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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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3
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Henry C, Kaur G, Cherry ME, Henrikus SS, Bonde N, Sharma N, Beyer H, Wood EA, Chitteni-Pattu S, van Oijen A, Robinson A, Cox M. RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes. Nucleic Acids Res 2023; 51:5714-5742. [PMID: 37125644 PMCID: PMC10287930 DOI: 10.1093/nar/gkad310] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/09/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023] Open
Abstract
The bacterial RecF, RecO, and RecR proteins are an epistasis group involved in loading RecA protein into post-replication gaps. However, the targeting mechanism that brings these proteins to appropriate gaps is unclear. Here, we propose that targeting may involve a direct interaction between RecF and DnaN. In vivo, RecF is commonly found at the replication fork. Over-expression of RecF, but not RecO or a RecF ATPase mutant, is extremely toxic to cells. We provide evidence that the molecular basis of the toxicity lies in replisome destabilization. RecF over-expression leads to loss of genomic replisomes, increased recombination associated with post-replication gaps, increased plasmid loss, and SOS induction. Using three different methods, we document direct interactions of RecF with the DnaN β-clamp and DnaG primase that may underlie the replisome effects. In a single-molecule rolling-circle replication system in vitro, physiological levels of RecF protein trigger post-replication gap formation. We suggest that the RecF interactions, particularly with DnaN, reflect a functional link between post-replication gap creation and gap processing by RecA. RecF's varied interactions may begin to explain how the RecFOR system is targeted to rare lesion-containing post-replication gaps, avoiding the potentially deleterious RecA loading onto thousands of other gaps created during replication.
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Affiliation(s)
- Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
| | - Gurleen Kaur
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Megan E Cherry
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Nina J Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
| | - Nischal Sharma
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Hope A Beyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706-1544, USA
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Henry C, Mbele N, Cox MM. RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR. Nucleic Acids Res 2023; 51:5699-5713. [PMID: 37125642 PMCID: PMC10287957 DOI: 10.1093/nar/gkad311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/09/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023] Open
Abstract
In bacteria, the repair of post-replication gaps by homologous recombination requires the action of the recombination mediator proteins RecF, RecO and RecR. Whereas the role of the RecOR proteins to displace the single strand binding protein (SSB) and facilitate RecA loading is clear, how RecF mediates targeting of the system to appropriate sites remains enigmatic. The most prominent hypothesis relies on specific RecF binding to gap ends. To test this idea, we present a detailed examination of RecF and RecFR binding to more than 40 DNA substrates of varying length and structure. Neither RecF nor the RecFR complex exhibited specific DNA binding that can explain the targeting of RecF(R) to post-replication gaps. RecF(R) bound to dsDNA and ssDNA of sufficient length with similar facility. DNA binding was highly ATP-dependent. Most measured Kd values fell into a range of 60-180 nM. The addition of ssDNA extensions on duplex substrates to mimic gap ends or CPD lesions produces only subtle increases or decreases in RecF(R) affinity. Significant RecFR binding cooperativity was evident with many DNA substrates. The results indicate that RecF or RecFR targeting to post-replication gaps must rely on factors not yet identified, perhaps involving interactions with additional proteins.
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Affiliation(s)
- Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Neema Mbele
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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Pham P, Wood EA, Cox MM, Goodman MF. RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli. Nucleic Acids Res 2023; 51:5527-5546. [PMID: 37070184 PMCID: PMC10287960 DOI: 10.1093/nar/gkad263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated 'ssGap-seq', we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, RecA and SSB assembly profiles coincide globally, concentrated on the lagging strand and enhanced after UV irradiation. Unexpected results also abound. Near the terminus, RecA binding is favored over SSB, binding patterns change in the absence of RecG, and the absence of XerD results in massive RecA assembly. RecA may substitute for the absence of XerCD to resolve chromosome dimers. A RecA loading pathway may exist that is independent of RecBCD and RecFOR. Two prominent and focused peaks of RecA binding revealed a pair of 222 bp and GC-rich repeats, equidistant from dif and flanking the Ter domain. The repeats, here named RRS for replication risk sequence, trigger a genomically programmed generation of post-replication gaps that may play a special role in relieving topological stress during replication termination and chromosome segregation. As demonstrated here, ssGap-seq provides a new window on previously inaccessible aspects of ssDNA metabolism.
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Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
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Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M. Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination. Nat Struct Mol Biol 2023; 30:650-660. [PMID: 37081315 DOI: 10.1038/s41594-023-00967-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/15/2023] [Indexed: 04/22/2023]
Abstract
In bacteria, one type of homologous-recombination-based DNA-repair pathway involves RecFOR proteins that bind at the junction between single-stranded (ss) and double-stranded (ds) DNA. They facilitate the replacement of SSB protein, which initially covers ssDNA, with RecA, which mediates the search for homologous sequences. However, the molecular mechanism of RecFOR cooperation remains largely unknown. We used Thermus thermophilus proteins to study this system. Here, we present a cryo-electron microscopy structure of the RecF-dsDNA complex, and another reconstruction that shows how RecF interacts with two different regions of the tetrameric RecR ring. Lower-resolution reconstructions of the RecR-RecO subcomplex and the RecFOR-DNA assembly explain how RecO is positioned to interact with ssDNA and SSB, which is proposed to lock the complex on a ssDNA-dsDNA junction. Our results integrate the biochemical data available for the RecFOR system and provide a framework for its complete understanding.
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Affiliation(s)
- Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Anuradha Chaudhary
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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Laureti L, Lee L, Philippin G, Kahi M, Pagès V. Single strand gap repair: The presynaptic phase plays a pivotal role in modulating lesion tolerance pathways. PLoS Genet 2022; 18:e1010238. [PMID: 35653392 PMCID: PMC9203016 DOI: 10.1371/journal.pgen.1010238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 06/16/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
During replication, the presence of unrepaired lesions results in the formation of single stranded DNA (ssDNA) gaps that need to be repaired to preserve genome integrity and cell survival. All organisms have evolved two major lesion tolerance pathways to continue replication: Translesion Synthesis (TLS), potentially mutagenic, and Homology Directed Gap Repair (HDGR), that relies on homologous recombination. In Escherichia coli, the RecF pathway repairs such ssDNA gaps by processing them to produce a recombinogenic RecA nucleofilament during the presynaptic phase. In this study, we show that the presynaptic phase is crucial for modulating lesion tolerance pathways since the competition between TLS and HDGR occurs at this stage. Impairing either the extension of the ssDNA gap (mediated by the nuclease RecJ and the helicase RecQ) or the loading of RecA (mediated by RecFOR) leads to a decrease in HDGR and a concomitant increase in TLS. Hence, we conclude that defects in the presynaptic phase delay the formation of the D-loop and increase the time window allowed for TLS. In contrast, we show that a defect in the postsynaptic phase that impairs HDGR does not lead to an increase in TLS. Unexpectedly, we also reveal a strong genetic interaction between recF and recJ genes, that results in a recA deficient-like phenotype in which HDGR is almost completely abolished.
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Affiliation(s)
- Luisa Laureti
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Lara Lee
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Gaëlle Philippin
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Michel Kahi
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Vincent Pagès
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
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Courcelle J, Worley TK, Courcelle CT. Recombination Mediator Proteins: Misnomers That Are Key to Understanding the Genomic Instabilities in Cancer. Genes (Basel) 2022; 13:genes13030437. [PMID: 35327990 PMCID: PMC8950967 DOI: 10.3390/genes13030437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy of PARP inhibitors in treating BRCA2 cancers and RECQ inhibitors in treating cancers with microsatellite instabilities. Thus, understanding the cellular role of recombination mediators is critically important, both to improve current therapies and develop new ones that target these pathways. Our mechanistic understanding of BRCA2 and RECQ began in Escherichia coli. Here, we review the cellular roles of RecF and RecQ, often considered functional homologs of these proteins in bacteria. Although these proteins were originally isolated as genes that were required during replication in sexual cell cycles that produce recombinant products, we now know that their function is similarly required during replication in asexual or mitotic-like cell cycles, where recombination is detrimental and generally not observed. Cells mutated in these gene products are unable to protect and process replication forks blocked at DNA damage, resulting in high rates of cell lethality and recombination events that compromise genome integrity during replication.
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Jain K, Wood EA, Romero ZJ, Cox MM. RecA-independent recombination: Dependence on the Escherichia coli RarA protein. Mol Microbiol 2021; 115:1122-1137. [PMID: 33247976 PMCID: PMC8160026 DOI: 10.1111/mmi.14655] [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: 08/21/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022]
Abstract
Most, but not all, homologous genetic recombination in bacteria is mediated by the RecA recombinase. The mechanistic origin of RecA-independent recombination has remained enigmatic. Here, we demonstrate that the RarA protein makes a major enzymatic contribution to RecA-independent recombination. In particular, RarA makes substantial contributions to intermolecular recombination and to recombination events involving relatively short (<200 bp) homologous sequences, where RecA-mediated recombination is inefficient. The effects are seen here in plasmid-based recombination assays and in vivo cloning processes. Vestigial levels of recombination remain even when both RecA and RarA are absent. Additional pathways for RecA-independent recombination, possibly mediated by helicases, are suppressed by exonucleases ExoI and RecJ. Translesion DNA polymerases may also contribute. Our results provide additional substance to a previous report of a functional overlap between RecA and RarA.
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Affiliation(s)
- Kanika Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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Dissecting the RecA-(In)dependent Response to Mitomycin C in Mycobacterium tuberculosis Using Transcriptional Profiling and Proteomics Analyses. Cells 2021; 10:cells10051168. [PMID: 34064944 PMCID: PMC8151990 DOI: 10.3390/cells10051168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Mycobacteria exploit at least two independent global systems in response to DNA damage: the LexA/RecA-dependent SOS response and the PafBC-regulated pathway. Intracellular pathogens, such as Mycobacterium tuberculosis, are exposed to oxidative and nitrosative stress during the course of infection while residing inside host macrophages. The current understanding of RecA-independent responses to DNA damage is based on the saprophytic model of Mycobacterium smegmatis, a free-living and nonpathogenic mycobacterium. The aim of the present study was to identify elements of RecA-independent responses to DNA damage in pathogenic intracellular mycobacteria. With the help of global transcriptional profiling, we were able to dissect RecA-dependent and RecA-independent pathways. We profiled the DNA damage responses of an M. tuberculosis strain lacking the recA gene, a strain with an undetectable level of the PafBC regulatory system, and a strain with both systems tuned down simultaneously. RNA-Seq profiling was correlated with the evaluation of cell survival in response to DNA damage to estimate the relevance of each system to the overall sensitivity to genotoxic agents. We also carried out whole-cell proteomics analysis of the M. tuberculosis strains in response to mitomycin C. This approach highlighted that LexA, a well-defined key element of the SOS system, is proteolytically inactivated during RecA-dependent DNA repair, which we found to be transcriptionally repressed in response to DNA-damaging agents in the absence of RecA. Proteomics profiling revealed that AlkB was significantly overproduced in the ΔrecA pafBCCRISPRi/dCas9 strain and that Holliday junction resolvase RuvX was a DNA damage response factor that was significantly upregulated regardless of the presence of functional RecA and PafBC systems, thus falling into a third category of DNA damage factors: RecA- and PafBC-independent. While invisible to the mass spectrometer, the genes encoding alkA, dnaB, and dnaE2 were significantly overexpressed in the ΔrecA pafBCCRISPRi/dCas9 strain at the transcript level.
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11
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Elucidating Recombination Mediator Function Using Biophysical Tools. BIOLOGY 2021; 10:biology10040288. [PMID: 33916151 PMCID: PMC8066028 DOI: 10.3390/biology10040288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary This review recapitulates the initial knowledge acquired with genetics and biochemical experiments on Recombination mediator proteins in different domains of life. We further address how recent in vivo and in vitro biophysical tools were critical to deepen the understanding of RMPs molecular mechanisms in DNA and replication repair, and unveiled unexpected features. For instance, in bacteria, genetic and biochemical studies suggest a close proximity and coordination of action of the RecF, RecR and RecO proteins in order to ensure their RMP function, which is to overcome the single-strand binding protein (SSB) and facilitate the loading of the recombinase RecA onto ssDNA. In contrary to this expectation, using single-molecule fluorescent imaging in living cells, we showed recently that RecO and RecF do not colocalize and moreover harbor different spatiotemporal behavior relative to the replication machinery, suggesting distinct functions. Finally, we address how new biophysics tools could be used to answer outstanding questions about RMP function. Abstract The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.
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Fallon AM. DNA recombination and repair in Wolbachia: RecA and related proteins. Mol Genet Genomics 2021; 296:437-456. [PMID: 33507381 DOI: 10.1007/s00438-020-01760-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022]
Abstract
Wolbachia is an obligate intracellular bacterium that has undergone extensive genomic streamlining in its arthropod and nematode hosts. Because the gene encoding the bacterial DNA recombination/repair protein RecA is not essential in Escherichia coli, abundant expression of this protein in a mosquito cell line persistently infected with Wolbachia strain wStri was unexpected. However, RecA's role in the lytic cycle of bacteriophage lambda provides an explanation for retention of recA in strains known to encode lambda-like WO prophages. To examine DNA recombination/repair capacities in Wolbachia, a systematic examination of RecA and related proteins in complete or nearly complete Wolbachia genomes from supergroups A, B, C, D, E, F, J and S was undertaken. Genes encoding proteins including RecA, RecF, RecO, RecR, RecG and Holliday junction resolvases RuvA, RuvB and RuvC are uniformly absent from Wolbachia in supergroup C and have reduced representation in supergroups D and J, suggesting that recombination and repair activities are compromised in nematode-associated Wolbachia, relative to strains that infect arthropods. An exception is filarial Wolbachia strain wMhie, assigned to supergroup F, which occurs in a nematode host from a poikilothermic lizard. Genes encoding LexA and error-prone polymerases are absent from all Wolbachia genomes, suggesting that the SOS functions induced by RecA-mediated activation of LexA do not occur, despite retention of genes encoding a few proteins that respond to LexA induction in E. coli. Three independent E. coli accessions converge on a single Wolbachia UvrD helicase, which interacts with mismatch repair proteins MutS and MutL, encoded in nearly all Wolbachia genomes. With the exception of MutL, which has been mapped to a eukaryotic association module in Phage WO, proteins involved in recombination/repair are uniformly represented by single protein annotations. Putative phage-encoded MutL proteins are restricted to Wolbachia supergroups A and B and show higher amino acid identity than chromosomally encoded MutL orthologs. This analysis underscores differences between nematode and arthropod-associated Wolbachia and describes aspects of DNA metabolism that potentially impact development of procedures for transformation and genetic manipulation of Wolbachia.
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Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul, MN, 55108, USA.
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13
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Double strand break (DSB) repair in Cyanobacteria: Understanding the process in an ancient organism. DNA Repair (Amst) 2020; 95:102942. [DOI: 10.1016/j.dnarep.2020.102942] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/19/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
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14
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Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res 2020; 48:8445-8460. [PMID: 32644157 PMCID: PMC7470958 DOI: 10.1093/nar/gkaa579] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/31/2023] Open
Abstract
DNA lesions or other barriers frequently compromise replisome progress. The SF2 helicase RecG is a key enzyme in the processing of postreplication gaps or regressed forks in Escherichia coli. A deletion of the recG gene renders cells highly sensitive to a range of DNA damaging agents. Here, we demonstrate that RecG function is at least partially complemented by another SF2 helicase, RadD. A ΔrecGΔradD double mutant exhibits an almost complete growth defect, even in the absence of stress. Suppressors appear quickly, primarily mutations that compromise priA helicase function or recA promoter mutations that reduce recA expression. Deletions of uup (encoding the UvrA-like ABC system Uup), recO, or recF also suppress the ΔrecGΔradD growth phenotype. RadD and RecG appear to avoid toxic situations in DNA metabolism, either resolving or preventing the appearance of DNA repair intermediates produced by RecA or RecA-independent template switching at stalled forks or postreplication gaps. Barriers to replisome progress that require intervention by RadD or RecG occur in virtually every replication cycle. The results highlight the importance of the RadD protein for general chromosome maintenance and repair. They also implicate Uup as a new modulator of RecG function.
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Affiliation(s)
- Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Stefanie H Chen
- Biotechnology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Armstrong
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Antoine van Oijen
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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15
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Myka KK, Marians KJ. Two components of DNA replication-dependent LexA cleavage. J Biol Chem 2020; 295:10368-10379. [PMID: 32513870 PMCID: PMC7383369 DOI: 10.1074/jbc.ra120.014224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA-RecA filament supported LexA cleavage. Surprisingly, replication of an undamaged template supported levels of LexA cleavage like that induced by a template carrying two site-specific cyclobutane pyrimidine dimers. We found that two processes generate ssDNA that could support LexA cleavage. 1) During unperturbed replication, single-stranded regions formed because of stochastic uncoupling of the leading-strand DNA polymerase from the replication fork DNA helicase, and 2) on the damaged template, nascent leading-strand gaps were generated by replisome lesion skipping. The two pathways differed in that RecF stimulated LexA cleavage during replication of the damaged template, but not normal replication. RecF appears to facilitate RecA filament formation on the leading-strand ssDNA gaps generated by replisome lesion skipping.
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Affiliation(s)
- Kamila K Myka
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
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16
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Romero ZJ, Armstrong TJ, Henrikus SS, Chen SH, Glass DJ, Ferrazzoli AE, Wood EA, Chitteni-Pattu S, van Oijen AM, Lovett ST, Robinson A, Cox MM. Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins. Nucleic Acids Res 2020; 48:212-230. [PMID: 31665437 PMCID: PMC7145654 DOI: 10.1093/nar/gkz960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
When replication forks encounter template DNA lesions, the lesion is simply skipped in some cases. The resulting lesion-containing gap must be converted to duplex DNA to permit repair. Some gap filling occurs via template switching, a process that generates recombination-like branched DNA intermediates. The Escherichia coli Uup and RadD proteins function in different pathways to process the branched intermediates. Uup is a UvrA-like ABC family ATPase. RadD is a RecQ-like SF2 family ATPase. Loss of both functions uncovers frequent and RecA-independent deletion events in a plasmid-based assay. Elevated levels of crossing over and repeat expansions accompany these deletion events, indicating that many, if not most, of these events are associated with template switching in postreplication gaps as opposed to simple replication slippage. The deletion data underpin simulations indicating that multiple postreplication gaps may be generated per replication cycle. Both Uup and RadD bind to branched DNAs in vitro. RadD protein suppresses crossovers and Uup prevents nucleoid mis-segregation. Loss of Uup and RadD function increases sensitivity to ciprofloxacin. We present Uup and RadD as genomic guardians. These proteins govern two pathways for resolution of branched DNA intermediates such that potentially deleterious genome rearrangements arising from frequent template switching are averted.
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Affiliation(s)
- Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas J Armstrong
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Stefanie H Chen
- Biotechnology Program, North Carolina State University, Raleigh, NC 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David J Glass
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Alexander E Ferrazzoli
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Susan T Lovett
- Department of Biology and Rosenstiel Center, Brandeis University, Waltham, MA 02453, USA
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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17
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Henrikus SS, Henry C, Ghodke H, Wood EA, Mbele N, Saxena R, Basu U, van Oijen AM, Cox MM, Robinson A. RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli. Nucleic Acids Res 2019; 47:2946-2965. [PMID: 30657965 PMCID: PMC6451095 DOI: 10.1093/nar/gkz003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/03/2018] [Accepted: 01/10/2019] [Indexed: 01/31/2023] Open
Abstract
In bacteria, genetic recombination is a major mechanism for DNA repair. The RecF, RecO and RecR proteins are proposed to initiate recombination by loading the RecA recombinase onto DNA. However, the biophysical mechanisms underlying this process remain poorly understood. Here, we used genetics and single-molecule fluorescence microscopy to investigate whether RecF and RecO function together, or separately, in live Escherichia coli cells. We identified conditions in which RecF and RecO functions are genetically separable. Single-molecule imaging revealed key differences in the spatiotemporal behaviours of RecF and RecO. RecF foci frequently colocalize with replisome markers. In response to DNA damage, colocalization increases and RecF dimerizes. The majority of RecF foci are dependent on RecR. Conversely, RecO foci occur infrequently, rarely colocalize with replisomes or RecF and are largely independent of RecR. In response to DNA damage, RecO foci appeared to spatially redistribute, occupying a region close to the cell membrane. These observations indicate that RecF and RecO have distinct functions in the DNA damage response. The observed localization of RecF to the replisome supports the notion that RecF helps to maintain active DNA replication in cells carrying DNA damage.
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Affiliation(s)
- Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2500, Australia
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Harshad Ghodke
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2500, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Neema Mbele
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Roopashi Saxena
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Upasana Basu
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2500, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2500, Australia
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18
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Raychaudhury P, Marians KJ. The recombination mediator proteins RecFOR maintain RecA* levels for maximal DNA polymerase V Mut activity. J Biol Chem 2018; 294:852-860. [PMID: 30482842 DOI: 10.1074/jbc.ra118.005726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
DNA template damage can potentially block DNA replication. Cells have therefore developed different strategies to repair template lesions. Activation of the bacterial lesion bypass DNA polymerase V (Pol V) requires both the cleavage of the UmuD subunit to UmuD' and the acquisition of a monomer of activated RecA recombinase, forming Pol V Mut. Both of these events are mediated by the generation of RecA* via the formation of a RecA-ssDNA filament during the SOS response. Formation of RecA* is itself modulated by competition with the ssDNA-binding protein (SSB) for binding to ssDNA. Previous observations have demonstrated that RecA filament formation on SSB-coated DNA can be favored in the presence of the recombination mediator proteins RecF, RecO, and RecR. We show here using purified proteins that in the presence of SSB and RecA, a stable RecA-ssDNA filament is not formed, although sufficient RecA* is generated to support some activation of Pol V. The presence of RecFOR increased RecA* generation and allowed Pol V to synthesize longer DNA products and to elongate from an unpaired primer terminus opposite template damage, also without the generation of a stable RecA-ssDNA filament.
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Affiliation(s)
- Paromita Raychaudhury
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kenneth J Marians
- From the Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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19
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Tang Q, Liu YP, Shan HH, Tian LF, Zhang JZ, Yan XX. ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair. Sci Rep 2018; 8:2127. [PMID: 29391496 PMCID: PMC5794780 DOI: 10.1038/s41598-018-20557-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/19/2018] [Indexed: 11/13/2022] Open
Abstract
RecF is a principal member of the RecF pathway. It interacts with RecO and RecR to initiate homologous recombination by loading RecA recombinases on single-stranded DNA and displacing single-stranded DNA-binding proteins. As an ATP-binding cassette ATPase, RecF exhibits ATP-dependent dimerization and structural homology with Rad50 and SMC proteins. However, the mechanism and action pattern of RecF ATP-dependent dimerization remains unclear. Here, We determined three crystal structures of TTERecF, TTERecF-ATP and TTERecF-ATPɤS from Thermoanaerobacter tengcongensis that reveal a novel ATP-driven RecF dimerization. RecF contains a positively charged tunnel on its dimer interface that is essential to ATP binding. Our structural and biochemical data indicate that the Walker A motif serves as a switch and plays a key role in ATP binding and RecF dimerization. Furthermore, Biolayer interferometry assay results showed that the TTERecF interacted with ATP and formed a dimer, displaying a higher affinity for DNA than that of the TTERecF monomer. Overall, our results provide a solid structural basis for understanding the process of RecF binding with ATP and the functional mechanism of ATP-dependent RecF dimerization.
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Affiliation(s)
- Qun Tang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan-Ping Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Huan Shan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Fei Tian
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie-Zhong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Abstract
Replication forks frequently are challenged by lesions on the DNA template, replication-impeding DNA secondary structures, tightly bound proteins or nucleotide pool imbalance. Studies in bacteria have suggested that under these circumstances the fork may leave behind single-strand DNA gaps that are subsequently filled by homologous recombination, translesion DNA synthesis or template-switching repair synthesis. This review focuses on the template-switching pathways and how the mechanisms of these processes have been deduced from biochemical and genetic studies. I discuss how template-switching can contribute significantly to genetic instability, including mutational hotspots and frequent genetic rearrangements, and how template-switching may be elicited by replication fork damage.
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Affiliation(s)
- Susan T Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 2454-9110, USA.
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21
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Korolev S. Advances in structural studies of recombination mediator proteins. Biophys Chem 2017; 225:27-37. [PMID: 27974172 DOI: 10.1016/j.bpc.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 12/25/2022]
Abstract
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event. This review summarizes structural studies of RMPs and their implications for understanding mechanism and function. Comparative analysis of RMPs is complicated due to their convergent evolution. In contrast to the evolutionary conserved ssbs and recombinases, RMPs are extremely diverse in sequence and structure. Structural studies are particularly important in such cases to reveal common features of the entire family and specific features of regulatory mechanisms for each member. All RMPs are characterized by specific DNA-binding domains and include variable protein interaction motifs. The complexity of such RMPs corresponds to the ever-growing number of DNA metabolism events they participate in under normal and pathological conditions and requires additional comprehensive structure-functional studies.
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Affiliation(s)
- S Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 S Grand Blvd., St. Louis, MO 63104, USA.
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22
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Bakhlanova IV, Dudkina AV, Wood EA, Lanzov VA, Cox MM, Baitin DM. DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype. PLoS One 2016; 11:e0154137. [PMID: 27124470 PMCID: PMC4849656 DOI: 10.1371/journal.pone.0154137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/09/2016] [Indexed: 12/04/2022] Open
Abstract
The RecA recombinase of Escherichia coli has not evolved to optimally promote DNA pairing and strand exchange, the key processes of recombinational DNA repair. Instead, the recombinase function of RecA protein represents an evolutionary compromise between necessary levels of recombinational DNA repair and the potentially deleterious consequences of RecA functionality. A RecA variant, RecA D112R, promotes conjugational recombination at substantially enhanced levels. However, expression of the D112R RecA protein in E. coli results in a reduction in cell growth rates. This report documents the consequences of the substantial selective pressure associated with the RecA-mediated hyperrec phenotype. With continuous growth, the deleterious effects of RecA D112R, along with the observed enhancements in conjugational recombination, are lost over the course of 70 cell generations. The suppression reflects a decline in RecA D112R expression, associated primarily with a deletion in the gene promoter or chromosomal mutations that decrease plasmid copy number. The deleterious effects of RecA D112R on cell growth can also be negated by over-expression of the RecX protein from Neisseria gonorrhoeae. The effects of the RecX proteins in vivo parallel the effects of the same proteins on RecA D112R filaments in vitro. The results indicate that the toxicity of RecA D112R is due to its persistent binding to duplex genomic DNA, creating barriers for other processes in DNA metabolism. A substantial selective pressure is generated to suppress the resulting barrier to growth.
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Affiliation(s)
- Irina V. Bakhlanova
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
| | - Alexandra V. Dudkina
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706–1544, United States of America
| | - Vladislav A. Lanzov
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706–1544, United States of America
| | - Dmitry M. Baitin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
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23
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Timmins J, Moe E. A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges. Comput Struct Biotechnol J 2016; 14:168-176. [PMID: 27924191 PMCID: PMC5128194 DOI: 10.1016/j.csbj.2016.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 10/27/2022] Open
Affiliation(s)
- Joanna Timmins
- Université Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Elin Moe
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Av da Republica (EAN), 2780-157 Oeiras, Portugal
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24
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Tang Q, Liu YP, Yan XX, Liang DC. Structural and functional characterization of Cys4 zinc finger motif in the recombination mediator protein RecR. DNA Repair (Amst) 2015; 24:10-14. [PMID: 25460918 DOI: 10.1016/j.dnarep.2014.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 11/18/2022]
Abstract
Zinc finger motif widely exists in protein structure, which can play different roles in different proteins. RecR is an important recombination mediator protein (RMP) in the RecFOR pathway and zinc finger motif is the most conserved domain in RecR protein. However, the function of this zinc finger motif in RecR is unclear. Here, we have studied the structures of the single cysteine and double cysteines mutation within the zinc finger motif in Thermoanaerobacter tengcongensis RecR (TTERecR). We have also studied the DNA binding ability as well as TTERecO protein binding ability of single, double and even triple cysteines mutation of the zinc finger motif, and the mutants do not alter DNA binding by RecR nor the interaction between RecR and RecO. The function of TTERecR zinc finger motif is to maintain the stability of the three-dimensional structure.
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Affiliation(s)
- Qun Tang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan-Ping Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dong-Cai Liang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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25
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Zhang M, Chen J, Zhang J, Du G. The effects of RecO deficiency in Lactococcus lactis NZ9000 on resistance to multiple environmental stresses. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:3125-3133. [PMID: 24648035 DOI: 10.1002/jsfa.6662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 02/24/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Multiple stresses could cause damage to DNA and other macromolecules. RecO, belonging to the family of DNA repair proteins, plays an important part in homologous recombination and replication repair. In order to explore the role of RecO in overcoming multiple stresses, a mutant of recO deletion is constructed in Lactococcus lactis ssp. cremoris NZ9000. RESULTS Compared with the mutant strain, the original strain L. lactis NZ9000 shows better performance in growth under multiple stresses. The survival rates of the original strain under acid, osmotic and chill stresses are 13.49-, 2.78- and 60.89-fold higher. In our deeper research on fermentation capability under osmotic stress, lactate dehydrogenase activity after 8 h fermentation, maximum lactate acid production, lactate yield and maximum lactate productivity of L. lactis NZ9000 are 1.63-, 1.28-, 1.28- and 1.5-fold higher, respectively. CONCLUSION Results indicate that RecO has positively improved the survival of L. lactis NZ9000, protected its key enzymes and enhanced its fermentation efficiencies. Our research confirms the role of RecO in enhancing tolerances to multiple stresses of L. lactis NZ9000, and puts forward the suggestion that RecO could be used in other industrial microorganisms as a new anti-stress component to improve their resistance to various stresses.
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Affiliation(s)
- Mengru Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, People's Republic of China; School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
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26
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Ryzhikov M, Gupta R, Glickman M, Korolev S. RecO protein initiates DNA recombination and strand annealing through two alternative DNA binding mechanisms. J Biol Chem 2014; 289:28846-55. [PMID: 25170075 DOI: 10.1074/jbc.m114.585117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Recombination mediator proteins (RMPs) are important for genome stability in all organisms. Several RMPs support two alternative reactions: initiation of homologous recombination and DNA annealing. We examined mechanisms of RMPs in both reactions with Mycobacterium smegmatis RecO (MsRecO) and demonstrated that MsRecO interacts with ssDNA by two distinct mechanisms. Zinc stimulates MsRecO binding to ssDNA during annealing, whereas the recombination function is zinc-independent and is regulated by interaction with MsRecR. Thus, different structural motifs or conformations of MsRecO are responsible for interaction with ssDNA during annealing and recombination. Neither annealing nor recombinase loading depends on MsRecO interaction with the conserved C-terminal tail of single-stranded (ss) DNA-binding protein (SSB), which is known to bind Escherichia coli RecO. However, similarly to E. coli proteins, MsRecO and MsRecOR do not dismiss SSB from ssDNA, suggesting that RMPs form a complex with SSB-ssDNA even in the absence of binding to the major protein interaction motif. We propose that alternative conformations of such complexes define the mechanism by which RMPs initiate the repair of stalled replication and support two different functions during recombinational repair of DNA breaks.
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Affiliation(s)
- Mikhail Ryzhikov
- From the Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Richa Gupta
- Division of Infectious Diseases and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Michael Glickman
- Division of Infectious Diseases and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Sergey Korolev
- From the Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, Missouri 63104 and
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Radzimanowski J, Dehez F, Round A, Bidon-Chanal A, McSweeney S, Timmins J. An 'open' structure of the RecOR complex supports ssDNA binding within the core of the complex. Nucleic Acids Res 2013; 41:7972-86. [PMID: 23814185 PMCID: PMC3763555 DOI: 10.1093/nar/gkt572] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 01/19/2023] Open
Abstract
Efficient DNA repair is critical for cell survival and the maintenance of genome integrity. The homologous recombination pathway is responsible for the repair of DNA double-strand breaks within cells. Initiation of this pathway in bacteria can be carried out by either the RecBCD or the RecFOR proteins. An important regulatory player within the RecFOR pathway is the RecOR complex that facilitates RecA loading onto DNA. Here we report new data regarding the assembly of Deinococcus radiodurans RecOR and its interaction with DNA, providing novel mechanistic insight into the mode of action of RecOR in homologous recombination. We present a higher resolution crystal structure of RecOR in an 'open' conformation in which the tetrameric RecR ring flanked by two RecO molecules is accessible for DNA binding. We show using small-angle neutron scattering and mutagenesis studies that DNA binding does indeed occur within the RecR ring. Binding of single-stranded DNA occurs without any major conformational changes of the RecOR complex while structural rearrangements are observed on double-stranded DNA binding. Finally, our molecular dynamics simulations, supported by our biochemical data, provide a detailed picture of the DNA binding motif of RecOR and reveal that single-stranded DNA is sandwiched between the two facing oligonucleotide binding domains of RecO within the RecR ring.
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Affiliation(s)
- Jens Radzimanowski
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - François Dehez
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Adam Round
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Axel Bidon-Chanal
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Sean McSweeney
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Joanna Timmins
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
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Fate of the replisome following arrest by UV-induced DNA damage in Escherichia coli. Proc Natl Acad Sci U S A 2013; 110:11421-6. [PMID: 23801750 DOI: 10.1073/pnas.1300624110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate replication in the presence of DNA damage is essential to genome stability and viability in all cells. In Escherichia coli, DNA replication forks blocked by UV-induced damage undergo a partial resection and RecF-catalyzed regression before synthesis resumes. These processing events generate distinct structural intermediates on the DNA that can be visualized in vivo using 2D agarose gels. However, the fate and behavior of the stalled replisome remains a central uncharacterized question. Here, we use thermosensitive mutants to show that the replisome's polymerases uncouple and transiently dissociate from the DNA in vivo. Inactivation of α, β, or τ subunits within the replisome is sufficient to signal and induce the RecF-mediated processing events observed following UV damage. By contrast, the helicase-primase complex (DnaB and DnaG) remains critically associated with the fork, leading to a loss of fork integrity, degradation, and aberrant intermediates when disrupted. The results reveal a dynamic replisome, capable of partial disassembly to allow access to the obstruction, while retaining subunits that maintain fork licensing and direct reassembly to the appropriate location after processing has occurred.
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Costes A, Lambert SAE. Homologous recombination as a replication fork escort: fork-protection and recovery. Biomolecules 2012; 3:39-71. [PMID: 24970156 PMCID: PMC4030885 DOI: 10.3390/biom3010039] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 01/03/2023] Open
Abstract
Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.
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Affiliation(s)
- Audrey Costes
- Institut Curie, Centre de Recherche, CNRS, UMR3348, Centre Universitaire, Bat110, 91405, Orsay, France.
| | - Sarah A E Lambert
- Institut Curie, Centre de Recherche, CNRS, UMR3348, Centre Universitaire, Bat110, 91405, Orsay, France.
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Cárdenas PP, Carrasco B, Defeu Soufo C, César CE, Herr K, Kaufenstein M, Graumann PL, Alonso JC. RecX facilitates homologous recombination by modulating RecA activities. PLoS Genet 2012; 8:e1003126. [PMID: 23284295 PMCID: PMC3527212 DOI: 10.1371/journal.pgen.1003126] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/15/2012] [Indexed: 12/31/2022] Open
Abstract
The Bacillus subtilis recH342 strain, which decreases interspecies recombination without significantly affecting the frequency of transformation with homogamic DNA, carried a point mutation in the putative recX (yfhG) gene, and the mutation was renamed as recX342. We show that RecX (264 residues long), which shares partial identity with the Proteobacterial RecX (<180 residues), is a genuine recombination protein, and its primary function is to modulate the SOS response and to facilitate RecA-mediated recombinational repair and genetic recombination. RecX-YFP formed discrete foci on the nucleoid, which were coincident in time with RecF, in response to DNA damage, and on the poles and/or the nucleoid upon stochastic induction of programmed natural competence. When DNA was damaged, the RecX foci co-localized with RecA threads that persisted for a longer time in the recX context. The absence of RecX severely impaired natural transformation both with plasmid and chromosomal DNA. We show that RecX suppresses the negative effect exerted by RecA during plasmid transformation, prevents RecA mis-sensing of single-stranded DNA tracts, and modulates DNA strand exchange. RecX, by modulating the “length or packing” of a RecA filament, facilitates the initiation of recombination and increases recombination across species. This study describes mechanisms employed by the bacterium Bacillus subtilis to survive DNA damages by recombinational repair (RR) and to provide genetic variation via genetic recombination (GR). At the center of homologous recombination (HR) is the recombinase RecA, which forms RecA·ssDNA filaments to mediate SOS induction and to promote DNA strand exchange, a step needed for both RR and GR. Genetic data presented here highlight the complexity of the network of RecA accessory factors that regulate HR activities, with RecX counteracting the role of RecF in SOS induction. The absence of both RecA modulators, however, blocked RR and GR. Insights into the spatio-temporal recruitment of RecA to preserve genome integrity, to overcome the barriers of gene flow, and its regulation by mediators and modulators are provided. Chromosomal transformation, which declines with increasing evolutionary distance, depends on HR. Indeed, the presence of the RecX modulator decreases the genetic barrier between closely related organisms. The role of RecA mediators and modulators on the preservation of genome integrity and long-term genome evolution is discussed.
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Affiliation(s)
- Paula P. Cárdenas
- Department of Microbial Biotechnology, Centro Nacional de Biotechnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotechnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Carolina E. César
- Department of Microbial Biotechnology, Centro Nacional de Biotechnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Katharina Herr
- Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Freiburg, Germany
| | - Miriam Kaufenstein
- Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Freiburg, Germany
| | - Peter L. Graumann
- Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Freiburg, Germany
| | - Juan C. Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotechnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
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Beaume N, Pathak R, Yadav VK, Kota S, Misra HS, Gautam HK, Chowdhury S. Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation. Nucleic Acids Res 2012; 41:76-89. [PMID: 23161683 PMCID: PMC3592403 DOI: 10.1093/nar/gks1071] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A remarkable number of guanine-rich sequences with potential to adopt non-canonical secondary structures called G-quadruplexes (or G4 DNA) are found within gene promoters. Despite growing interest, regulatory role of quadruplex DNA motifs in intrinsic cellular function remains poorly understood. Herein, we asked whether occurrence of potential G4 (PG4) DNA in promoters is associated with specific function(s) in bacteria. Using a normalized promoter-PG4-content (PG4P) index we analysed >60 000 promoters in 19 well-annotated species for (a) function class(es) and (b) gene(s) with enriched PG4P. Unexpectedly, PG4-associated functional classes were organism specific, suggesting that PG4 motifs may impart specific function to organisms. As a case study, we analysed radioresistance. Interestingly, unsupervised clustering using PG4P of 21 genes, crucial for radioresistance, grouped three radioresistant microorganisms including Deinococcus radiodurans. Based on these predictions we tested and found that in presence of nanomolar amounts of the intracellular quadruplex-binding ligand N-methyl mesoporphyrin (NMM), radioresistance of D. radiodurans was attenuated by ∼60%. In addition, important components of the RecF recombinational repair pathway recA, recF, recO, recR and recQ genes were found to harbour promoter-PG4 motifs and were also down-regulated in presence of NMM. Together these results provide first evidence that radioresistance may involve G4 DNA-mediated regulation and support the rationale that promoter-PG4s influence selective functions.
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Affiliation(s)
- Nicolas Beaume
- GNR Knowledge Centre for Genome Informatics, Division of Comparative Genomics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Abstract
Homologous recombination is an ubiquitous process that shapes genomes and repairs DNA damage. The reaction is classically divided into three phases: presynaptic, synaptic, and postsynaptic. In Escherichia coli, the presynaptic phase involves either RecBCD or RecFOR proteins, which act on DNA double-stranded ends and DNA single-stranded gaps, respectively; the central synaptic steps are catalyzed by the ubiquitous DNA-binding protein RecA; and the postsynaptic phase involves either RuvABC or RecG proteins, which catalyze branch-migration and, in the case of RuvABC, the cleavage of Holliday junctions. Here, we review the biochemical properties of these molecular machines and analyze how, in light of these properties, the phenotypes of null mutants allow us to define their biological function(s). The consequences of point mutations on the biochemical properties of recombination enzymes and on cell phenotypes help refine the molecular mechanisms of action and the biological roles of recombination proteins. Given the high level of conservation of key proteins like RecA and the conservation of the principles of action of all recombination proteins, the deep knowledge acquired during decades of studies of homologous recombination in bacteria is the foundation of our present understanding of the processes that govern genome stability and evolution in all living organisms.
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Tang Q, Gao P, Liu YP, Gao A, An XM, Liu S, Yan XX, Liang DC. RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA. Nucleic Acids Res 2012; 40:11115-25. [PMID: 23019218 PMCID: PMC3510498 DOI: 10.1093/nar/gks889] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
RecR is an important recombination mediator protein in the RecFOR pathway. RecR together with RecO and RecF facilitates RecA nucleoprotein filament formation and homologous pairing. Structural and biochemical studies of Thermoanaerobacter tengcongensis RecR (TTERecR) and its series mutants revealed that TTERecR uses the N-N dimer as a basic functional unit to interact with TTERecO monomer. Two TTERecR N-N dimers form a ring-shaped tetramer via an interaction between their C-terminal regions. The tetramer is a result of crystallization only. Hydrophobic interactions between the entire helix-hairpin-helix domains within the N-terminal regions of two TTERecR monomers are necessary for formation of a RecR functional N-N dimer. The TTERecR N-N dimer conformation also affects formation of a hydrophobic patch, which creates a binding site for TTERecO in the TTERecR Toprim domain. In addition, we demonstrate that TTERecR does not bind single-stranded DNA (ssDNA) and binds double-stranded DNA very weakly, whereas TTERecOR complex can stably bind DNA, with a higher affinity for ssDNA than double-stranded DNA. Based on these results, we propose an interaction model for the RecOR:ssDNA complex.
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Affiliation(s)
- Qun Tang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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UvrD Participation in Nucleotide Excision Repair Is Required for the Recovery of DNA Synthesis following UV-Induced Damage in Escherichia coli. J Nucleic Acids 2012; 2012:271453. [PMID: 23056919 PMCID: PMC3465929 DOI: 10.1155/2012/271453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022] Open
Abstract
UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structures in vitro and is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we characterized the role UvrD has in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occur normally. In addition, damage-induced replication intermediates persist and accumulate in uvrD mutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that, following arrest by DNA damage, UvrD is not required to catalyze fork regression in vivo and suggest that the failure of uvrD mutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.
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A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms. BMC Microbiol 2012; 12:189. [PMID: 22943491 PMCID: PMC3478200 DOI: 10.1186/1471-2180-12-189] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/21/2012] [Indexed: 02/08/2023] Open
Abstract
Background The Gram negative anaerobe Fusobacterium nucleatum has been implicated in the aetiology of periodontal diseases. Although frequently isolated from healthy dental plaque, its numbers and proportion increase in plaque associated with disease. One of the significant physico-chemical changes in the diseased gingival sulcus is increased environmental pH. When grown under controlled conditions in our laboratory, F. nucleatum subspecies polymorphum formed mono-culture biofilms when cultured at pH 8.2. Biofilm formation is a survival strategy for bacteria, often associated with altered physiology and increased virulence. A proteomic approach was used to understand the phenotypic changes in F. nucleatum cells associated with alkaline induced biofilms. The proteomic based identification of significantly altered proteins was verified where possible using additional methods including quantitative real-time PCR (qRT-PCR), enzyme assay, acidic end-product analysis, intracellular polyglucose assay and Western blotting. Results Of 421 proteins detected on two-dimensional electrophoresis gels, spot densities of 54 proteins varied significantly (p < 0.05) in F. nucleatum cultured at pH 8.2 compared to growth at pH 7.4. Proteins that were differentially produced in biofilm cells were associated with the functional classes; metabolic enzymes, transport, stress response and hypothetical proteins. Our results suggest that biofilm cells were more metabolically efficient than planktonic cells as changes to amino acid and glucose metabolism generated additional energy needed for survival in a sub-optimal environment. The intracellular concentration of stress response proteins including heat shock protein GroEL and recombinational protein RecA increased markedly in the alkaline environment. A significant finding was the increased abundance of an adhesin, Fusobacterial outer membrane protein A (FomA). This surface protein is known for its capacity to bind to a vast number of bacterial species and human epithelial cells and its increased abundance was associated with biofilm formation. Conclusion This investigation identified a number of proteins that were significantly altered by F. nucleatum in response to alkaline conditions similar to those reported in diseased periodontal pockets. The results provide insight into the adaptive mechanisms used by F. nucleatum biofilms in response to pH increase in the host environment.
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Morimatsu K, Wu Y, Kowalczykowski SC. RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5' terminus: implication for repair of stalled replication forks. J Biol Chem 2012; 287:35621-35630. [PMID: 22902627 DOI: 10.1074/jbc.m112.397034] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The repair of single-stranded gaps in duplex DNA by homologous recombination requires the proteins of the RecF pathway. The assembly of RecA protein onto gapped DNA (gDNA) that is complexed with the single-stranded DNA-binding protein is accelerated by the RecF, RecO, and RecR (RecFOR) proteins. Here, we show the RecFOR proteins specifically target RecA protein to gDNA even in the presence of a thousand-fold excess of single-stranded DNA (ssDNA). The binding constant of RecF protein, in the presence of the RecOR proteins, to the junction of ssDNA and dsDNA within a gap is 1-2 nm, suggesting that a few RecF molecules in the cell are sufficient to recognize gDNA. We also found that the nucleation of a RecA filament on gDNA in the presence of the RecFOR proteins occurs at a faster rate than filament elongation, resulting in a RecA nucleoprotein filament on ssDNA for 1000-2000 nucleotides downstream (5' → 3') of the junction with duplex DNA. Thus, RecA loading by RecFOR is localized to a region close to a junction. RecFOR proteins also recognize RNA at the 5'-end of an RNA-DNA junction within an ssDNA gap, which is compatible with their role in the repair of lagging strand gaps at stalled replication forks.
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Affiliation(s)
- Katsumi Morimatsu
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Yun Wu
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Stephen C Kowalczykowski
- Department of Microbiology and of Molecular and Cellular Biology, University of California, Davis, California 95616.
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Cellular characterization of the primosome and rep helicase in processing and restoration of replication following arrest by UV-induced DNA damage in Escherichia coli. J Bacteriol 2012; 194:3977-86. [PMID: 22636770 DOI: 10.1128/jb.00290-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Following arrest by UV-induced DNA damage, replication is restored through a sequence of steps that involve partial resection of the nascent DNA by RecJ and RecQ, branch migration and processing of the fork DNA surrounding the lesion by RecA and RecF-O-R, and resumption of DNA synthesis once the blocking lesion has been repaired or bypassed. In vitro, the primosomal proteins (PriA, PriB, and PriC) and Rep are capable of initiating replication from synthetic DNA fork structures, and they have been proposed to catalyze these events when replication is disrupted by certain impediments in vivo. Here, we characterized the role that PriA, PriB, PriC, and Rep have in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that the partial degradation and processing of the arrested replication fork occurs normally in both rep and primosome mutants. In each mutant, the nascent degradation ceases and DNA synthesis initially resumes in a timely manner, but the recovery then stalls in the absence of PriA, PriB, or Rep. The results demonstrate a role for the primosome and Rep helicase in overcoming replication forks arrested by UV-induced damage in vivo and suggest that these proteins are required for the stability and efficiency of the replisome when DNA synthesis resumes but not to initiate de novo replication downstream of the lesion.
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Liu J, Ehmsen KT, Heyer WD, Morrical SW. Presynaptic filament dynamics in homologous recombination and DNA repair. Crit Rev Biochem Mol Biol 2011; 46:240-70. [PMID: 21599536 DOI: 10.3109/10409238.2011.576007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Homologous recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments-helical filaments of a recombinase enzyme bound to single-stranded DNA (ssDNA). Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we reviewed the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments; some intrinsic such as recombinase ATP-binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examined dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examined the biochemical properties of recombination proteins from four model systems (T4 phage, Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We proposed that the presynaptic filament has evolved to rely on multiple external factors for increased multilevel regulation of HR processes in genomes with greater structural and sequence complexity.
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Affiliation(s)
- Jie Liu
- Departments of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA, USA
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Ryzhikov M, Koroleva O, Postnov D, Tran A, Korolev S. Mechanism of RecO recruitment to DNA by single-stranded DNA binding protein. Nucleic Acids Res 2011; 39:6305-14. [PMID: 21504984 PMCID: PMC3152348 DOI: 10.1093/nar/gkr199] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/18/2011] [Accepted: 03/21/2011] [Indexed: 12/26/2022] Open
Abstract
RecO is a recombination mediator protein (RMP) important for homologous recombination, replication repair and DNA annealing in bacteria. In all pathways, the single-stranded (ss) DNA binding protein, SSB, plays an inhibitory role by protecting ssDNA from annealing and recombinase binding. Conversely, SSB may stimulate each reaction through direct interaction with RecO. We present a crystal structure of Escherichia coli RecO bound to the conserved SSB C-terminus (SSB-Ct). SSB-Ct binds the hydrophobic pocket of RecO in a conformation similar to that observed in the ExoI/SSB-Ct complex. Hydrophobic interactions facilitate binding of SSB-Ct to RecO and RecO/RecR complex in both low and moderate ionic strength solutions. In contrast, RecO interaction with DNA is inhibited by an elevated salt concentration. The SSB mutant lacking SSB-Ct also inhibits RecO-mediated DNA annealing activity in a salt-dependent manner. Neither RecO nor RecOR dissociates SSB from ssDNA. Therefore, in E. coli, SSB recruits RMPs to ssDNA through SSB-Ct, and RMPs are likely to alter the conformation of SSB-bound ssDNA without SSB dissociation to initiate annealing or recombination. Intriguingly, Deinococcus radiodurans RecO does not bind SSB-Ct and weakly interacts with the peptide in the presence of RecR, suggesting the diverse mechanisms of DNA repair pathways mediated by RecO in different organisms.
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Affiliation(s)
| | | | | | | | - Sergey Korolev
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, 1100 S Grand Blvd., St Louis, MO 63021, USA
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Uranga LA, Balise VD, Benally CV, Grey A, Lusetti SL. The Escherichia coli DinD protein modulates RecA activity by inhibiting postsynaptic RecA filaments. J Biol Chem 2011; 286:29480-91. [PMID: 21697094 DOI: 10.1074/jbc.m111.245373] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli dinD is an SOS gene up-regulated in response to DNA damage. We find that the purified DinD protein is a novel inhibitor of RecA-mediated DNA strand exchange activities. Most modulators of RecA protein activity act by controlling the amount of RecA protein bound to single-stranded DNA by affecting either the loading of RecA protein onto DNA or the disassembly of RecA nucleoprotein filaments bound to single-stranded DNA. The DinD protein, however, acts postsynaptically to inhibit RecA during an on-going DNA strand exchange, likely through the disassembly of RecA filaments. DinD protein does not affect RecA single-stranded DNA filaments but efficiently disassembles RecA when bound to two or more DNA strands, effectively halting RecA-mediated branch migration. By utilizing a nonspecific duplex DNA-binding protein, YebG, we show that the DinD effect is not simply due to duplex DNA sequestration. We present a model suggesting that the negative effects of DinD protein are targeted to a specific conformational state of the RecA protein and discuss the potential role of DinD protein in the regulation of recombinational DNA repair.
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Affiliation(s)
- Lee A Uranga
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, USA
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Curtis FA, Reed P, Wilson LA, Bowers LY, Yeo RP, Sanderson JM, Walmsley AR, Sharples GJ. The C-terminus of the phage λ Orf recombinase is involved in DNA binding. J Mol Recognit 2011; 24:333-40. [PMID: 21360615 DOI: 10.1002/jmr.1079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 11/11/2022]
Abstract
Phage λ Orf substitutes for the activities of the Escherichia coli RecFOR proteins in vivo and is therefore implicated as a recombination mediator, encouraging the assembly of bacterial RecA onto single-stranded DNA (ssDNA) coated with SSB. Orf exists as a dimer in solution, associates with E. coli SSB and binds preferentially to ssDNA. To help identify interacting domains we analysed Orf and SSB proteins carrying mutations or truncations in the C-terminal region. A cluster of acidic residues at the carboxy-terminus of SSB is known to attract multiple protein partners to assist in DNA replication and repair. In this case an alternative domain must be utilized since Orf association with SSB was unaffected by an SSB113 point mutant (P176S) or removal of the last ten residues (ΔC10). Structurally the Orf C-terminus consists of a helix with a flexible tail that protrudes from each side of the dimer and could serve as a binding site for either SSB or DNA. Eliminating the six residue flexible tail (ΔC6) or the entire helix (ΔC19) had no significant impact on the Orf-SSB interaction. However, the OrfΔC6 protein exhibited reduced DNA binding, a feature shared by single amino acid substitutions within (W141F) or adjacent (R140A) to this region. The OrfΔC19 mutant bound poorly to DNA and secondary structure analysis in solution revealed that this truncation induces protein misfolding and aggregation. The results show that the carboxy-terminus of Orf is involved in nucleic acid recognition and also plays an unexpected role in maintaining structural integrity.
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Affiliation(s)
- Fiona A Curtis
- School of Biological and Biomedical Sciences, University of Durham, Science Site, Durham DH1 3LE, UK
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Zhang X, Wanda SY, Brenneman K, Kong W, Zhang X, Roland K, Curtiss R. Improving Salmonella vector with rec mutation to stabilize the DNA cargoes. BMC Microbiol 2011; 11:31. [PMID: 21303535 PMCID: PMC3047425 DOI: 10.1186/1471-2180-11-31] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/08/2011] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Salmonella has been employed to deliver therapeutic molecules against cancer and infectious diseases. As the carrier for target gene(s), the cargo plasmid should be stable in the bacterial vector. Plasmid recombination has been reduced in E. coli by mutating several genes including the recA, recE, recF and recJ. However, to our knowledge, there have been no published studies of the effect of these or any other genes that play a role in plasmid recombination in Salmonella enterica. RESULTS The effect of recA, recF and recJ deletions on DNA recombination was examined in three serotypes of Salmonella enterica. We found that (1) intraplasmid recombination between direct duplications was RecF-independent in Typhimurium and Paratyphi A, but could be significantly reduced in Typhi by a ΔrecA or ΔrecF mutation; (2) in all three Salmonella serotypes, both ΔrecA and ΔrecF mutations reduced intraplasmid recombination when a 1041 bp intervening sequence was present between the duplications; (3) ΔrecA and ΔrecF mutations resulted in lower frequencies of interplasmid recombination in Typhimurium and Paratyphi A, but not in Typhi; (4) in some cases, a ΔrecJ mutation could reduce plasmid recombination but was less effective than ΔrecA and ΔrecF mutations. We also examined chromosome-related recombination. The frequencies of intrachromosomal recombination and plasmid integration into the chromosome were 2 and 3 logs lower than plasmid recombination frequencies in Rec+ strains. A ΔrecA mutation reduced both intrachromosomal recombination and plasmid integration frequencies. CONCLUSIONS The ΔrecA and ΔrecF mutations can reduce plasmid recombination frequencies in Salmonella enterica, but the effect can vary between serovars. This information will be useful for developing Salmonella delivery vectors able to stably maintain plasmid cargoes for vaccine development and gene therapy.
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Affiliation(s)
- Xiangmin Zhang
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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Costes A, Lecointe F, McGovern S, Quevillon-Cheruel S, Polard P. The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks. PLoS Genet 2010; 6:e1001238. [PMID: 21170359 PMCID: PMC3000357 DOI: 10.1371/journal.pgen.1001238] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 11/04/2010] [Indexed: 11/18/2022] Open
Abstract
We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB(Cter)) as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB(Cter) interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB(Cter) deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssbΔCter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB(Cter) acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.
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Affiliation(s)
- Audrey Costes
- Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
| | - François Lecointe
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, Jouy-en-Josas, France
| | - Stephen McGovern
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, Jouy-en-Josas, France
| | - Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, Centre National de la Recherche Scientifique, UMR8619, IFR115, Orsay, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- * E-mail:
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Michel-Marks E, Courcelle CT, Korolev S, Courcelle J. ATP binding, ATP hydrolysis, and protein dimerization are required for RecF to catalyze an early step in the processing and recovery of replication forks disrupted by DNA damage. J Mol Biol 2010; 401:579-89. [PMID: 20558179 DOI: 10.1016/j.jmb.2010.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/06/2010] [Accepted: 06/08/2010] [Indexed: 12/30/2022]
Abstract
In Escherichia coli, the recovery of replication following disruption by UV-induced DNA damage requires the RecF protein and occurs through a process that involves stabilization of replication fork DNA, resection of nascent DNA to allow the offending lesion to be repaired, and reestablishment of a productive replisome on the DNA. RecF forms a homodimer and contains an ATP binding cassette ATPase domain that is conserved among eukaryotic SMC (structural maintenance of chromosome) proteins, including cohesin, condensin, and Rad50. Here, we investigated the functions of RecF dimerization, ATP binding, and ATP hydrolysis in the progressive steps involved in recovering DNA synthesis following disruption by DNA damage. RecF point mutations with altered biochemical properties were constructed in the chromosome. We observed that protein dimerization, ATP binding, and ATP hydrolysis were essential for maintaining and processing the arrested replication fork, as well as for restoring DNA synthesis. In contrast, stabilization of the RecF protein dimer partially protected the DNA at the arrested fork from degradation, although overall processing and recovery remained severely impaired.
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Hinz JM. Role of homologous recombination in DNA interstrand crosslink repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:582-603. [PMID: 20658649 DOI: 10.1002/em.20577] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Homologous recombination repair (HRR) encompasses mechanisms that employ homologous DNA sequences as templates for repair or tolerance of a wide range of DNA lesions that inhibit DNA replication in S phase. Arguably the most imposing of these DNA lesions is that of the interstrand crosslink (ICL), consisting of a covalently attached chemical bridge between opposing DNA strands. ICL repair requires the coordinated activities of HRR and a number of proteins from other DNA repair and damage response systems, including nucleotide excision repair, base excision repair, mismatch repair, and translesion DNA synthesis (TLS). Interestingly, different organisms favor alternative methods of HRR in the ICL repair process. E. coli perform ICL repair using a homology-driven damage bypass mechanism analogous to daughter strand gap repair. Eukaryotes from yeast to humans initiate ICL repair primarily during DNA replication, relying on HRR activity to restart broken replication forks associated with double-strand break intermediates induced by nucleolytic activities of other excision repair factors. Higher eukaryotes also employ several additional factors, including members of the Fanconi anemia damage-response network, which further promote replication-associated ICL repair through the activation and coordination of various DNA excision repair, TLS, and HRR proteins. This review focuses on the proteins and general mechanisms of HRR associated with ICL repair in different model organisms.
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Affiliation(s)
- John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
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Dudkina AV, Bakhlanova IV, Baitin DM. The new mechanism of the frequency of recombination exchanges increase by improving the synaptase activity of the RecA protein from Escherichia coli. DOKL BIOCHEM BIOPHYS 2010; 432:120-2. [DOI: 10.1134/s1607672910030075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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KHOONTAWAD J, WONGKHAM C, HIRAKU Y, YONGVANIT P, PRAKOBWONG S, BOONMARS T, PINLAOR P, PINLAOR S. Proteomic identification of peroxiredoxin 6 for host defence againstOpisthorchis viverriniinfection. Parasite Immunol 2010; 32:314-23. [DOI: 10.1111/j.1365-3024.2009.01189.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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49
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Chang X, Yang L, Zhao Q, Fu W, Chen H, Qiu Z, Chen JA, Hu R, Shu W. Involvement of recF in 254 nm Ultraviolet Radiation Resistance in Deinococcus radiodurans and Escherichia coli. Curr Microbiol 2010; 61:458-64. [DOI: 10.1007/s00284-010-9638-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 03/24/2010] [Indexed: 11/28/2022]
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50
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Rolfsmeier ML, Haseltine CA. The Single-Stranded DNA Binding Protein of Sulfolobus solfataricus Acts in the Presynaptic Step of Homologous Recombination. J Mol Biol 2010; 397:31-45. [DOI: 10.1016/j.jmb.2010.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 12/13/2009] [Accepted: 01/05/2010] [Indexed: 12/31/2022]
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