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Yang M, Liang X, Song X, Wu F, Xu Y, Liu M, Zhang T, Zeng X, Wu Z, Pan D, Luo H, Guo Y. Proteomic Analysis of Milk Fat Globule Membrane Protein Modulation of Differently Expressed Proteins in Lactobacillus plantarum under Bile Salt Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13125-13137. [PMID: 38805674 DOI: 10.1021/acs.jafc.4c01747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Tolerance to bile stress is a crucial property for lactic acid bacteria (LAB) to survive in the gastrointestinal tract and exert their beneficial effects. Whey powder enriched with milk fat globule membrane proteins (M-WPI) as a functional component is protective for strains under stress conditions. The current study investigated the key mechanisms of action involved in Lactobacillus plantarum (L. plantarum) CGMCC 23701 survival in the presence of bile and the protective mechanism of M-WPI. According to proteomic analysis (proteomics), there could be several reasons for the greater protective effect of M-WPI. These include promoting the synthesis of fatty acids and peptidoglycans to repair the structure of the cell surface, regulating the metabolism of carbohydrates and amino acids to release energy and produce a range of precursors, enabling the expression of the repair system to repair damaged DNA, and promoting the expression of proteins associated with the multidrug efflux pump, which facilitates the exocytosis of intracellular bile salts. This study helps us to better understand the changes in proteome of L. plantarum CGMCC 23701 under bile salt stress and M-WPI protection, which will provide a new method for the protection and development of functional LAB.
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Affiliation(s)
- Mengxue Yang
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Xiaohui Liang
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Xingye Song
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Fan Wu
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Yingjie Xu
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Mingzhen Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Tao Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaoqun Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Haibo Luo
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
| | - Yuxing Guo
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, P. R. China
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2
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Adebali O, Yang Y, Neupane P, Dike NI, Boltz JL, Kose C, Braunstein M, Selby CP, Sancar A, Lindsey-Boltz LA. The Mfd protein is the transcription-repair coupling factor (TRCF) in Mycobacterium smegmatis. J Biol Chem 2023; 299:103009. [PMID: 36775124 PMCID: PMC10023983 DOI: 10.1016/j.jbc.2023.103009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
In vitro and in vivo experiments with Escherichia coli have shown that the Mfd translocase is responsible for transcription-coupled repair, a subpathway of nucleotide excision repair involving the faster rate of repair of the transcribed strand than the nontranscribed strand. Even though the mfd gene is conserved in all bacterial lineages, there is only limited information on whether it performs the same function in other bacterial species. Here, by genome scale analysis of repair of UV-induced cyclobutane pyrimidine dimers, we find that the Mfd protein is the transcription-repair coupling factor in Mycobacterium smegmatis. This finding, combined with the inverted strandedness of UV-induced mutations in WT and mfd-E. coli and Bacillus subtilis indicate that the Mfd protein is the universal transcription-repair coupling factor in bacteria.
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Affiliation(s)
- Ogun Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Türkiye; Department of Computational Science - Biological Sciences, TÜBİTAK Research Institute for Fundamental Sciences, Gebze, Türkiye
| | - Yanyan Yang
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pradeep Neupane
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nneka I Dike
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julia L Boltz
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cansu Kose
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
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3
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Joseph AM, Nahar K, Daw S, Hasan MM, Lo R, Le TBK, Rahman KM, Badrinarayanan A. Mechanistic insight into the repair of C8-linked pyrrolobenzodiazepine monomer-mediated DNA damage. RSC Med Chem 2022; 13:1621-1633. [PMID: 36561066 PMCID: PMC9749960 DOI: 10.1039/d2md00194b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Pyrrolobenzodiazepines (PBDs) are naturally occurring DNA binding compounds that possess anti-tumor and anti-bacterial activity. Chemical modifications of PBDs can result in improved DNA binding, sequence specificity and enhanced efficacy. More recently, synthetic PBD monomers have shown promise as payloads for antibody drug conjugates and anti-bacterial agents. The precise mechanism of action of these PBD monomers and their role in causing DNA damage remains to be elucidated. Here we characterized the damage-inducing potential of two C8-linked PBD bi-aryl monomers in Caulobacter crescentus and investigated the strategies employed by cells to repair the same. We show that these compounds cause DNA damage and efficiently kill bacteria, in a manner comparable to the extensively used DNA cross-linking agent mitomycin-C (MMC). However, in stark contrast to MMC which employs a mutagenic lesion tolerance pathway, we implicate essential functions for error-free mechanisms in repairing PBD monomer-mediated damage. We find that survival is severely compromised in cells lacking nucleotide excision repair and to a lesser extent, in cells with impaired recombination-based repair. Loss of nucleotide excision repair leads to significant increase in double-strand breaks, underscoring the critical role of this pathway in mediating repair of PBD-induced DNA lesions. Together, our study provides comprehensive insights into how mono-alkylating DNA-targeting therapeutic compounds like PBD monomers challenge cell growth, and identifies the specific mechanisms employed by the cell to counter the same.
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Affiliation(s)
- Asha Mary Joseph
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
| | - Kazi Nahar
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Saheli Daw
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
| | - Md Mahbub Hasan
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Rebecca Lo
- John Innes Centre, Department of Molecular Microbiology Colney Lane Norwich NR4 7UH UK
| | - Tung B K Le
- John Innes Centre, Department of Molecular Microbiology Colney Lane Norwich NR4 7UH UK
| | - Khondaker Miraz Rahman
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London Franklin-Wilkins Building, 150 Stamford Street London SE1 9NH UK
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences (Tata Institute of Fundamental Research) Bangalore India
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4
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Vanderlinden W, Skoruppa E, Kolbeck PJ, Carlon E, Lipfert J. DNA fluctuations reveal the size and dynamics of topological domains. PNAS NEXUS 2022; 1:pgac268. [PMID: 36712371 PMCID: PMC9802373 DOI: 10.1093/pnasnexus/pgac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here, we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real time and at the single-molecule level. Our approach is based on quantifying the extension fluctuations-in addition to the mean extension-of supercoiled DNA in magnetic tweezers (MT). Using a combination of high-speed MT experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime, the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how the transient (partial) dissociation of DNA-bridging proteins results in the dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our results to further the understanding and optimization of magnetic tweezer measurements and to enable quantification of the dynamics and reaction pathways of DNA processing enzymes in the context of physiologically relevant forces and supercoiling densities.
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Affiliation(s)
| | | | - Pauline J Kolbeck
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amalienstrasse 54, 80799 Munich, Germany,Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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5
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Schaich MA, Van Houten B. Searching for DNA Damage: Insights From Single Molecule Analysis. Front Mol Biosci 2021; 8:772877. [PMID: 34805281 PMCID: PMC8602339 DOI: 10.3389/fmolb.2021.772877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/18/2021] [Indexed: 01/26/2023] Open
Abstract
DNA is under constant threat of damage from a variety of chemical and physical insults, such as ultraviolet rays produced by sunlight and reactive oxygen species produced during respiration or inflammation. Because damaged DNA, if not repaired, can lead to mutations or cell death, multiple DNA repair pathways have evolved to maintain genome stability. Two repair pathways, nucleotide excision repair (NER) and base excision repair (BER), must sift through large segments of nondamaged nucleotides to detect and remove rare base modifications. Many BER and NER proteins share a common base-flipping mechanism for the detection of modified bases. However, the exact mechanisms by which these repair proteins detect their damaged substrates in the context of cellular chromatin remains unclear. The latest generation of single-molecule techniques, including the DNA tightrope assay, atomic force microscopy, and real-time imaging in cells, now allows for nearly direct visualization of the damage search and detection processes. This review describes several mechanistic commonalities for damage detection that were discovered with these techniques, including a combination of 3-dimensional and linear diffusion for surveying damaged sites within long stretches of DNA. We also discuss important findings that DNA repair proteins within and between pathways cooperate to detect damage. Finally, future technical developments and single-molecule studies are described which will contribute to the growing mechanistic understanding of DNA damage detection.
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Affiliation(s)
- Matthew A Schaich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, Pittsburgh, PA, United States
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6
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Deaconescu AM. Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability. Transcription 2021; 12:156-170. [PMID: 34674614 PMCID: PMC8632110 DOI: 10.1080/21541264.2021.1982628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
For survival, bacteria need to continuously evolve and adapt to complex environments, including those that may impact the integrity of the DNA, the repository of genetic information to be passed on to future generations. The multiple factors of DNA repair share the substrate on which they operate with other key cellular machineries, principally those of replication and transcription, implying a high degree of coordination of DNA-based activities. In this review, I focus on progress made in the understanding of the protein factors operating at the crossroads of these three fundamental processes, with emphasis on the mutation frequency decline protein (Mfd, aka TRCF). Although Mfd research has a rich history that goes back in time for more than half a century, recent reports hint that much remains to be uncovered. I argue that besides being a transcription-repair coupling factor (TRCF), Mfd is also a global regulator of transcription and a pro-mutagenic factor, and that the way it interfaces with transcription, replication and nucleotide excision repair makes it an attractive candidate for the development of strategies to curb molecular evolution, hence, antibiotic resistance.
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Affiliation(s)
- Alexandra M. Deaconescu
- CONTACT Alexandra M. Deaconescu Molecular Biology, Cell Biology and Biochemistry, Laboratories of Molecular Medicine, Brown University, 70 Ship St. G-E4, Providence, RI02903, USA
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7
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Lindsey-Boltz LA, Sancar A. The Transcription-Repair Coupling Factor Mfd Prevents and Promotes Mutagenesis in a Context-Dependent Manner. Front Mol Biosci 2021; 8:668290. [PMID: 34095223 PMCID: PMC8174841 DOI: 10.3389/fmolb.2021.668290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
The mfd (mutation frequency decline) gene was identified by screening an auxotrophic Escherichia coli strain exposed to UV and held in a minimal medium before plating onto rich or minimal agar plates. It was found that, under these conditions, holding cells in minimal (nongrowth) conditions resulted in mutations that enabled cells to grow on minimal media. Using this observation as a starting point, a mutant was isolated that failed to mutate to auxotrophy under the prescribed conditions, and the gene responsible for this phenomenon (mutation frequency decline) was named mfd. Later work revealed that mfd encoded a translocase that recognizes a stalled RNA polymerase (RNAP) at damage sites and binds to the stalled RNAP, recruits the nucleotide excision repair damage recognition complex UvrA2UvrB to the site, and facilitates damage recognition and repair while dissociating the stalled RNAP from the DNA along with the truncated RNA. Recent single-molecule and genome-wide repair studies have revealed time-resolved features and structural aspects of this transcription-coupled repair (TCR) phenomenon. Interestingly, recent work has shown that in certain bacterial species, mfd also plays roles in recombination, bacterial virulence, and the development of drug resistance.
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Affiliation(s)
- Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
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8
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Kouzminova EA, Kuzminov A. Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis. Nucleic Acids Res 2021; 49:3888-3906. [PMID: 33693789 PMCID: PMC8053090 DOI: 10.1093/nar/gkab147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022] Open
Abstract
Ultraviolet (UV) induces pyrimidine dimers (PDs) in DNA and replication-dependent fragmentation in chromosomes. The rnhAB mutants in Escherichia coli, accumulating R-loops and single DNA-rNs, are generally resistant to DNA damage, but are surprisingly UV-sensitive, even though they remove PDs normally, suggesting irreparable chromosome lesions. We show here that the RNase H defect does not cause additional chromosome fragmentation after UV, but inhibits DNA synthesis after replication restart. Genetic analysis implies formation of R-loop-anchored transcription elongation complexes (R-loop-aTECs) in UV-irradiated rnhAB mutants, predicting that their chromosomal DNA will accumulate: (i) RNA:DNA hybrids; (ii) a few slow-to-remove PDs. We confirm both features and also find that both, surprisingly, depend on replication restart. Finally, enriching for the UV-induced RNA:DNA hybrids in the rnhAB uvrA mutants also co-enriches for PDs, showing their co-residence in the same structures. We propose that PD-triggered R-loop-aTECs block head-on replication in RNase H-deficient mutants.
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Affiliation(s)
- Elena A Kouzminova
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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9
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Tiwari V, Baptiste BA, Okur MN, Bohr VA. Current and emerging roles of Cockayne syndrome group B (CSB) protein. Nucleic Acids Res 2021; 49:2418-2434. [PMID: 33590097 DOI: 10.1093/nar/gkab085] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cockayne syndrome (CS) is a segmental premature aging syndrome caused primarily by defects in the CSA or CSB genes. In addition to premature aging, CS patients typically exhibit microcephaly, progressive mental and sensorial retardation and cutaneous photosensitivity. Defects in the CSB gene were initially thought to primarily impair transcription-coupled nucleotide excision repair (TC-NER), predicting a relatively consistent phenotype among CS patients. In contrast, the phenotypes of CS patients are pleiotropic and variable. The latter is consistent with recent work that implicates CSB in multiple cellular systems and pathways, including DNA base excision repair, interstrand cross-link repair, transcription, chromatin remodeling, RNAPII processing, nucleolin regulation, rDNA transcription, redox homeostasis, and mitochondrial function. The discovery of additional functions for CSB could potentially explain the many clinical phenotypes of CSB patients. This review focuses on the diverse roles played by CSB in cellular pathways that enhance genome stability, providing insight into the molecular features of this complex premature aging disease.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Mustafa N Okur
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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10
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Han S, Gong Z, Liang T, Chen Y, Xie J. The role of Mfd in Mycobacterium tuberculosis physiology and underlying regulatory network. Microbiol Res 2021; 246:126718. [PMID: 33588338 DOI: 10.1016/j.micres.2021.126718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis with millions of deaths annually, remains one of the most formidable pathogen to global public health. As the most successful intracellular pathogens, Mtb can spatiotemporally coordinate the transcription and translation timely to reconcile the inevitable transcription-replication conflicts. Mutation frequency decline (Mfd) is a bacterial ATP-dependent DNA translocase that couples DNA repair to transcription via hydrolyzing ATP as energy, which preferentially acts on the damaged DNA transcribed strand to rescue stalled RNAP or dissociate RNAP to terminate the transcription depending on impediment severity, mitigating the damage to bacteria. In addition to the traditional damage repair effect, Mfd may also promote bacteria mutagenesis under stresses and boost the drug resistance. Mfd is widespread among bacteria and intensively studied, but there are very few studies in Mycobacteria, especially Mtb. In this review, the structure, function and mechanism characteristics of Mfd in Mtb (MtbMfd, Rv1020) are explored, with emphasis on the regulatory network of MtbMfd and its potential as a prime target for antibiotic drugs against tuberculosis.
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Affiliation(s)
- Shuang Han
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Tian Liang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Yu Chen
- Department of Tuberculosis, Shenyang Tenth People's Hospital and Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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11
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Selby CP, Lindsey-Boltz LA, Yang Y, Sancar A. Mycobacteria excise DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair. J Biol Chem 2020; 295:17374-17380. [PMID: 33087442 PMCID: PMC7863889 DOI: 10.1074/jbc.ac120.016325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/16/2020] [Indexed: 12/29/2022] Open
Abstract
In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11-13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24-32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nt from the 3´ end and 9 nt from the 5´ end flanking the damage. To test this model, we used the in vivo excision assay and the excision repair sequencing genome-wide repair mapping method developed in our laboratory to determine the repair pattern and genome-wide repair map of Mycobacterium smegmatis We find that M. smegmatis, which possesses homologs of the Escherichia coli uvrA, uvrB, and uvrC genes, removes cyclobutane pyrimidine dimers from the genome in a manner identical to the prokaryotic pattern by incising 7 nt 5´ and 3 or 4 nt 3´ to the photoproduct, and performs transcription-coupled repair in a manner similar to E. coli.
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Affiliation(s)
- Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Yanyan Yang
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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12
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Agapov A, Ignatov A, Turtola M, Belogurov G, Esyunina D, Kulbachinskiy A. Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase. J Biol Chem 2020; 295:9583-9595. [PMID: 32439804 DOI: 10.1074/jbc.ra119.011844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 05/20/2020] [Indexed: 11/06/2022] Open
Abstract
DNA lesions can severely compromise transcription and block RNA synthesis by RNA polymerase (RNAP), leading to subsequent recruitment of DNA repair factors to the stalled transcription complex. Recent structural studies have uncovered molecular interactions of several DNA lesions within the transcription elongation complex. However, little is known about the role of key elements of the RNAP active site in translesion transcription. Here, using recombinantly expressed proteins, in vitro transcription, kinetic analyses, and in vivo cell viability assays, we report that point amino acid substitutions in the trigger loop, a flexible element of the active site involved in nucleotide addition, can stimulate translesion RNA synthesis by Escherichia coli RNAP without altering the fidelity of nucleotide incorporation. We show that these substitutions also decrease transcriptional pausing and strongly affect the nucleotide addition cycle of RNAP by increasing the rate of nucleotide addition but also decreasing the rate of translocation. The secondary channel factors DksA and GreA modulated translesion transcription by RNAP, depending on changes in the trigger loop structure. We observed that although the mutant RNAPs stimulate translesion synthesis, their expression is toxic in vivo, especially under stress conditions. We conclude that the efficiency of translesion transcription can be significantly modulated by mutations affecting the conformational dynamics of the active site of RNAP, with potential effects on cellular stress responses and survival.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Aitken SJ, Anderson CJ, Connor F, Pich O, Sundaram V, Feig C, Rayner TF, Lukk M, Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes SV, Davies SE, Drews RM, Ewing A, Kaiser VB, Khamseh A, López-Arribillaga E, Redmond AM, Santoyo-Lopez J, Sentís I, Talmane L, Yates AD, Semple CA, López-Bigas N, Flicek P, Odom DT, Taylor MS. Pervasive lesion segregation shapes cancer genome evolution. Nature 2020; 583:265-270. [PMID: 32581361 PMCID: PMC7116693 DOI: 10.1038/s41586-020-2435-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion1,2. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.
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Affiliation(s)
- Sarah J Aitken
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Craig J Anderson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Frances Connor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Vasavi Sundaram
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Christine Feig
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Tim F Rayner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Margus Lukk
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Juliet Luft
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sjoerd V Beentjes
- School of Mathematics and Maxwell Institute, University of Edinburgh, Edinburgh, UK
| | - Susan E Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ruben M Drews
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ava Khamseh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Higgs Centre for Theoretical Physics, University of Edinburgh, Edinburgh, UK
| | - Erika López-Arribillaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lana Talmane
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paul Flicek
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany.
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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15
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Ebright RH, Werner F, Zhang X. RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes. J Mol Biol 2019; 431:3945-3946. [PMID: 31356803 DOI: 10.1016/j.jmb.2019.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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