMID: 14642565 DOI: 10.1016/j.dnarep.2003.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Replication of damaged DNA, also termed as translesion synthesis (TLS), involves specialized DNA polymerases that bypass DNA lesions. In Escherichia coli, although TLS can involve one or a combination of DNA polymerases depending on the nature of the lesion, it generally requires the Pol V DNA polymerase (formed by two SOS proteins, UmuD' and UmuC) and the RecA protein. In addition to being an essential component of translesion DNA synthesis, Pol V is also an antagonist of RecA-mediated recombination. We have recently isolated umuD' and umuC mutants on the basis of their increased capacity to inhibit homologous recombination. Despite the capacity of these mutants to form a Pol V complex and to interact with the RecA polymer, most of them exhibit a defect in TLS. Here, we further characterize the TLS activity of these Pol V mutants in vivo by measuring the extent of error-free and mutagenic bypass at a single (6-4)TT lesion located in double stranded plasmid DNA. TLS is markedly decreased in most Pol V mutants that we analyzed (8/9) with the exception of one UmuC mutant (F287L) that exhibits wild-type bypass activity. Somewhat unexpectedly, Pol V mutants that are partially deficient in TLS are more severely affected in mutagenic bypass compared to error-free synthesis. The defect in bypass activity of the Pol V mutant polymerases is discussed in light of the location of the respective mutations in the 3D structure of UmuD' and the DinB/UmuC homologous protein Dpo4 of Sulfolobus solfataricus.
Collapse
Affiliation(s)
- Suzanne Sommer
- Institut de Génétique et Microbiologie, Bât. 409, Université Paris-Sud, F-91405, Orsay, France.
| | | | | | | | | |
Collapse
|
30
|
Fuchs RP, Fujii S, Wagner J. Properties and functions of Escherichia coli: Pol IV and Pol V. ADVANCES IN PROTEIN CHEMISTRY 2004; 69:229-64. [PMID: 15588845 DOI: 10.1016/s0065-3233(04)69008-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Escherichia coli possesses two members of the newly discovered class of Y DNA polymerases (Ohmori et al., 2001): Pol IV (dinB) and Pol V (umuD'C). Polymerases that belong to this family are often referred to as specialized or error-prone DNA polymerases to distinguish them from the previously discovered DNA polymerases (Pol I, II, and III) that are essentially involved in DNA replication or error-free DNA repair. Y-family DNA polymerases are characterized by their capacity to replicate DNA, through chemically damaged template bases, or to elongate mismatched primer termini. These properties stem from their capacity to accommodate and use distorted primer templates within their active site and from the lack of an associated exonuclease activity. Even though both belong to the Y-family, Pol IV and Pol V appear to perform distinct physiological functions. Although Pol V is clearly the major lesion bypass polymerase involved in damage-induced mutagenesis, the role of Pol IV remains enigmatic. Indeed, compared to a wild-type strain, a dinB mutant exhibits no clear phenotype with respect to survival or mutagenesis following treatment with DNA-damaging agents. Subtler dinB phenotypes will be discussed below. Moreover, despite the fact that both dinB and umuDC loci are controlled by the SOS response, their constitutive and induced levels of expression are dramatically different. In noninduced cells, Pol V is undetectable by Western analysis. In contrast, it is estimated that there are about 250 copies of Pol IV per cell. On SOS induction, it is believed that only about 15 molecules of Pol V are assembled per cell (S. Sommer, personal communication), whereas Pol IV levels reach approximately 2500 molecules. In fact, despite extensive knowledge of the individual enzymatic properties of all five E. coli DNA polymerases, much more work is needed to understand how their activities are orchestrated within a living cell.
Collapse
Affiliation(s)
- Robert P Fuchs
- Cancérogenèse et Mutagenèse Moléculaire et Structurale, CNRS ESBS, 67400 Strasbourg, France
| | | | | |
Collapse
|
31
|
Goodman MF, Woodgate R. The biochemical basis and in vivo regulation of SOS-induced mutagenesis promoted by Escherichia coli DNA polymerase V (UmuD'2C). COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 65:31-40. [PMID: 12760018 DOI: 10.1101/sqb.2000.65.31] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- M F Goodman
- University of Southern California, Hedco Molecular Biology Laboratory, Department of Biological Sciences and Chemistry, Los Angeles, California 90089-1340, USA
| | | |
Collapse
|
32
|
Janion C, Sikora A, Nowosielska A, Grzesiuk E. E. coli BW535, a triple mutant for the DNA repair genes xth, nth, and nfo, chronically induces the SOS response. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2003; 41:237-242. [PMID: 12717778 DOI: 10.1002/em.10154] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A strong chronic induction of the SOS response system occurs in E. coli BW535, a strain defective in nth, nfo and xth genes, and hence severely deficient in the repair of abasic sites in DNA. This was shown here by visualization of filamentous growth of the BW535 strain and by measuring the level of beta-galactosidase expressed in BW535/pSK1002 in comparison to the AB1157/pSK1002 strain. The plasmid pSK1002 bears an umuC::lacZ fusion in which lacZ is under the control of the umuC promoter and regulated under the SOS regulon. Increases in the expression of beta-galactosidase occur in BW535 without any exogenous SOS inducer. Chronic induction of the SOS response was observed previously in E. coli strains bearing mutations in certain genes that have mutator activity and BW535 is a moderate mutator strain. However, not all mutators show this property, since chronic induction of SOS was not observed in mutT or mutY mutators. MutT and MutY proteins, when active, protect bacteria from mutations induced by 8-oxoG lesions in DNA. This suggests that accumulation of abasic sites, but not 8-oxoG residues in DNA, induce the SOS response.
Collapse
Affiliation(s)
- Celina Janion
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | | | | | | |
Collapse
|
33
|
Abstract
DNA repair is crucial to the well-being of all organisms from unicellular life forms to humans. A rich tapestry of mechanistic studies on DNA repair has emerged thanks to the recent discovery of Y-family DNA polymerases. Many Y-family members carry out aberrant DNA synthesis-poor replication accuracy, the favored formation of non-Watson-Crick base pairs, efficient mismatch extension, and most importantly, an ability to replicate through DNA damage. This review is devoted primarily to a discussion of Y-family polymerase members that exhibit error-prone behavior. Roles for these remarkable enzymes occur in widely disparate DNA repair pathways, such as UV-induced mutagenesis, adaptive mutation, avoidance of skin cancer, and induction of somatic cell hypermutation of immunoglobulin genes. Individual polymerases engaged in multiple repair pathways pose challenging questions about their roles in targeting and trafficking. Macromolecular assemblies of replication-repair "factories" could enable a cell to handle the complex logistics governing the rapid migration and exchange of polymerases.
Collapse
Affiliation(s)
- Myron F Goodman
- Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratory, University of Southern California, Los Angeles, California 90089-1340, USA.
| |
Collapse
|
34
|
Pham P, Seitz EM, Saveliev S, Shen X, Woodgate R, Cox MM, Goodman MF. Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc Natl Acad Sci U S A 2002; 99:11061-6. [PMID: 12177433 PMCID: PMC123210 DOI: 10.1073/pnas.172197099] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2002] [Indexed: 11/18/2022] Open
Abstract
SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.
Collapse
Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-1340, USA
| | | | | | | | | | | | | |
Collapse
|
35
|
Gawel D, Maliszewska-Tkaczyk M, Jonczyk P, Schaaper RM, Fijalkowska IJ. Lack of strand bias in UV-induced mutagenesis in Escherichia coli. J Bacteriol 2002; 184:4449-54. [PMID: 12142415 PMCID: PMC135265 DOI: 10.1128/jb.184.16.4449-4454.2002] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We have investigated whether UV-induced mutations are created with equal efficiency on the leading and lagging strands of DNA replication. We employed an assay system that permits measurement of mutagenesis in the lacZ gene in pairs of near-identical strains. Within each pair, the strains differ only in the orientation of the lacZ gene with respect to the origin of DNA replication. Depending on this orientation, any lacZ target sequence will be replicated in one orientation as a leading strand and as a lagging strand in the other orientation. In contrast to previous results obtained for mutations resulting from spontaneous replication errors or mutations resulting from the spontaneous SOS mutator effect, measurements of UV-induced mutagenesis in uvrA strains fail to show significant differences between the two target orientations. These data suggest that SOS-mediated mutagenic translesion synthesis on the Escherichia coli chromosome may occur with equal or similar probability on leading and lagging strands.
Collapse
Affiliation(s)
- Damian Gawel
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02 106 Warsaw, Poland
| | | | | | | | | |
Collapse
|
36
|
Abstract
Increases in ultraviolet radiation at the Earth's surface due to the depletion of the stratospheric ozone layer have recently fuelled interest in the mechanisms of various effects it might have on organisms. DNA is certainly one of the key targets for UV-induced damage in a variety of organisms ranging from bacteria to humans. UV radiation induces two of the most abundant mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) and their Dewar valence Isomers. However, cells have developed a number of repair or tolerance mechanism to counteract the DNA damage caused by UV or any other stressors. Photoreactivation with the help of the enzyme photolyase is one of the most important and frequently occurring repair mechanisms in a variety of organisms. Excision repair, which can be distinguished into base excision repair (BER) and nucleotide excision repair (NER), also plays an important role in DNA repair in several organisms with the help of a number of glycosylases and polymerases, respectively. In addition, mechanisms such as mutagenic repair or dimer bypass, recombinational repair, cell-cycle checkpoints, apoptosis and certain alternative repair pathways are also operative in various organisms. This review deals with UV-induced DNA damage and the associated repair mechanisms as well as methods of detecting DNA damage and its future perspectives.
Collapse
Affiliation(s)
- Rajeshwar P Sinha
- Institut für Botanik und Pharmazeutische Biologie, Friedrich-Alexander-Universität, Staudtstr. 5, D-91058 Erlangen, Germany
| | | |
Collapse
|
37
|
Abstract
It has recently become clear that the recombinational repair of stalled replication forks is the primary function of homologous recombination systems in bacteria. In spite of the rapid progress in many related lines of inquiry that have converged to support this view, much remains to be done. This review focuses on several key gaps in understanding. Insufficient data currently exists on: (a) the levels and types of DNA damage present as a function of growth conditions, (b) which types of damage and other barriers actually halt replication, (c) the structures of the stalled/collapsed replication forks, (d) the number of recombinational repair paths available and their mechanistic details, (e) the enzymology of some of the key reactions required for repair, (f) the role of certain recombination proteins that have not yet been studied, and (g) the molecular origin of certain in vivo observations associated with recombinational DNA repair during the SOS response. The current status of each of these topics is reviewed.
Collapse
Affiliation(s)
- M M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.
| |
Collapse
|
38
|
Pham P, Rangarajan S, Woodgate R, Goodman MF. Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc Natl Acad Sci U S A 2001; 98:8350-4. [PMID: 11459974 PMCID: PMC37442 DOI: 10.1073/pnas.111007198] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD(2)(') proteins, working in conjunction with RecA, single-stranded DNA (ssDNA)-binding protein (SSB), beta sliding clamp, and gamma clamp loading complex, are responsible for most SOS lesion-targeted mutations in Escherichia coli, by catalyzing translesion synthesis (TLS). DNA polymerase II, the product of the damage-inducible polB (dinA ) gene plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Replication-restart takes place almost immediately after the DNA is damaged (approximately 2 min post-UV irradiation), whereas TLS occurs after pol V is induced approximately 50 min later. We discuss recent data for pol V-catalyzed TLS and pol II-catalyzed replication-restart. Specific roles during TLS for pol V and each of its accessory factors have been recently determined. Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins.
Collapse
Affiliation(s)
- P Pham
- Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089-1340, USA
| | | | | | | |
Collapse
|
39
|
Livneh Z. DNA damage control by novel DNA polymerases: translesion replication and mutagenesis. J Biol Chem 2001; 276:25639-42. [PMID: 11371576 DOI: 10.1074/jbc.r100019200] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Z Livneh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
40
|
Sutton MD, Smith BT, Godoy VG, Walker GC. The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Annu Rev Genet 2001; 34:479-497. [PMID: 11092836 DOI: 10.1146/annurev.genet.34.1.479] [Citation(s) in RCA: 221] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Be they prokaryotic or eukaryotic, organisms are exposed to a multitude of deoxyribonucleic acid (DNA) damaging agents ranging from ultraviolet (UV) light to fungal metabolites, like Aflatoxin B1. Furthermore, DNA damaging agents, such as reactive oxygen species, can be produced by cells themselves as metabolic byproducts and intermediates. Together, these agents pose a constant threat to an organism's genome. As a result, organisms have evolved a number of vitally important mechanisms to repair DNA damage in a high fidelity manner. They have also evolved systems (cell cycle checkpoints) that delay the resumption of the cell cycle after DNA damage to allow more time for these accurate processes to occur. If a cell cannot repair DNA damage accurately, a mutagenic event may occur. Most bacteria, including Escherichia coli, have evolved a coordinated response to these challenges to the integrity of their genomes. In E. coli, this inducible system is termed the SOS response, and it controls both accurate and potentially mutagenic DNA repair functions [reviewed comprehensively in () and also in ()]. Recent advances have focused attention on the umuD(+)C(+)-dependent, translesion DNA synthesis (TLS) process that is responsible for SOS mutagenesis (). Here we discuss the SOS response of E. coli and concentrate in particular on the roles of the umuD(+)C(+) gene products in promoting cell survival after DNA damage via TLS and a primitive DNA damage checkpoint.
Collapse
Affiliation(s)
- M D Sutton
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | |
Collapse
|
41
|
Abstract
The products of the SOS-regulated umuDC genes are required for most UV and chemical mutagenesis in Escherichia coli. Recently it has been recognized that UmuC is the founding member of a superfamily of novel DNA polymerases found in all three kingdoms of life. Key findings leading to these insights are reviewed, placing a particular emphasis on contributions made by Bryn Bridges and on his interest in the importance of interactions between the umuDC gene products and the replicative DNA polymerase.
Collapse
Affiliation(s)
- G C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
42
|
Abstract
It is quite remarkable how our understanding of translesion DNA synthesis (TLS) has changed so dramatically in the past 2 years. Until very recently, little was known about the molecular mechanisms of TLS in higher eukaryotes and what we did know, was largely based upon Escherichia coli and Saccharomyces cerevisiae model systems. The paradigm, proposed by Bryn Bridges and I [Mutat. Res. 150 (1985) 133] in 1985, was that error-prone TLS occurred in two steps; namely a misinsertion event opposite a lesion, followed by extension of the mispair so as to facilitate complete bypass of the lesion. The initial concept was that at least for E. coli, the misinsertion event was performed by the cell's main replicase, DNA polymerase III holoenzyme, and that elongation was achieved through the actions of specialized polymerase accessory proteins, such as UmuD and UmuC. Some 15 years later, we now know that this view is likely to be incorrect in that both misinsertion and bypass are performed by the Umu proteins (now called pol V). As pol V is normally a distributive enzyme, pol III may only be required to "fix" the misincorporation as a mutation by completing chromosome duplication. However, while the role of the E. coli proteins involved in TLS have changed, the initial concept of misincorporation followed by extension/bypass remains valid. Indeed, recent evidence suggests that it can equally be applied to TLS in eukaryotic cells where there are many more DNA polymerases to choose from. The aim of this review is, therefore, to provide a historical perspective to the "two-step" model for UV-mutagenesis, how it has recently evolved, and in particular, to highlight the seminal contributions made to it by Bryn Bridges.
Collapse
Affiliation(s)
- R Woodgate
- Section on DNA Replication, Repair and Mutagenesis, National Institute of Child Health and Human Development, Bethesda, MD 20892-2725, USA.
| |
Collapse
|
43
|
Reuven NB, Arad G, Stasiak AZ, Stasiak A, Livneh Z. Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament. J Biol Chem 2001; 276:5511-7. [PMID: 11084028 DOI: 10.1074/jbc.m006828200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Translesion replication is carried out in Escherichia coli by the SOS-inducible DNA polymerase V (UmuC), an error-prone polymerase, which is specialized for replicating through lesions in DNA, leading to the formation of mutations. Lesion bypass by pol V requires the SOS-regulated proteins UmuD' and RecA and the single-strand DNA-binding protein (SSB). Using an in vitro assay system for translesion replication based on a gapped plasmid carrying a site-specific synthetic abasic site, we show that the assembly of a RecA nucleoprotein filament is required for lesion bypass by pol V. This is based on the reaction requirements for stoichiometric amounts of RecA and for single-stranded gaps longer than 100 nucleotides and on direct visualization of RecA-DNA filaments by electron microscopy. SSB is likely to facilitate the assembly of the RecA nucleoprotein filament; however, it has at least one additional role in lesion bypass. ATPgammaS, which is known to strongly increase binding of RecA to DNA, caused a drastic inhibition of pol V activity. Lesion bypass does not require stoichiometric binding of UmuD' along RecA filaments. In summary, the RecA nucleoprotein filament, previously known to be required for SOS induction and homologous recombination, is also a critical intermediate in translesion replication.
Collapse
Affiliation(s)
- N B Reuven
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | |
Collapse
|
44
|
Sutton MD, Murli S, Opperman T, Klein C, Walker GC. umuDC-dnaQ Interaction and its implications for cell cycle regulation and SOS mutagenesis in Escherichia coli. J Bacteriol 2001; 183:1085-9. [PMID: 11208808 PMCID: PMC94977 DOI: 10.1128/jb.183.3.1085-1089.2001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2000] [Accepted: 10/20/2000] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli SOS-regulated umuDC gene products participate in a DNA damage checkpoint control and in translesion DNA synthesis. Specific interactions involving the UmuD and UmuD' proteins, both encoded by the umuD gene, and components of the replicative DNA polymerase, Pol III, appear to be important for regulating these two biological activities of the umuDC gene products. Here we show that overproduction of the epsilon proofreading subunit of Pol III suppresses the cold sensitivity normally associated with overexpression of the umuDC gene products. Our results suggest that this suppression is attributable to specific interactions between UmuD or UmuD' and the C-terminal domain of epsilon.
Collapse
Affiliation(s)
- M D Sutton
- Biology Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | |
Collapse
|
45
|
Tippin B, Goodman MF. A new class of errant DNA polymerases provides candidates for somatic hypermutation. Philos Trans R Soc Lond B Biol Sci 2001; 356:47-51. [PMID: 11205329 PMCID: PMC1087690 DOI: 10.1098/rstb.2000.0747] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanism of somatic hypermutation of the immunoglobulin genes remains a mystery after nearly 30 years of intensive research in the field. While many clues to the process have been discovered in terms of the genetic elements required in the immunoglobulin genes, the key enzymatic players that mediate the introduction of mutations into the variable region are unknown. The recent wave of newly discovered eukaryotic DNA polymerases have given a fresh supply of potential candidates and a renewed vigour in the search for the elusive mutator factor governing affinity maturation. In this paper, we discuss the relevant genetic and biochemical evidence known to date regarding both somatic hypermutation and the new DNA polymerases and address how the two fields can be brought together to identify the strongest candidates for further study. In particular we discuss evidence for the in vitro biochemical misincorporation properties of human Rad30B/Pol iota and how it compares to the in vivo somatic hypermutation spectra.
Collapse
Affiliation(s)
- B Tippin
- Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles 90089-1340, USA
| | | |
Collapse
|
46
|
Friedberg EC. Why do cells have multiple error-prone DNA polymerases? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2001; 38:105-110. [PMID: 11746742 DOI: 10.1002/em.1059] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent years have witnessed the emergence of a plethora of so-called novel DNA polymerases in both eukaryotic and prokaryotic cells. Many of these DNA polymerases are characterized by poor replicational fidelity and low processivity, and are devoid of 3' --> 5' exonuclease activity. This article describes the discovery of these error-prone polymerases and what is known about their biological function.
Collapse
Affiliation(s)
- E C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9072, USA
| |
Collapse
|
47
|
Goldsmith M, Sarov-Blat L, Livneh Z. Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA', RecA, and SSB. Proc Natl Acad Sci U S A 2000; 97:11227-31. [PMID: 11016960 PMCID: PMC17182 DOI: 10.1073/pnas.200361997] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replication through damaged sites in DNA requires in Escherichia coli the SOS stress-inducible DNA polymerase V (UmuC), which is specialized for lesion bypass. Homologs of the umuC gene were found on native conjugative plasmids, which often carry multiple antibiotic-resistant genes. MucB is a UmuC homolog present on plasmid R46, and its variant plasmid pKM101 has been introduced into Salmonella strains for use in the Ames test for mutagens. Using a translesion replication assay based on a gapped plasmid carrying a site-specific synthetic abasic site in the single-stranded DNA region, we show that MucB is a DNA polymerase, termed pol RI, which is specialized for lesion bypass. The activity of pol RI requires the plasmid-encoded MucA' protein and the E. coli RecA and single-strand DNA binding proteins. Elimination of any of the proteins from the reaction abolished lesion bypass and polymerase activity. The unprocessed MucA could not substitute for MucA' in the bypass reaction. The presence of a lesion bypass DNA polymerase on a native conjugative plasmid, which has a broad host range specificity and carries multiple antibiotic-resistant genes, raises the possibility that mutagenesis caused by pol RI plays a role in the spreading of antibiotic resistance among bacterial pathogens.
Collapse
Affiliation(s)
- M Goldsmith
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
48
|
Chattopadhyaya R, Ghosh K, Namboodiri VM. Model of a LexA repressor dimer bound to recA operator. J Biomol Struct Dyn 2000; 18:181-97. [PMID: 11089640 DOI: 10.1080/07391102.2000.10506657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A complete three dimensional model (RCSB000408; PDB code 1qaa) for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor is proposed. A model of interaction of the N-terminal operator binding domain 1-72 with the operator was available. We have modelled residues 106-202 of LexA on the basis of the crystal structure of a homologous protein, UmuD'. Residues 70-105 have been modelled by us, residues 70-77 comprising the real hinge, followed by a beta-strand and an alpha-helix, both interacting with the rest of the C-domain. The preexponential Arrhenius factor for the LexA autocleavage is shown to be approximately 10(9) s(-1) at 298K whereas the exponential factor is approximately 2 x 10(-12), demanding that the autocleavage site is quite close to the catalytic site but reaction is slow due to an activation energy barrier. We propose that in the operator bound form, Ala 84- Gly 85 is about 7-10A from the catalytic groups, but the reaction does not occur as the geometry is not suitable for a nucleophilic attack from Ser 119 Ogamma, since Pro 87 is held in the cis conformation. When pH is elevated or under the action of activated RecA, cleavage may occur following a cis --> trans isomerization at Pro 87 and/or a rotation of the region beta9-beta10 about beta7-beta8 following the disruption of two hydrogen bonds. We show that the C-C interaction comprises the approach of two negatively charged surfaces neutralized by sodium ions, the C-domains of the monomers making a new beta barrel at the interface burying 710A2 of total surface area of each monomer.
Collapse
|
49
|
Ravin V, Ravin N, Casjens S, Ford ME, Hatfull GF, Hendrix RW. Genomic sequence and analysis of the atypical temperate bacteriophage N15. J Mol Biol 2000; 299:53-73. [PMID: 10860722 DOI: 10.1006/jmbi.2000.3731] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
N15 is a temperate bacteriophage that forms stable lysogens in Escherichia coli. While its virion is morphologically very similar to phage lambda and its close relatives, it is unusual in that the prophage form replicates autonomously as a linear DNA molecule with closed hairpin telomeres. Here, we describe the genomic architecture of N15, and its global pattern of gene expression, which reveal that N15 contains several plasmid-derived genes that are expressed in N15 lysogens. The tel site, at which processing occurs to form the prophage ends is close to the center of the genome in a similar location to that occupied by the attachment site, attP, in lambda and its relatives and defines the boundary between the left and right arms. The left arm contains a long cluster of structural genes that are closely related to those of the lambda-like phages, but also includes homologs of umuD', which encodes a DNA polymerase accessory protein, and the plasmid partition genes, sopA and sopB. The right arm likewise contains a mixture of apparently phage- and plasmid-derived genes including genes encoding plasmid replication functions, a phage repressor, a transcription antitermination system, as well as phage host cell lysis genes and two putative DNA methylases. The unique structure of the N15 genome suggests that the large global population of bacteriophages may exhibit a much greater diversity of genomic architectures than was previously recognized.
Collapse
MESH Headings
- Bacteriolysis
- Bacteriophage lambda/genetics
- Bacteriophages/enzymology
- Bacteriophages/genetics
- Bacteriophages/ultrastructure
- Base Composition
- Base Sequence
- Escherichia coli/physiology
- Escherichia coli/virology
- Gene Expression Regulation, Bacterial
- Genes, Viral/genetics
- Genome, Viral
- Lysogeny/genetics
- Microscopy, Electron
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Response Elements/genetics
- Sequence Analysis, DNA
- Terminator Regions, Genetic/genetics
- Transcription, Genetic/genetics
- Viral Proteins/genetics
Collapse
Affiliation(s)
- V Ravin
- Center for Bioengineering, Russian Academy of Science, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
50
|
Tang M, Pham P, Shen X, Taylor JS, O'Donnell M, Woodgate R, Goodman MF. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 2000; 404:1014-8. [PMID: 10801133 DOI: 10.1038/35010020] [Citation(s) in RCA: 345] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The expression of the Escherichia coli DNA polymerases pol V (UmuD'2C complex) and pol IV (DinB) increases in response to DNA damage. The induction of pol V is accompanied by a substantial increase in mutations targeted at DNA template lesions in a process called SOS-induced error-prone repair. Here we show that the common DNA template lesions, TT (6-4) photoproducts, TT cis-syn photodimers and abasic sites, are efficiently bypassed within 30 seconds by pol V in the presence of activated RecA protein (RecA*), single-stranded binding protein (SSB) and pol III's processivity beta,gamma-complex. There is no detectable bypass by either pol IV or pol III on this time scale. A mutagenic 'signature' for pol V is its incorporation of guanine opposite the 3'-thymine of a TT (6-4) photoproduct, in agreement with mutational spectra. In contrast, pol III and pol IV incorporate adenine almost exclusively. When copying undamaged DNA, pol V exhibits low fidelity with error rates of around 10(-3) to 10(-4), with pol IV being 5- to 10-fold more accurate. The effects of RecA protein on pol V, and beta,gamma-complex on pol IV, cause a 15,000- and 3,000-fold increase in DNA synthesis efficiency, respectively. However, both polymerases exhibit low processivity, adding 6 to 8 nucleotides before dissociating. Lesion bypass by pol V does not require beta,gamma-complex in the presence of non-hydrolysable ATPgammaS, indicating that an intact RecA filament may be required for translesion synthesis.
Collapse
Affiliation(s)
- M Tang
- Department of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles 90089-1340, USA
| | | | | | | | | | | | | |
Collapse
|