1
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Paudel BP, Xu ZQ, Jergic S, Oakley AJ, Sharma N, Brown SHJ, Bouwer JC, Lewis PJ, Dixon NE, van Oijen AM, Ghodke H. Mechanism of transcription modulation by the transcription-repair coupling factor. Nucleic Acids Res 2022; 50:5688-5712. [PMID: 35641110 PMCID: PMC9177983 DOI: 10.1093/nar/gkac449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022] Open
Abstract
Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Simon H J Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - James C Bouwer
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Peter J Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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2
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Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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3
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [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: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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4
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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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5
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Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y. Structural basis of Mfd-dependent transcription termination. Nucleic Acids Res 2021; 48:11762-11772. [PMID: 33068413 PMCID: PMC7672476 DOI: 10.1093/nar/gkaa904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 11/16/2022] Open
Abstract
Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite extensive studies, the molecular mechanism of Mfd-dependent transcription termination in bacteria remains unclear, with several long-standing puzzles. How Mfd is activated by stalled RNA polymerase (RNAP) and how activated Mfd translocates along the DNA are unknown. Here, we report the single-particle cryo-electron microscopy structures of T. thermophilus Mfd-RNAP complex with and without ATPγS. The structures reveal that Mfd undergoes profound conformational changes upon activation, contacts the RNAP β1 domain and its clamp, and pries open the RNAP clamp. These structures provide a foundation for future studies aimed at dissecting the precise mechanism of Mfd-dependent transcription termination and pave the way for rational drug design targeting Mfd for the purpose of tackling the antimicrobial resistance crisis.
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Affiliation(s)
- Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou 310058, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Minxing Zhao
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Sha Jin
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shi
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shuling Dong
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiaoting Hua
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310058, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou 310058, China
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6
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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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7
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Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA. Structural basis for transcription complex disruption by the Mfd translocase. eLife 2021; 10:62117. [PMID: 33480355 PMCID: PMC7864632 DOI: 10.7554/elife.62117] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC. We used cryo-electron microscopy to visualize Mfd engaging with a stalled EC and attempting to dislodge the RNAP. We visualized seven distinct Mfd-EC complexes in both ATP and ADP-bound states. The structures explain how Mfd is remodeled from its repressed conformation, how the UvrA-interacting surface of Mfd is hidden during most of the remodeling process to prevent premature engagement with the NER pathway, how Mfd alters the RNAP conformation to facilitate disassembly, and how Mfd forms a processive translocation complex after dislodging the RNAP. Our results reveal an elaborate mechanism for how Mfd kinetically discriminates paused from stalled ECs and disassembles stalled ECs to initiate TCR.
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Affiliation(s)
- Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Joshua Brewer
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
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8
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Kraithong T, Hartley S, Jeruzalmi D, Pakotiprapha D. A Peek Inside the Machines of Bacterial Nucleotide Excision Repair. Int J Mol Sci 2021; 22:ijms22020952. [PMID: 33477956 PMCID: PMC7835731 DOI: 10.3390/ijms22020952] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). Below, we discuss the architecture of key proteins in bacterial NER and recent biochemical, structural and single-molecule studies that shed light on the lesion recognition steps of both the GGR and the TCR sub-pathways. Although a great deal has been learned about both of these sub-pathways, several important questions, including damage discrimination, roles of ATP and the orchestration of protein binding and conformation switching, remain to be addressed.
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Affiliation(s)
- Thanyalak Kraithong
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Silas Hartley
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence: (D.J.); (D.P.)
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (D.J.); (D.P.)
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9
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Ding W, Tan HY, Zhang JX, Wilczek LA, Hsieh KR, Mulkin JA, Bianco PR. The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function. Protein Sci 2020; 29:1211-1227. [PMID: 32196797 PMCID: PMC7184773 DOI: 10.1002/pro.3855] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
The Escherichia coli single-strand DNA binding protein (SSB) is essential to viability where it functions to regulate SSB interactome function. Here it binds to single-stranded DNA and to target proteins that comprise the interactome. The region of SSB that links these two essential protein functions is the intrinsically disordered linker. Key to linker function is the presence of three, conserved PXXP motifs that mediate binding to oligosaccharide-oligonucleotide binding folds (OB-fold) present in SSB and its interactome partners. Not surprisingly, partner OB-fold deletions eliminate SSB binding. Furthermore, single point mutations in either the PXXP motifs or, in the RecG OB-fold, obliterate SSB binding. The data also demonstrate that, and in contrast to the view currently held in the field, the C-terminal acidic tip of SSB is not required for interactome partner binding. Instead, we propose the tip has two roles. First, and consistent with the proposal of Dixon, to regulate the structure of the C-terminal domain in a biologically active conformation that prevents linkers from binding to SSB OB-folds until this interaction is required. Second, as a secondary binding domain. Finally, as OB-folds are present in SSB and many of its partners, we present the SSB interactome as the first family of OB-fold genome guardians identified in prokaryotes.
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Affiliation(s)
- Wenfei Ding
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Hui Yin Tan
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndianaUnited States
| | - Jia Xiang Zhang
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Luke A. Wilczek
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of ChemistryBrown UniversityProvidenceRhode IslandUnited States
| | - Karin R. Hsieh
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Jeffrey A. Mulkin
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Piero R. Bianco
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
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10
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Bianco PR. DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication forks in Escherichia coli. Genes (Basel) 2020; 11:E471. [PMID: 32357475 PMCID: PMC7290993 DOI: 10.3390/genes11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 01/25/2023] Open
Abstract
In Escherichia coli, DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so that repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls helicase-fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, NY 14221, USA
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11
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Sun Z, Wang Y, Bianco PR, Lyubchenko YL. Nanoscale interaction of RecG with mobile fork DNA. NANOSCALE ADVANCES 2020; 2:1318-1324. [PMID: 33791509 PMCID: PMC8009289 DOI: 10.1039/c9na00712a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/10/2020] [Indexed: 06/12/2023]
Abstract
The RecG DNA helicase is a guardian of the bacterial genome where it dominates stalled DNA replication fork rescue. The single-stranded DNA binding protein (SSB) is involved in this process and promotes the binding of RecG to stalled replication forks. Atomic force microscopy (AFM) was used to investigate the interaction of RecG and SSB on a mobile fork substrate capable of being regressed. In the absence of proteins, the fork undergoes spontaneous dynamics between two states defined by the length of the DNA complementarity at the fork. Binding of SSB does not affect these dynamics as it binds to single-stranded regions as expected. In contrast, RecG interacts with the two states quite differently. We demonstrate that RecG has two modes of interaction with fork DNA in the presence of SSB and ATP. In the first mode, RecG translocates over the duplex region and this activity is defined by SSB-mediated remodeling of the helicase. In the second mode, RecG utilizes its helicase activity to regress the fork, in an ATP-dependent manner, displacing SSB on the ssDNA. Overall, our results highlight two functions of RecG that can be employed in the regulation of stalled DNA replication fork rescue.
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Affiliation(s)
- Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical CenterOmahaNE 68198-6025USA
| | - Yaqing Wang
- Department of Pharmaceutical Sciences, University of Nebraska Medical CenterOmahaNE 68198-6025USA
| | - Piero R. Bianco
- Center for Single Molecule Biophysics, Department of Microbiology and Immunology, University at BuffaloSUNYBuffaloNY 14214USA
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical CenterOmahaNE 68198-6025USA
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12
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Strick TR, Portman JR. Transcription-Coupled Repair: From Cells to Single Molecules and Back Again. J Mol Biol 2019; 431:4093-4102. [PMID: 31175845 DOI: 10.1016/j.jmb.2019.05.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 11/19/2022]
Abstract
Transcription-coupled repair is mediated by the Mfd protein. TCR is defined as the preferential repair of DNA lesions in the transcribed strand of actively transcribed genes, and is opposed to the strand-aspecific global genome repair. The Mfd protein mediates TCR by binding to and displacing RNA polymerase, which is stalled at a DNA lesion on the transcribed strand of DNA, then recruiting UvrA and UvrB. The repair cascade results in the recruitment of, and DNA excision by, UvrC; removal of the damage-bearing oligonucleotide by UvrD; "filling-in" of the DNA by DNA polymerase; and sealing of the strands by DNA ligase. The gene required for Mfd was originally identified as a gene needed for the "mutation frequency decline" phenotype in which the repair of certain UV-induced lesions in the transcribed strand of tRNA genes is increased when cells are forced to delay replication immediately following UV exposure. This review will focus on the genetics that led to the discovery of the Mfd gene; summarize the subsequent biochemical, structural and single-molecule interrogations of the Mfd protein; and explore the more recent findings of Mfd in mutagenesis.
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Affiliation(s)
- T R Strick
- Institut Jacques Monod, CNRS and Université Paris 7, Paris Université, Paris, France; Institut de Biologie de l'Ecole normale supérieure, PSL Université, INSERM, CNRS, Paris, France; Equipe Labellisée de la Ligue Nationale Contre le Cancer, Paris, France; Horizons 2020 Innovative Training Network, DNAREPAIRMAN, Paris, France.
| | - J R Portman
- Institut Jacques Monod, CNRS and Université Paris 7, Paris Université, Paris, France; Institut de Biologie de l'Ecole normale supérieure, PSL Université, INSERM, CNRS, Paris, France; Horizons 2020 Innovative Training Network, DNAREPAIRMAN, Paris, France
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13
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Warren GM, Stein RA, Mchaourab HS, Eichman BF. Movement of the RecG Motor Domain upon DNA Binding Is Required for Efficient Fork Reversal. Int J Mol Sci 2018; 19:ijms19103049. [PMID: 30301235 PMCID: PMC6213257 DOI: 10.3390/ijms19103049] [Citation(s) in RCA: 11] [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: 09/01/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/20/2023] Open
Abstract
RecG catalyzes reversal of stalled replication forks in response to replication stress in bacteria. The protein contains a fork recognition (“wedge”) domain that binds branched DNA and a superfamily II (SF2) ATPase motor that drives translocation on double-stranded (ds)DNA. The mechanism by which the wedge and motor domains collaborate to catalyze fork reversal in RecG and analogous eukaryotic fork remodelers is unknown. Here, we used electron paramagnetic resonance (EPR) spectroscopy to probe conformational changes between the wedge and ATPase domains in response to fork DNA binding by Thermotoga maritima RecG. Upon binding DNA, the ATPase-C lobe moves away from both the wedge and ATPase-N domains. This conformational change is consistent with a model of RecG fully engaged with a DNA fork substrate constructed from a crystal structure of RecG bound to a DNA junction together with recent cryo-electron microscopy (EM) structures of chromatin remodelers in complex with dsDNA. We show by mutational analysis that a conserved loop within the translocation in RecG (TRG) motif that was unstructured in the RecG crystal structure is essential for fork reversal and DNA-dependent conformational changes. Together, this work helps provide a more coherent model of fork binding and remodeling by RecG and related eukaryotic enzymes.
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Affiliation(s)
- Garrett M Warren
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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14
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Sun Z, Hashemi M, Warren G, Bianco PR, Lyubchenko YL. Dynamics of the Interaction of RecG Protein with Stalled Replication Forks. Biochemistry 2018; 57:1967-1976. [PMID: 29432678 DOI: 10.1021/acs.biochem.7b01235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As a guardian of the bacterial genome, the RecG DNA helicase repairs DNA replication and rescues stalled replication. We applied atomic force microscopy (AFM) to directly visualize dynamics of RecG upon the interaction with replication fork substrates in the presence and absence of SSB using high-speed AFM. We directly visualized that RecG moves back and forth over dozens of base pairs in the presence of SSB. There is no RecG translocation in the absence of SSB. Computational modeling was performed to build models of Escherichia coli RecG in a free state and in complex with the fork. The simulations revealed the formation of complexes of RecG with the fork and identified conformational transitions that may be responsible for RecG remodeling that can facilitate RecG translocation along the DNA duplex. Such complexes do not form with the DNA duplex, which is in line with experimental data. Overall, our results provide mechanistic insights into the modes of interaction of RecG with the replication fork, suggesting a novel role of RecG in the repair of stalled DNA replication forks.
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Affiliation(s)
- Zhiqiang Sun
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Galina Warren
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Piero R Bianco
- Department of Microbiology and Immunology , University at Buffalo, State University of New York , Buffalo , New York 14214 , United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
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15
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Sedman T, Garber N, Gaidutšik I, Sillamaa S, Paats J, Piljukov VJ, Sedman J. Mitochondrial helicase Irc3 translocates along double-stranded DNA. FEBS Lett 2017; 591:3831-3841. [PMID: 29113022 DOI: 10.1002/1873-3468.12903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 12/12/2022]
Abstract
Irc3 is a superfamily II helicase required for mitochondrial DNA stability in Saccharomyces cerevisiae. Irc3 remodels branched DNA structures, including substrates without extensive single-stranded regions. Therefore, it is unlikely that Irc3 uses the conventional single-stranded DNA translocase mechanism utilized by most helicases. Here, we demonstrate that Irc3 disrupts partially triple-stranded DNA structures in an ATP-dependent manner. Our kinetic experiments indicate that the rate of ATP hydrolysis by Irc3 is dependent on the length of the double-stranded DNA cosubstrate. Furthermore, the previously uncharacterized C-terminal region of Irc3 is essential for these two characteristic features and forms a high affinity complex with branched DNA. Together, our experiments demonstrate that Irc3 has double-stranded DNA translocase activity.
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Affiliation(s)
- Tiina Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Natalja Garber
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Ilja Gaidutšik
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Sirelin Sillamaa
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Joosep Paats
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Vlad J Piljukov
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
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16
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Bianco PR, Lyubchenko YL. SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork. Protein Sci 2017; 26:638-649. [PMID: 28078722 DOI: 10.1002/pro.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022]
Abstract
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.
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Affiliation(s)
- Piero R Bianco
- SUNY Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, 321 Cary Hall, 3435 Main St, Buffalo, New York 14214.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, 68198-6025
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17
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Azeroglu B, Leach DRF. RecG controls DNA amplification at double-strand breaks and arrested replication forks. FEBS Lett 2017; 591:1101-1113. [PMID: 28155219 PMCID: PMC5412681 DOI: 10.1002/1873-3468.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/16/2022]
Abstract
DNA amplification is a powerful mutational mechanism that is a hallmark of cancer and drug resistance. It is therefore important to understand the fundamental pathways that cells employ to avoid over‐replicating sections of their genomes. Recent studies demonstrate that, in the absence of RecG, DNA amplification is observed at sites of DNA double‐strand break repair (DSBR) and of DNA replication arrest that are processed to generate double‐strand ends. RecG also plays a role in stabilising joint molecules formed during DSBR. We propose that RecG prevents a previously unrecognised mechanism of DNA amplification that we call reverse‐restart, which generates DNA double‐strand ends from incorrect loading of the replicative helicase at D‐loops formed by recombination, and at arrested replication forks.
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Affiliation(s)
- Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
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18
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Selby CP. Mfd Protein and Transcription-Repair Coupling in Escherichia coli. Photochem Photobiol 2017; 93:280-295. [PMID: 27864884 DOI: 10.1111/php.12675] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/18/2016] [Indexed: 01/30/2023]
Abstract
In 1989, transcription-repair coupling (TRC) was first described in Escherichia coli, as the transcription-dependent, preferential nucleotide excision repair (NER) of UV photoproducts located in the template DNA strand. This finding led to pioneering biochemical studies of TRC in the laboratory of Professor Aziz Sancar, where, at the time, major contributions were being made toward understanding the roles of the UvrA, UvrB and UvrC proteins in NER. When the repair studies were extended to TRC, template but not coding strand lesions were found to block RNA polymerase (RNAP) in vitro, and unexpectedly, the blocked RNAP inhibited NER. A transcription-repair coupling factor, also called Mfd protein, was found to remove the blocked RNAP, deliver the repair enzyme to the lesion and thereby mediate more rapid repair of the transcription-blocking lesion compared with lesions elsewhere. Structural and functional analyses of Mfd protein revealed helicase motifs responsible for ATP hydrolysis and DNA binding, and regions that interact with RNAP and UvrA. These and additional studies provided a basis upon which other investigators, in following decades, have characterized fascinating and unexpected structural and mechanistic features of Mfd, revealed the possible existence of additional pathways of TRC and discovered additional roles of Mfd in the cell.
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Affiliation(s)
- Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
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19
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Beyene GT, Balasingham SV, Frye SA, Namouchi A, Homberset H, Kalayou S, Riaz T, Tønjum T. Characterization of the Neisseria meningitidis Helicase RecG. PLoS One 2016; 11:e0164588. [PMID: 27736945 PMCID: PMC5063381 DOI: 10.1371/journal.pone.0164588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.
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Affiliation(s)
| | | | - Stephan A. Frye
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | | | - Shewit Kalayou
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- * E-mail:
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20
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Wallet C, Le Ret M, Bergdoll M, Bichara M, Dietrich A, Gualberto JM. The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis. THE PLANT CELL 2015; 27:2907-25. [PMID: 26462909 PMCID: PMC4682331 DOI: 10.1105/tpc.15.00680] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/14/2015] [Accepted: 09/25/2015] [Indexed: 05/24/2023]
Abstract
The mitochondria of flowering plants have considerably larger and more complex genomes than the mitochondria of animals or fungi, mostly due to recombination activities that modulate their genomic structures. These activities most probably participate in the repair of mitochondrial DNA (mtDNA) lesions by recombination-dependent processes. Rare ectopic recombination across short repeats generates new genomic configurations that contribute to mtDNA heteroplasmy, which drives rapid evolution of the sequence organization of plant mtDNAs. We found that Arabidopsis thaliana RECG1, an ortholog of the bacterial RecG translocase, is an organellar protein with multiple roles in mtDNA maintenance. RECG1 targets to mitochondria and plastids and can complement a bacterial recG mutant that shows defects in repair and replication control. Characterization of Arabidopsis recG1 mutants showed that RECG1 is required for recombination-dependent repair and for suppression of ectopic recombination in mitochondria, most likely because of its role in recovery of stalled replication forks. The analysis of alternative mitotypes present in a recG1 line and of their segregation following backcross allowed us to build a model to explain how a new stable mtDNA configuration, compatible with normal plant development, can be generated by stoichiometric shift.
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Affiliation(s)
- Clémentine Wallet
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Monique Le Ret
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Marc Bergdoll
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Marc Bichara
- CNRS UMR7242, IREBS, Université de Strasbourg, 67412 Illkirch, France
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, 67084 Strasbourg, France
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21
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Thakur RS, Basavaraju S, Khanduja JS, Muniyappa K, Nagaraju G. Mycobacterium tuberculosis RecG protein but not RuvAB or RecA protein is efficient at remodeling the stalled replication forks: implications for multiple mechanisms of replication restart in mycobacteria. J Biol Chem 2015; 290:24119-39. [PMID: 26276393 DOI: 10.1074/jbc.m115.671164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant DNA replication, defects in the protection, and restart of stalled replication forks are major causes of genome instability in all organisms. Replication fork reversal is emerging as an evolutionarily conserved physiological response for restart of stalled forks. Escherichia coli RecG, RuvAB, and RecA proteins have been shown to reverse the model replication fork structures in vitro. However, the pathways and the mechanisms by which Mycobacterium tuberculosis, a slow growing human pathogen, responds to different types of replication stress and DNA damage are unclear. Here, we show that M. tuberculosis RecG rescues E. coli ΔrecG cells from replicative stress. The purified M. tuberculosis RecG (MtRecG) and RuvAB (MtRuvAB) proteins catalyze fork reversal of model replication fork structures with and without a leading strand single-stranded DNA gap. Interestingly, single-stranded DNA-binding protein suppresses the MtRecG- and MtRuvAB-mediated fork reversal with substrates that contain lagging strand gap. Notably, our comparative studies with fork structures containing template damage and template switching mechanism of lesion bypass reveal that MtRecG but not MtRuvAB or MtRecA is proficient in driving the fork reversal. Finally, unlike MtRuvAB, we find that MtRecG drives efficient reversal of forks when fork structures are tightly bound by protein. These results provide direct evidence and valuable insights into the underlying mechanism of MtRecG-catalyzed replication fork remodeling and restart pathways in vivo.
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Affiliation(s)
- Roshan Singh Thakur
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Shivakumar Basavaraju
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Jasbeer Singh Khanduja
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Ganesh Nagaraju
- From the Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
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22
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Bianco PR. I came to a fork in the DNA and there was RecG. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:166-173. [PMID: 25613916 PMCID: PMC4417463 DOI: 10.1016/j.pbiomolbio.2015.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Abstract
RecG is a potent, atypical, monomeric DNA helicase. It simultaneously couples ATP hydrolysis to duplex unwinding and rewinding, and to the displacement of proteins bound to the DNA. A model is presented for the localization of the enzyme to the inner membrane via its binding to SSB. Upon fork stalling, SSB targets the enzyme to the fork where it can act. RecG displays a strong preference for processing the fork in the regression direction, that is, away from the site of damage that initially led to fork arrest. Regression is mediated by strong binding of the wedge domain to the fork arms as well as to parental duplex DNA by the helicase domains. Once RecG has regressed the fork, it will dissociate leaving the now relaxed, Holliday junction-like DNA, available for further processing by enzymes such as RuvAB.
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Affiliation(s)
- Piero R Bianco
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA; Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214, USA.
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23
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Chen SH, Byrne RT, Wood EA, Cox MM. Escherichia coli radD (yejH) gene: a novel function involved in radiation resistance and double-strand break repair. Mol Microbiol 2015; 95:754-68. [PMID: 25425430 DOI: 10.1111/mmi.12885] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 11/28/2022]
Abstract
A transposon insertion screen implicated the yejH gene in the repair of ionizing radiation-induced damage. The yejH gene, which exhibits significant homology to the human transcription-coupled DNA repair gene XPB, is involved in the repair of double-strand DNA breaks. Deletion of yejH significantly sensitized cells to agents that cause double-strand breaks (ionizing radiation, UV radiation, ciprofloxacin). In addition, deletion of both yejH and radA hypersensitized the cells to ionizing radiation, UV and ciprofloxacin damage, indicating that these two genes have complementary repair functions. The ΔyejH ΔradA double deletion also showed a substantial decline in viability following an induced double-strand DNA break, of a magnitude comparable with the defect measured when the recA, recB, recG or priA genes are deleted. The ATPase activity and C-terminal zinc finger motif of yejH play an important role in its repair function, as targeted mutant alleles of yejH did not rescue sensitivity. We propose that yejH be renamed radD, reflecting its role in the DNA repair of radiation damage.
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Affiliation(s)
- Stefanie H Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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24
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Bhattacharyya B, Keck JL. Grip it and rip it: structural mechanisms of DNA helicase substrate binding and unwinding. Protein Sci 2014; 23:1498-507. [PMID: 25131811 DOI: 10.1002/pro.2533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 07/30/2014] [Accepted: 08/04/2014] [Indexed: 11/07/2022]
Abstract
Maintenance and faithful transmission of genomic information depends on the efficient execution of numerous DNA replication, recombination, and repair pathways. Many of the enzymes that catalyze steps within these pathways require access to sequence information that is buried in the interior of the DNA double helix, which makes DNA unwinding an essential cellular reaction. The unwinding process is mediated by specialized molecular motors called DNA helicases that couple the chemical energy derived from nucleoside triphosphate hydrolysis to the otherwise non-spontaneous unwinding reaction. An impressive number of high-resolution helicase structures are now available that, together with equally important mechanistic studies, have begun to define the features that allow this class of enzymes to function as molecular motors. In this review, we explore the structural features within DNA helicases that are used to bind and unwind DNA. We focus in particular on "aromatic-rich loops" that allow some helicases to couple single-stranded DNA binding to ATP hydrolysis and "wedge/pin" elements that provide mechanical tools for DNA strand separation when connected to translocating motor domains.
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Affiliation(s)
- Basudeb Bhattacharyya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706; Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, La Crosse, Wisconsin, 53601
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25
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Upton AL, Grove JI, Mahdi AA, Briggs GS, Milner DS, Rudolph CJ, Lloyd RG. Cellular location and activity of Escherichia coli RecG proteins shed light on the function of its structurally unresolved C-terminus. Nucleic Acids Res 2014; 42:5702-14. [PMID: 24692661 PMCID: PMC4027168 DOI: 10.1093/nar/gku228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RecG is a DNA translocase encoded by most species of bacteria. The Escherichia coli protein targets branched DNA substrates and drives the unwinding and rewinding of DNA strands. Its ability to remodel replication forks and to genetically interact with PriA protein have led to the idea that it plays an important role in securing faithful genome duplication. Here we report that RecG co-localises with sites of DNA replication and identify conserved arginine and tryptophan residues near its C-terminus that are needed for this localisation. We establish that the extreme C-terminus, which is not resolved in the crystal structure, is vital for DNA unwinding but not for DNA binding. Substituting an alanine for a highly conserved tyrosine near the very end results in a substantial reduction in the ability to unwind replication fork and Holliday junction structures but has no effect on substrate affinity. Deleting or substituting the terminal alanine causes an even greater reduction in unwinding activity, which is somewhat surprising as this residue is not uniformly present in closely related RecG proteins. More significantly, the extreme C-terminal mutations have little effect on localisation. Mutations that do prevent localisation result in only a slight reduction in the capacity for DNA repair.
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Affiliation(s)
- Amy L Upton
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane I Grove
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Akeel A Mahdi
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Geoffrey S Briggs
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - David S Milner
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Christian J Rudolph
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK School of Health Sciences and Social Care, Division of Biosciences, Brunel University, Uxbridge, London UB8 3PH, UK
| | - Robert G Lloyd
- Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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26
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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27
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Baharoglu Z, Babosan A, Mazel D. Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase. Nucleic Acids Res 2013; 42:2366-79. [PMID: 24319148 PMCID: PMC3936754 DOI: 10.1093/nar/gkt1259] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.
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Affiliation(s)
- Zeynep Baharoglu
- Département Génomes et Génétique, Unité Plasticité du Génome Bactérien, Institut Pasteur, 75015 Paris, France and Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France
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28
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Deaconescu AM. RNA polymerase between lesion bypass and DNA repair. Cell Mol Life Sci 2013; 70:4495-509. [PMID: 23807206 PMCID: PMC11113250 DOI: 10.1007/s00018-013-1384-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/13/2013] [Accepted: 05/23/2013] [Indexed: 11/29/2022]
Abstract
DNA damage leads to heritable changes in the genome via DNA replication. However, as the DNA helix is the site of numerous other transactions, notably transcription, DNA damage can have diverse repercussions on cellular physiology. In particular, DNA lesions have distinct effects on the passage of transcribing RNA polymerases, from easy bypass to almost complete block of transcription elongation. The fate of the RNA polymerase positioned at a lesion is largely determined by whether the lesion is structurally subtle and can be accommodated and eventually bypassed, or bulky, structurally distorting and requiring remodeling/complete dissociation of the transcription elongation complex, excision, and repair. Here we review cellular responses to DNA damage that involve RNA polymerases with a focus on bacterial transcription-coupled nucleotide excision repair and lesion bypass via transcriptional mutagenesis. Emphasis is placed on the explosion of new structural information on RNA polymerases and relevant DNA repair factors and the mechanistic models derived from it.
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Affiliation(s)
- Alexandra M Deaconescu
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South St., MS029, Waltham, MA, 02454, USA,
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29
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Zegeye ED, Balasingham SV, Laerdahl JK, Homberset H, Kristiansen PE, Tønjum T. Effects of conserved residues and naturally occurring mutations on Mycobacterium tuberculosis RecG helicase activity. MICROBIOLOGY-SGM 2013; 160:217-227. [PMID: 24169816 DOI: 10.1099/mic.0.072140-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RecG is a helicase that is conserved in nearly all bacterial species. The prototypical Escherichia coli RecG promotes regression of stalled replication forks, participates in DNA recombination and DNA repair, and prevents aberrant replication. Mycobacterium tuberculosis RecG (RecGMtb) is a DNA-dependent ATPase that unwinds a variety of DNA substrates, although its preferred substrate is a Holliday junction. Here, we performed site-directed mutagenesis of selected residues in the wedge domain and motifs Q, I, Ib and VI of RecGMtb. Three of the 10 substitution mutations engineered were detected previously as naturally occurring SNPs in the gene encoding RecGMtb. Alanine substitution mutations at residues Q292, F286, K321 and R627 abolished the RecGMtb unwinding activity, whilst RecGMtb F99A, P285S and T408A mutants exhibited ~25-50 % lower unwinding activity than WT. We also found that RecGMtb bound ATP in the absence of a DNA cofactor.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Jon K Laerdahl
- Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Per E Kristiansen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
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30
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Thakur RS, Basavaraju S, Somyajit K, Jain A, Subramanya S, Muniyappa K, Nagaraju G. Evidence for the role of Mycobacterium tuberculosis RecG helicase in DNA repair and recombination. FEBS J 2013; 280:1841-60. [PMID: 23438087 DOI: 10.1111/febs.12208] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/05/2013] [Accepted: 02/18/2013] [Indexed: 11/28/2022]
Abstract
In order to survive and replicate in a variety of stressful conditions during its life cycle, Mycobacterium tuberculosis must possess mechanisms to safeguard the integrity of the genome. Although DNA repair and recombination related genes are thought to play key roles in the repair of damaged DNA in all organisms, so far only a few of them have been functionally characterized in the tubercle bacillus. In this study, we show that M. tuberculosis RecG (MtRecG) expression was induced in response to different genotoxic agents. Strikingly, expression of MtRecG in Escherichia coli ∆recG mutant strain provided protection against mitomycin C, methyl methane sulfonate and UV induced cell death. Purified MtRecG exhibited higher binding affinity for the Holliday junction (HJ) compared with a number of canonical recombinational DNA repair intermediates. Notably, although MtRecG binds at the core of the mobile and immobile HJs, and with higher binding affinity for the immobile HJ, branch migration was evident only in the case of the mobile HJ. Furthermore, immobile HJs stimulate MtRecG ATPase activity less efficiently than mobile HJs. In addition to HJ substrates, MtRecG exhibited binding affinity for a variety of branched DNA structures including three-way junctions, replication forks, flap structures, forked duplex and a D-loop structure, but demonstrated strong unwinding activity on replication fork and flap DNA structures. Together, these results support that MtRecG plays an important role in processes related to DNA metabolism under normal as well as stress conditions.
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Affiliation(s)
- Roshan S Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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31
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Luo D, Kohlway A, Pyle AM. Duplex RNA activated ATPases (DRAs): platforms for RNA sensing, signaling and processing. RNA Biol 2012; 10:111-20. [PMID: 23228901 PMCID: PMC3590228 DOI: 10.4161/rna.22706] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Double-stranded RNAs are an important class of functional macromolecules in living systems. They are usually found as part of highly specialized intracellular machines that control diverse cellular events, ranging from virus replication, antiviral defense, RNA interference, to regulation of gene activities and genomic integrity. Within different intracellular machines, the RNA duplex is often found in association with specific RNA-dependent ATPases, including Dicer, RIG-I and DRH-3 proteins. These duplex RNA-activated ATPases represent an emerging group of motor proteins within the large and diverse super family 2 nucleic acid-dependent ATPases (which are historically defined as SF2 helicases). The duplex RNA-activated ATPases share characteristic molecular features for duplex RNA recognition, including motifs (e.g., motifs IIa and Vc) and an insertion domain (HEL2i), and they require double-strand RNA binding for their enzymatic activities. Proteins in this family undergo large conformational changes concomitant with RNA binding, ATP binding and ATP hydrolysis in order to achieve their functions, which include the release of signaling domains and the recruitment of partner proteins. The duplex RNA-activated ATPases represent a distinct and fascinating group of nanomechanical molecular motors that are essential for duplex RNA sensing and processing in diverse cellular pathways.
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Affiliation(s)
- Dahai Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
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32
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Dib L, Carbone A. Protein fragments: functional and structural roles of their coevolution networks. PLoS One 2012; 7:e48124. [PMID: 23139761 PMCID: PMC3489791 DOI: 10.1371/journal.pone.0048124] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 09/27/2012] [Indexed: 11/19/2022] Open
Abstract
Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Indeed, coevolving fragments are indicators of important information explaining folding intermediates, peptide assembly, key mutations with known roles in genetic diseases, distinguished subfamily-dependent motifs and differentiated evolutionary pressures on protein regions. Coevolution analysis detects networks of fragments interaction and highlights a high order organization of fragments demonstrating the importance of studying at a deeper level this structure. We demonstrate that it can be applied to protein families that are highly conserved or represented by few sequences, enlarging in this manner, the class of proteins where coevolution analysis can be performed and making large-scale coevolution studies a feasible goal.
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Affiliation(s)
- Linda Dib
- Université Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France
- CNRS, UMR 7238, Laboratoire de Génomique des Microorganismes, Paris, France
| | - Alessandra Carbone
- Université Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France
- CNRS, UMR 7238, Laboratoire de Génomique des Microorganismes, Paris, France
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33
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Abstract
ATP-dependent nucleic acid helicases and translocases play essential roles in many aspects of DNA and RNA biology. In order to ensure that these proteins act only in specific contexts, their activity is often regulated by intramolecular contacts and interaction with partner proteins. We have studied the bacterial Mfd protein, which is an ATP-dependent DNA translocase that relocates or displaces transcription ECs in a variety of cellular contexts. When bound to RNAP, Mfd exhibits robust ATPase and DNA translocase activities, but when released from its substrate these activities are repressed by autoinhibitory interdomain contacts. In this work, we have identified an interface within the Mfd protein that is important for regulating the activity of the protein, and whose disruption permits Mfd to act indiscriminately at transcription complexes that lack the usual determinants of Mfd specificity. Our results indicate that regulation of Mfd occurs through multiple nodes, and that activation of Mfd may be a multi-stage process.
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Affiliation(s)
- Abigail J Smith
- DNA-protein interactions unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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34
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Toseland CP, Powell B, Webb MR. ATPase cycle and DNA unwinding kinetics of RecG helicase. PLoS One 2012; 7:e38270. [PMID: 22701618 PMCID: PMC3368886 DOI: 10.1371/journal.pone.0038270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/07/2012] [Indexed: 11/18/2022] Open
Abstract
The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states.
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Affiliation(s)
| | - Ben Powell
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Martin R. Webb
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- * E-mail: .
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35
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Zegeye ED, Balasingham SV, Laerdahl JK, Homberset H, Tønjum T. Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions. MICROBIOLOGY-SGM 2012; 158:1982-1993. [PMID: 22628485 PMCID: PMC3542137 DOI: 10.1099/mic.0.058693-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The RecG enzyme, a superfamily 2 helicase, is present in nearly all bacteria. Here we report for the first time that the recG gene is also present in the genomes of most vascular plants as well as in green algae, but is not found in other eukaryotes or archaea. The precise function of RecG is poorly understood, although ample evidence shows that it plays critical roles in DNA repair, recombination and replication. We further demonstrate that Mycobacterium tuberculosis RecG (RecGMtb) DNA binding activity had a broad substrate specificity, whereas it only unwound branched-DNA substrates such as Holliday junctions (HJs), replication forks, D-loops and R-loops, with a strong preference for the HJ as a helicase substrate. In addition, RecGMtb preferentially bound relatively long (≥40 nt) ssDNA, exhibiting a higher affinity for the homopolymeric nucleotides poly(dT), poly(dG) and poly(dC) than for poly(dA). RecGMtb helicase activity was supported by hydrolysis of ATP or dATP in the presence of Mg2+, Mn2+, Cu2+ or Fe2+. Like its Escherichia coli orthologue, RecGMtb is also a strictly DNA-dependent ATPase.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Jon K Laerdahl
- Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
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36
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Mfd is required for rapid recovery of transcription following UV-induced DNA damage but not oxidative DNA damage in Escherichia coli. J Bacteriol 2012; 194:2637-45. [PMID: 22427630 DOI: 10.1128/jb.06725-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Transcription-coupled repair (TCR) is a cellular process by which some forms of DNA damage are repaired more rapidly from transcribed strands of active genes than from nontranscribed strands or the overall genome. In humans, the TCR coupling factor, CSB, plays a critical role in restoring transcription following both UV-induced and oxidative DNA damage. It also contributes indirectly to the global repair of some forms of oxidative DNA damage. The Escherichia coli homolog, Mfd, is similarly required for TCR of UV-induced lesions. However, its contribution to the restoration of transcription and to global repair of oxidative damage has not been examined. Here, we report the first direct study of transcriptional recovery following UV-induced and oxidative DNA damage in E. coli. We observed that mutations in mfd or uvrA reduced the rate that transcription recovered following UV-induced damage. In contrast, no difference was detected in the rate of transcription recovery in mfd, uvrA, fpg, nth, or polB dinB umuDC mutants relative to wild-type cells following oxidative damage. mfd mutants were also fully resistant to hydrogen peroxide (H(2)O(2)) and removed oxidative lesions from the genome at rates comparable to wild-type cells. The results demonstrate that Mfd promotes the rapid recovery of gene expression following UV-induced damage in E. coli. In addition, these findings imply that Mfd may be functionally distinct from its human CSB homolog in that it does not detectably contribute to the recovery of gene expression or global repair following oxidative damage.
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37
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Tate J, Gollnick P. Role of forward translocation in nucleoside triphosphate phosphohydrolase I (NPH I)-mediated transcription termination of vaccinia virus early genes. J Biol Chem 2011; 286:44764-75. [PMID: 22069335 PMCID: PMC3247973 DOI: 10.1074/jbc.m111.263822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 10/28/2011] [Indexed: 01/04/2023] Open
Abstract
Termination of transcription of vaccinia virus early genes requires the virion form of the viral RNA polymerase (RNAP), a termination signal (UUUUUNU) in the nascent RNA, vaccinia termination factor, nucleoside triphosphate phosphohydrolase I (NPH I), and ATP. NPH I uses ATP hydrolysis to mediate transcript release, and in vitro, ATPase activity requires single-stranded DNA. NPH I shows sequence similarity with the DEXH-box family of proteins, which includes an Escherichia coli ATP-dependent motor protein, Mfd. Mfd releases transcripts and rescues arrested transcription complexes by moving the transcription elongation complex downstream on the DNA template in the absence of transcription elongation. This mechanism is known as forward translocation. In this study, we demonstrate that NPH I also uses forward translocation to catalyze transcript release from viral RNAP. Moreover, we show that NPH I-mediated release can occur at a stalled RNAP in the absence of vaccinia termination factor and U(5)NU when transcription elongation is prevented.
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Affiliation(s)
- Jessica Tate
- From the Department of Biological Sciences, University at Buffalo, Buffalo, New York 14226
| | - Paul Gollnick
- From the Department of Biological Sciences, University at Buffalo, Buffalo, New York 14226
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38
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Prabha S, Rao DN, Nagaraja V. Distinct properties of hexameric but functionally conserved Mycobacterium tuberculosis transcription-repair coupling factor. PLoS One 2011; 6:e19131. [PMID: 21559463 PMCID: PMC3084762 DOI: 10.1371/journal.pone.0019131] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 03/17/2011] [Indexed: 12/04/2022] Open
Abstract
Transcription coupled nucleotide excision repair (TC-NER) is involved in correcting UV-induced damage and other road-blocks encountered in the transcribed strand. Mutation frequency decline (Mfd) is a transcription repair coupling factor, involved in repair of template strand during transcription. Mfd from M. tuberculosis (MtbMfd) is 1234 amino-acids long harboring characteristic modules for different activities. Mtbmfd complemented Escherichia coli mfd (Ecomfd) deficient strain, enhanced survival of UV irradiated cells and increased the road-block repression in vivo. The protein exhibited ATPase activity, which was stimulated ∼1.5-fold in the presence of DNA. While the C-terminal domain (CTD) comprising amino acids 630 to 1234 showed ∼2-fold elevated ATPase activity than MtbMfd, the N-terminal domain (NTD) containing the first 433 amino acid residues was able to bind ATP but deficient in hydrolysis. Overexpression of NTD of MtbMfd led to growth defect and hypersensitivity to UV light. Deletion of 184 amino acids from the C-terminal end of MtbMfd (MfdΔC) increased the ATPase activity by ∼10-fold and correspondingly exhibited efficient translocation along DNA as compared to the MtbMfd and CTD. Surprisingly, MtbMfd was found to be distributed in monomer and hexamer forms both in vivo and in vitro and the monomer showed increased susceptibility to proteases compared to the hexamer. MfdΔC, on the other hand, was predominantly monomeric in solution implicating the extreme C-terminal region in oligomerization of the protein. Thus, although the MtbMfd resembles EcoMfd in many of its reaction characteristics, some of its hitherto unknown distinct properties hint at its species specific role in mycobacteria during transcription-coupled repair.
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Affiliation(s)
- Swayam Prabha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Desirazu N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail: (DNR); (VN)
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- * E-mail: (DNR); (VN)
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39
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Srivastava DB, Darst SA. Derepression of bacterial transcription-repair coupling factor is associated with a profound conformational change. J Mol Biol 2010; 406:275-84. [PMID: 21185303 DOI: 10.1016/j.jmb.2010.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/28/2010] [Accepted: 12/02/2010] [Indexed: 11/16/2022]
Abstract
Transcription-repair coupling factor (TRCF; the product of the mfd gene) is a widely conserved bacterial protein that couples DNA repair with transcription. TRCF recognizes RNA polymerase stalled at a noncoding lesion in the DNA template strand, uses the energy from ATP hydrolysis to disrupt the transcription complex, and stimulates DNA repair by recruiting UvrA, a component of the nucleotide excision repair machinery, to the site. TRCF is a large (130 kDa) multifunctional protein with a complex structure-function relationship consisting of a compact arrangement of eight structured domains linked by flexible linkers. Through a conserved, intramolecular, interdomain interaction, TRCF is held in a conformation in which its enzymatic activities (ATPase activity and DNA translocase activity) are strongly repressed. Disruption of the repressive interdomain interaction by amino acid substitutions within the interface derepresses ATPase and DNA translocase activities. In this work, we have shown that derepressed TRCF mutants are dramatically sensitized to limited proteolysis compared with repressed TRCF, pointing to an altered conformational state. Analysis of the protease cleavage sites mapped onto the structure of the repressed TRCF conformation indicates that (1) the cleavage sites tend to cluster at linkers connecting the TRCF structured domains, and (2) many of the cleavage sites sensitized in the derepressed TRCF are partially or completely buried to protease access in the repressed TRCF structure. We conclude that TRCF derepression is associated with profound conformational changes that primarily involve a reorganization of the interdomain interactions.
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40
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Abstract
DNA and RNA helicases are organized into six superfamilies of enzymes on the basis of sequence alignments, biochemical data, and available crystal structures. DNA helicases, members of which are found in each of the superfamilies, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5'-triphosphates. The purpose of this DNA unwinding is to provide nascent, single-stranded DNA (ssDNA) for the processes of DNA repair, replication, and recombination. Not surprisingly, DNA helicases share common biochemical properties that include the binding of single- and double-stranded DNA, nucleoside 5'-triphosphate binding and hydrolysis, and nucleoside 5'-triphosphate hydrolysis-coupled, polar unwinding of duplex DNA. These enzymes participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination, and repair can occur. In Escherichia coli, there are currently twelve DNA helicases that perform a variety of tasks ranging from simple strand separation at the replication fork to more sophisticated processes in DNA repair and genetic recombination. In this chapter, the superfamily classification, role(s) in DNA metabolism, effects of mutations, biochemical analysis, oligomeric nature, and interacting partner proteins of each of the twelve DNA helicases are discussed.
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41
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Promoting and avoiding recombination: contrasting activities of the Escherichia coli RuvABC Holliday junction resolvase and RecG DNA translocase. Genetics 2010; 185:23-37. [PMID: 20157002 DOI: 10.1534/genetics.110.114413] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RuvABC and RecG are thought to provide alternative pathways for the late stages of recombination in Escherichia coli. Inactivation of both blocks the recovery of recombinants in genetic crosses. RuvABC resolves Holliday junctions, with RuvAB driving branch migration and RuvC catalyzing junction cleavage. RecG also drives branch migration, but no nuclease has been identified that might act with RecG to cleave junctions, apart from RusA, which is not normally expressed. We searched for an alternative nuclease using a synthetic lethality assay to screen for mutations causing inviability in the absence of RuvC, on the premise that a strain without any ability to cut junctions might be inviable. All the mutations identified mapped to polA, dam, or uvrD. None of these genes encodes a nuclease that cleaves Holliday junctions. Probing the reason for the inviability using the RusA Holliday junction resolvase provided strong evidence in each case that the RecG pathway is very ineffective at removing junctions and indicated that a nuclease component most probably does not exist. It also revealed new suppressors of recG, which were located to the ssb gene. Taken together with the results from the synthetic lethality assays, the properties of the mutant SSB proteins provide evidence that, rather than promoting recombination, a major function of RecG is to curb potentially pathological replication initiated via PriA protein at sites remote from oriC.
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Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K. An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Nucleic Acids Res 2009; 37:6042-53. [PMID: 19700770 PMCID: PMC2764443 DOI: 10.1093/nar/gkp680] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, making the lesion accessible for repair. Structural and biochemical data on the bacterial transcription-repair coupling factor Mfd suggest that this enzyme undergoes large conformational changes from a dormant state to an active state upon substrate binding. Mfd can be functionally dissected into an N-terminal part instrumental in recruiting DNA repair proteins (domains 1–3, MfdN), and a C-terminal part harboring motor activity (domains 4–7, MfdC). We show that isolated MfdC has elevated ATPase and motor activities compared to the full length protein. While MfdN has large effects on MfdC activity and thermostability in cis, these effects are not observed in trans. The structure of MfdN is independent of interactions with MfdC, implying that MfdN acts as a clamp that restrains motions of the motor domains in the dormant state. We conclude that releasing MfdN:MfdC interactions serves as a central molecular switch that upregulates Mfd functions during transcription-coupled DNA repair.
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Affiliation(s)
- Michael N Murphy
- Department of Chemistry, Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
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43
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Abstract
Little is known about what happens when forks meet to complete DNA replication in any organism. In this study we present data suggesting that the collision of replication forks is a potential threat to genomic stability. We demonstrate that Escherichia coli cells lacking RecG helicase suffer major defects in chromosome replication following UV irradiation, and that this is associated with high levels of DNA synthesis initiated independently of the initiator protein DnaA. This UV-induced stable DNA replication is dependent on PriA helicase and continues long after UV-induced lesions have been excised. We suggest UV irradiation triggers the assembly of new replication forks, leading to multiple fork collisions outside the terminus area. Such collisions may generate branched DNAs that serve to establish further new forks, resulting in uncontrolled DNA amplification. We propose that RecG reduces the likelihood of this pathological cascade being set in motion by reducing initiation of replication at D- and R-loops, and other structures generated as a result of fork collisions. Our results shed light on why replication initiation in bacteria is limited to a single origin and why termination is carefully orchestrated to a single event within a restricted area each cell cycle.
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Affiliation(s)
- Christian J Rudolph
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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44
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Atkinson J, McGlynn P. Replication fork reversal and the maintenance of genome stability. Nucleic Acids Res 2009; 37:3475-92. [PMID: 19406929 PMCID: PMC2699526 DOI: 10.1093/nar/gkp244] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The progress of replication forks is often threatened in vivo, both by DNA damage and by proteins bound to the template. Blocked forks must somehow be restarted, and the original blockage cleared, in order to complete genome duplication, implying that blocked fork processing may be critical for genome stability. One possible pathway that might allow processing and restart of blocked forks, replication fork reversal, involves the unwinding of blocked forks to form four-stranded structures resembling Holliday junctions. This concept has gained increasing popularity recently based on the ability of such processing to explain many genetic observations, the detection of unwound fork structures in vivo and the identification of enzymes that have the capacity to catalyse fork regression in vitro. Here, we discuss the contexts in which fork regression might occur, the factors that may promote such a reaction and the possible roles of replication fork unwinding in normal DNA metabolism.
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Affiliation(s)
- John Atkinson
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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45
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Nelson SW, Perumal SK, Benkovic SJ. Processive and unidirectional translocation of monomeric UvsW helicase on single-stranded DNA. Biochemistry 2009; 48:1036-46. [PMID: 19154117 DOI: 10.1021/bi801792q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UvsW protein from bacteriophage T4 controls the transition from origin-dependent to origin-independent initiation of replication through the unwinding of R-loops bound to the T4 origins of replication. UvsW has also been implicated through genetic and biochemical experiments to play a role in DNA repair processes such as replication fork regression and Holliday junction branch migration. UvsW is capable of unwinding a wide variety of substrates, many of which contain only duplex DNA without single-stranded regions. Based on this observation, it has been suggested that UvsW is a dsDNA translocase. In this work we examine the ability of UvsW to translocate on ssDNA. Kinetic analysis indicates that the rate of ATP hydrolysis is strongly dependent on the length of the ssDNA lattice, whereas the K(M)-DNA remains relatively constant, demonstrating that UvsW translocates on ssDNA in an ATP-dependent fashion. Experiments using streptavidin blocks or poly dT sequences located at either end of the ssDNA substrate indicate that UvsW translocates in a 3' to 5' direction. Mutant competition and heparin trapping experiments reveal that UvsW is extremely processive during ATP-driven translocation with a half-life on the order of several minutes. Finally, functional assays provide evidence that UvsW is monomeric while translocating on ssDNA. The ability of UvsW to unwind DNA duplexes is likely to be mechanistically linked to its ability to processively translocate on ssDNA in a 3' to 5' unidirectional fashion.
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Affiliation(s)
- Scott W Nelson
- Department of Chemistry, 414 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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46
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Rajagopal V, Patel SS. Viral Helicases. VIRAL GENOME REPLICATION 2009. [PMCID: PMC7121818 DOI: 10.1007/b135974_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Helicases are motor proteins that use the free energy of NTP hydrolysis to catalyze the unwinding of duplex nucleic acids. Helicases participate in almost all processes involving nucleic acids. Their action is critical for replication, recombination, repair, transcription, translation, splicing, mRNA editing, chromatin remodeling, transport, and degradation (Matson and Kaiser-Rogers 1990; Matson et al. 1994; Mendonca et al. 1995; Luking et al. 1998).
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Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 2008; 43:289-318. [PMID: 18937104 PMCID: PMC2583361 DOI: 10.1080/10409230802341296] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When duplex DNA is altered in almost any way (replicated, recombined, or repaired), single strands of DNA are usually intermediates, and single-stranded DNA binding (SSB) proteins are present. These proteins have often been described as inert, protective DNA coatings. Continuing research is demonstrating a far more complex role of SSB that includes the organization and/or mobilization of all aspects of DNA metabolism. Escherichia coli SSB is now known to interact with at least 14 other proteins that include key components of the elaborate systems involved in every aspect of DNA metabolism. Most, if not all, of these interactions are mediated by the amphipathic C-terminus of SSB. In this review, we summarize the extent of the eubacterial SSB interaction network, describe the energetics of interactions with SSB, and highlight the roles of SSB in the process of recombination. Similar themes to those highlighted in this review are evident in all biological systems.
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Affiliation(s)
- Robert D Shereda
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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48
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DNA double strand break repair and crossing over mediated by RuvABC resolvase and RecG translocase. DNA Repair (Amst) 2008; 7:1517-30. [PMID: 18606573 DOI: 10.1016/j.dnarep.2008.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 05/02/2008] [Accepted: 05/16/2008] [Indexed: 10/21/2022]
Abstract
DNA double-strand breaks threaten the stability of the genome, and yet are induced deliberately during meiosis in order to provoke homologous recombination and generate the crossovers needed to promote faithful chromosome transmission. Crossovers are secured via biased resolution of the double Holliday junction intermediates formed when both ends of the broken chromosome engage an intact homologue. To investigate whether the enzymes catalysing branch migration and resolution of Holliday junctions are directed to favour production of either crossover or noncrossover products, we engineered a genetic system based on DNA breakage induced by the I-SceI endonuclease to detect analogous exchanges in Escherichia coli where the enzymology of recombination is more fully understood. Analysis of the recombinants generated revealed approximately equal numbers of crossover and noncrossover products, regardless of whether repair is mediated via RecG, RuvABC, or the RusA resolvase. We conclude that there little or no control of crossing over at the level of Holliday junction resolution. Thus, if similar resolvases function during meiosis, additional factors must act to bias recombination in favour of crossover progeny.
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Wen Q, Scorah J, Phear G, Rodgers G, Rodgers S, Meuth M. A mutant allele of MRE11 found in mismatch repair-deficient tumor cells suppresses the cellular response to DNA replication fork stress in a dominant negative manner. Mol Biol Cell 2008; 19:1693-705. [PMID: 18256278 PMCID: PMC2291432 DOI: 10.1091/mbc.e07-09-0975] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 01/16/2008] [Accepted: 01/29/2008] [Indexed: 01/26/2023] Open
Abstract
The interaction of ataxia-telangiectasia mutated (ATM) and the Mre11/Rad50/Nbs1 (MRN) complex is critical for the response of cells to DNA double-strand breaks; however, little is known of the role of these proteins in response to DNA replication stress. Here, we report a mutant allele of MRE11 found in a colon cancer cell line that sensitizes cells to agents causing replication fork stress. The mutant Mre11 weakly interacts with Rad50 relative to wild type and shows little affinity for Nbs1. The mutant protein lacks 3'-5' exonuclease activity as a result of loss of part of the conserved nuclease domain; however, it retains binding affinity for single-stranded DNA (ssDNA), double-stranded DNA with a 3' single-strand overhang, and fork-like structures containing ssDNA regions. In cells, the mutant protein shows a time- and dose-dependent accumulation in chromatin after thymidine treatment that corresponds with increased recruitment and hyperphosphorylation of replication protein A. ATM autophosphorylation, Mre11 foci, and thymidine-induced homologous recombination are suppressed in cells expressing the mutant allele. Together, our results suggest that the mutant Mre11 suppresses the cellular response to replication stress by binding to ssDNA regions at disrupted forks and impeding replication restart in a dominant negative manner.
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Affiliation(s)
- Qin Wen
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
| | - Jennifer Scorah
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
| | - Geraldine Phear
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
| | - Gary Rodgers
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
| | - Sheila Rodgers
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
| | - Mark Meuth
- Institute for Cancer Studies, University of Sheffield, School of Medicine and Biomedical Sciences, Sheffield S10 2RX, United Kingdom
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50
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Singleton MR, Dillingham MS, Wigley DB. Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 2007; 76:23-50. [PMID: 17506634 DOI: 10.1146/annurev.biochem.76.052305.115300] [Citation(s) in RCA: 948] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Helicases and translocases are a ubiquitous, highly diverse group of proteins that perform an extraordinary variety of functions in cells. Consequently, this review sets out to define a nomenclature for these enzymes based on current knowledge of sequence, structure, and mechanism. Using previous definitions of helicase families as a basis, we delineate six superfamilies of enzymes, with examples of crystal structures where available, and discuss these structures in the context of biochemical data to outline our present understanding of helicase and translocase activity. As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized.
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Affiliation(s)
- Martin R Singleton
- Macromolecular Structure and Function Laboratory, The London Research Institute, London WC2A 3PX, United Kingdom.
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