1
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Nautiyal A, Thakur M. Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution. ACS OMEGA 2024; 9:12515-12538. [PMID: 38524412 PMCID: PMC10956419 DOI: 10.1021/acsomega.3c09866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.
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Affiliation(s)
- Astha Nautiyal
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Thakur
- Sri
Venkateswara College, Benito Juarez Road, University of Delhi, New Delhi 110021, India
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2
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Kamat A, Tran NT, Sharda M, Sontakke N, Le TBK, Badrinarayanan A. Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria. PLoS Biol 2024; 22:e3002540. [PMID: 38466718 PMCID: PMC10957082 DOI: 10.1371/journal.pbio.3002540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/21/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Ngat T. Tran
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
| | - Mohak Sharda
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Neha Sontakke
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
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3
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Keller LML, Flattich K, Weber-Ban E. Novel WYL domain-containing transcriptional activator acts in response to genotoxic stress in rapidly growing mycobacteria. Commun Biol 2023; 6:1222. [PMID: 38042942 PMCID: PMC10693628 DOI: 10.1038/s42003-023-05592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023] Open
Abstract
The WYL domain is a nucleotide-sensing module that controls the activity of transcription factors involved in the regulation of DNA damage response and phage defense mechanisms in bacteria. In this study, we investigated a WYL domain-containing transcription factor in Mycobacterium smegmatis that we termed stress-involved WYL domain-containing regulator (SiwR). We found that SiwR controls adjacent genes that belong to the DinB/YfiT-like putative metalloenzymes superfamily by upregulating their expression in response to various genotoxic stress conditions, including upon exposure to H2O2 or the natural antibiotic zeocin. We show that SiwR binds different forms of single-stranded DNA (ssDNA) with high affinity, primarily through its characteristic WYL domain. In combination with complementation studies of a M. smegmatis siwR deletion strain, our findings support a role of the WYL domains as signal-sensing activity switches of WYL domain-containing transcription factors (WYL TFs). Our study provides evidence that WYL TFs are involved in the adaptation of bacteria to changing environments and encountered stress conditions.
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Affiliation(s)
| | - Kim Flattich
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland.
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4
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Deng MZ, Liu Q, Cui SJ, Fu H, Gan M, Xu YY, Cai X, Sha W, Zhao GP, Fortune SM, Lyu LD. Mycobacterial DnaQ is an Alternative Proofreader Ensuring DNA Replication Fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563508. [PMID: 37961690 PMCID: PMC10634781 DOI: 10.1101/2023.10.24.563508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Remove of mis-incorporated nucleotides ensures replicative fidelity. Although the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, proofreading in mycobacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase despite the presence of an alternative DnaQ homolog. Here, we show that depletion of DnaQ in Mycolicibacterium smegmatis results in increased mutation rate, leading to AT-biased mutagenesis and elevated insertions/deletions in homopolymer tract. We demonstrated that mycobacterial DnaQ binds to the b-clamp and functions synergistically with the PHP domain to correct replication errors. Further, we found that the mycobacterial DnaQ sustains replicative fidelity upon chromosome topological stress. Intriguingly, we showed that a naturally evolved DnaQ variant prevalent in clinical Mycobacterium tuberculosis isolates enables hypermutability and is associated with extensive drug resistance. These results collectively establish that the alternative DnaQ functions in proofreading, and thus reveal that mycobacteria deploy two proofreaders to maintain replicative fidelity.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- These authors contributed equally
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- These authors contributed equally
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102, P.R.China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
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5
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Schwarz MGA, Corrêa PR, Mendonça-Lima L. Transcriptional Profiling of Homologous Recombination Pathway Genes in Mycobacterium bovis BCG Moreau. Microorganisms 2023; 11:2534. [PMID: 37894192 PMCID: PMC10609372 DOI: 10.3390/microorganisms11102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 10/29/2023] Open
Abstract
Mycobacterium bovis BCG Moreau is the main Brazilian strain for vaccination against tuberculosis. It is considered an early strain, more like the original BCG, whereas BCG Pasteur, largely used as a reference, belongs to the late strain clade. BCG Moreau, contrary to Pasteur, is naturally deficient in homologous recombination (HR). In this work, using a UV exposure test, we aimed to detect differences in the survival of various BCG strains after DNA damage. Transcription of core and regulatory HR genes was further analyzed using RT-qPCR, aiming to identify the molecular agent responsible for this phenotype. We show that early strains share the Moreau low survival rate after UV exposure, whereas late strains mimic the Pasteur phenotype, indicating that this increase in HR efficiency is linked to the evolutionary clade history. Additionally, RT-qPCR shows that BCG Moreau has an overall lower level of these transcripts than Pasteur, indicating a correlation between this gene expression profile and HR efficiency. Further assays should be performed to fully identify the molecular mechanism that may explain this differential phenotype between early and late BCG strains.
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Affiliation(s)
- Marcos Gustavo Araujo Schwarz
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (P.R.C.); (L.M.-L.)
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6
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Gessner S, Martin ZAM, Reiche MA, Santos JA, Dinkele R, Ramudzuli A, Dhar N, de Wet TJ, Anoosheh S, Lang DM, Aaron J, Chew TL, Herrmann J, Müller R, McKinney JD, Woodgate R, Mizrahi V, Venclovas Č, Lamers MH, Warner DF. Investigating the composition and recruitment of the mycobacterial ImuA'-ImuB-DnaE2 mutasome. eLife 2023; 12:e75628. [PMID: 37530405 PMCID: PMC10421592 DOI: 10.7554/elife.75628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in Mycobacterium tuberculosis during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded 'mycobacterial mutasome' - minimally comprising DnaE2 polymerase and ImuA' and ImuB accessory proteins - remain elusive. Following exposure of mycobacteria to DNA damaging agents, we observe that DnaE2 and ImuB co-localize with the DNA polymerase III β subunit (β clamp) in distinct intracellular foci. Notably, genetic inactivation of the mutasome in an imuBAAAAGG mutant containing a disrupted β clamp-binding motif abolishes ImuB-β clamp focus formation, a phenotype recapitulated pharmacologically by treating bacilli with griselimycin and in biochemical assays in which this β clamp-binding antibiotic collapses pre-formed ImuB-β clamp complexes. These observations establish the essentiality of the ImuB-β clamp interaction for mutagenic DNA repair in mycobacteria, identifying the mutasome as target for adjunctive therapeutics designed to protect anti-TB drugs against emerging resistance.
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Affiliation(s)
- Sophia Gessner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Zela Alexandria-Mae Martin
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Michael A Reiche
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Joana A Santos
- Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Ryan Dinkele
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Atondaho Ramudzuli
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Neeraj Dhar
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Department of Integrative Biomedical Sciences, University of Cape TownCape TownSouth Africa
| | - Saber Anoosheh
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Dirk M Lang
- Confocal and Light Microscope Imaging Facility, Department of Human Biology, University of Cape TownCape TownSouth Africa
| | - Jesse Aaron
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical InstituteAshburnUnited States
| | - Jennifer Herrmann
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner Site Hannover-BraunschweigBraunschweigGermany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research SaarlandSaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner Site Hannover-BraunschweigBraunschweigGermany
| | - John D McKinney
- Laboratory of Microbiology and Microsystems, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
| | | | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
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7
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Dupuy P, Ghosh S, Fay A, Adefisayo O, Gupta R, Shuman S, Glickman MS. Roles for mycobacterial DinB2 in frameshift and substitution mutagenesis. eLife 2023; 12:e83094. [PMID: 37141254 PMCID: PMC10159617 DOI: 10.7554/elife.83094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Translesion synthesis by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are the widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. Mycobacterium smegmatis encodes two additional DinBs (DinB2 and DinB3) and Mycobacterium tuberculosis encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here, we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Shreya Ghosh
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Allison Fay
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
| | - Richa Gupta
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Michael S Glickman
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
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8
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Kamat A, Badrinarayanan A. SOS-independent bacterial DNA damage responses: diverse mechanisms, unifying function. Curr Opin Microbiol 2023; 73:102323. [PMID: 37148591 DOI: 10.1016/j.mib.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 05/08/2023]
Abstract
Cells across domains of life have dedicated pathways to sense and respond to DNA damage. These responses are broadly termed as DNA damage responses (DDRs). In bacteria, the best studied DDR is the Save our Soul (SOS) response. More recently, several SOS-independent DDRs have also been discovered. Studies further report diversity in the types of repair proteins present across bacterial species as well as differences in their mechanisms of action. Although the primary function of DDRs is preservation of genome integrity, the diverse organization, conservation, and function of bacterial DDRs raises important questions about how genome error correction mechanisms could influence or be influenced by the genomes that encode them. In this review, we discuss recent insights on three SOS-independent bacterial DDRs. We consider open questions in our understanding of how diversity in response and repair mechanisms is generated, and how action of these pathways is regulated in cells to ensure maintenance of genome integrity.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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9
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Keller LM, Weber-Ban E. An emerging class of nucleic acid-sensing regulators in bacteria: WYL domain-containing proteins. Curr Opin Microbiol 2023; 74:102296. [PMID: 37027901 DOI: 10.1016/j.mib.2023.102296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 04/09/2023]
Abstract
Transcriptional regulation plays a central role in adaptation to changing environments for all living organisms. Recently, proteins belonging to a novel widespread class of bacterial transcription factors have been characterized in mycobacteria and Proteobacteria. Those multidomain proteins carry a WYL domain that is almost exclusive to the domain of bacteria. WYL domain-containing proteins act as regulators in different cellular contexts, including the DNA damage response and bacterial immunity. WYL domains have an Sm-like fold with five antiparallel β-strands arranged into a β-sandwich preceded by an α-helix. A common feature of WYL domains is their ability to bind nucleic acids that regulate their activity. In this review, we discuss recent progress made toward the understanding of WYL domain-containing proteins as transcriptional regulators, their structural features, and molecular mechanisms, as well as their functional roles in bacterial physiology.
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Affiliation(s)
- Lena Ml Keller
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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10
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Warren GM, Ejaz A, Fay A, Glickman MS, Shuman S. Mycobacterial helicase Lhr abets resistance to DNA crosslinking agents mitomycin C and cisplatin. Nucleic Acids Res 2023; 51:218-235. [PMID: 36610794 PMCID: PMC9841417 DOI: 10.1093/nar/gkac1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium smegmatis Lhr exemplifies a novel clade of helicases composed of an N-terminal ATPase/helicase domain (Lhr-Core) and a large C-terminal domain (Lhr-CTD) that nucleates a unique homo-tetrameric quaternary structure. Expression of Lhr, and its operonic neighbor Nei2, is induced in mycobacteria exposed to mitomycin C (MMC). Here we report that lhr deletion sensitizes M. smegmatis to killing by DNA crosslinkers MMC and cisplatin but not to killing by monoadduct-forming alkylating agent methyl methanesulfonate or UV irradiation. Testing complementation of MMC and cisplatin sensitivity by expression of Lhr mutants in Δlhr cells established that: (i) Lhr-CTD is essential for DNA repair activity, such that Lhr-Core does not suffice; (ii) ATPase-defective mutant D170A/E171A fails to complement; (iii) ATPase-active, helicase-defective mutant W597A fails to complement and (iv) alanine mutations at the CTD-CTD interface that interdict homo-tetramer formation result in failure to complement. Our results instate Lhr's ATP-driven motor as an agent of inter-strand crosslink repair in vivo, contingent on Lhr's tetrameric quaternary structure. We characterize M. smegmatis Nei2 as a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Counter to previous reports, we find Nei2 is inactive as a lyase at a THF abasic site and has feeble uracil glycosylase activity.
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Affiliation(s)
- Garrett M Warren
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Anam Ejaz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Allison Fay
- Immunology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, NY, NY 10065, USA
| | - Stewart Shuman
- To whom correspondence should be addressed. Tel: +1 212 639 7145; E-mail:
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11
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Thakur M, Muniyappa K. Macrophage activation highlight an important role for NER proteins in the survival, latency and multiplication of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2023; 138:102284. [PMID: 36459831 DOI: 10.1016/j.tube.2022.102284] [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: 08/15/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Nucleotide excision repair (NER) is one of the most extensively studied DNA repair processes in both prokaryotes and eukaryotes. The NER pathway is a highly conserved, ATP-dependent multi-step process involving several proteins/enzymes that function in a concerted manner to recognize and excise a wide spectrum of helix-distorting DNA lesions and bulky adducts by nuclease cleavage on either side of the damaged bases. As such, the NER pathway of Mycobacterium tuberculosis (Mtb) is essential for its survival within the hostile environment of macrophages and disease progression. This review focuses on present published knowledge about the crucial roles of Mtb NER proteins in the survival and multiplication of the pathogen within the macrophages and as potential targets for drug discovery.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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12
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Dupuy P, Ghosh S, Adefisayo O, Buglino J, Shuman S, Glickman MS. Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis. Nat Commun 2022; 13:4493. [PMID: 35918328 PMCID: PMC9346131 DOI: 10.1038/s41467-022-32022-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance of Mycobacterium tuberculosis is exclusively a consequence of chromosomal mutations. Translesion synthesis (TLS) is a widely conserved mechanism of DNA damage tolerance and mutagenesis, executed by translesion polymerases such as DinBs. In mycobacteria, DnaE2 is the only known agent of TLS and the role of DinB polymerases is unknown. Here we demonstrate that, when overexpressed, DinB1 promotes missense mutations conferring resistance to rifampicin, with a mutational signature distinct from that of DnaE2, and abets insertion and deletion frameshift mutagenesis in homo-oligonucleotide runs. DinB1 is the primary mediator of spontaneous −1 frameshift mutations in homo-oligonucleotide runs whereas DnaE2 and DinBs are redundant in DNA damage-induced −1 frameshift mutagenesis. These results highlight DinB1 and DnaE2 as drivers of mycobacterial genome diversification with relevance to antimicrobial resistance and host adaptation. This manuscript elucidates new mechanisms of mutagenesis in mycobacteria by implicating two translesion DNA polymerases in genome diversification, including creating the mutations that underlie all antibiotic resistance in these global pathogens.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Shreya Ghosh
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA
| | - John Buglino
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | - Michael S Glickman
- Immunology Program, Sloan Kettering Institute, New York, NY, 10065, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY, 10065, USA.
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13
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Abstract
Streptococcus suis is an important zoonotic pathogen. Due to the indiscriminate use of macrolides, S. suis has developed a high level of drug resistance, which has led to a serious threat to human and animal health. However, it takes a long time to develop new antibacterial drugs. Therefore, we consider the perspective of bacterial physiological metabolism to ensure that the development of bacterial resistance to existing drugs is alleviated and bacterial susceptibility to drugs is restored. In the present study, an untargeted metabolomics analysis showed that the serine catabolic pathway was inhibited in drug-resistant S. suis. The addition of l-serine restored the fungicidal effect of macrolides on S. suisin vivo and in vitro by enhancing the serine metabolic pathway. Further studies showed that l-serine, stimulated by its serine catabolic pathway, inhibited intracellular H2S production, reduced Fe-S cluster production, and restored the normal occurrence of the Fenton reaction in cells. It also attenuated the production of glutathione, an important marker of the intracellular oxidation-reduction reaction. All these phenomena eventually contribute to an increase in the level of reactive oxygen species, which leads to intracellular DNA damage and bacterial death. Our study provides a potential new approach for the treatment of diseases caused by drug-resistant S. suis. IMPORTANCE The emergence of antimicrobial resistance is a global challenge. However, new drug development efforts consume considerable resources and time, and alleviating the pressure on existing drugs is the focus of our work. We investigated the mechanism of action of l-serine supplementation in restoring the use of macrolides in S. suis, based on the role of the serine catabolic pathway on reactive oxygen species levels and oxidative stress in S. suis. This pathway provides a theoretical basis for the rational use of macrolides in clinical practice and also identifies a possible target for restoring drug sensitivity in S. suis.
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14
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Chengalroyen MD, Mason MK, Borsellini A, Tassoni R, Abrahams GL, Lynch S, Ahn YM, Ambler J, Young K, Crowley BM, Olsen DB, Warner DF, Barry III CE, Boshoff HIM, Lamers MH, Mizrahi V. DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:612-625. [PMID: 35143160 PMCID: PMC8922275 DOI: 10.1021/acsinfecdis.1c00643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Natural products
provide a rich source of potential antimicrobials
for treating infectious diseases for which drug resistance has emerged.
Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial
activity of nargenicin, a natural product that targets the replicative
DNA polymerase of Staphylococcus aureus, revealed that it is a bactericidal genotoxin that induces a DNA
damage response in Mycobacterium tuberculosis (Mtb) and inhibits growth by blocking the replicative
DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding
of nargenicin to Mtb DnaE1 requires the DNA substrate
such that nargenicin is wedged between the terminal base pair and
the polymerase and occupies the position of both the incoming nucleotide
and templating base. Comparative analysis across three bacterial species
suggests that the activity of nargenicin is partly attributable to
the DNA binding affinity of the replicative polymerase. This work
has laid the foundation for target-led drug discovery efforts focused
on Mtb DnaE1.
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Affiliation(s)
- Melissa D. Chengalroyen
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Mandy K. Mason
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Alessandro Borsellini
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Raffaella Tassoni
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Garth L. Abrahams
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Sasha Lynch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Yong-Mo Ahn
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Jon Ambler
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Katherine Young
- Infectious Disease, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - Brendan M. Crowley
- Discovery Chemistry, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - David B. Olsen
- Infectious Disease, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - Digby F. Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Clifton E. Barry III
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Meindert H. Lamers
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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