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Liljegren MM, Gama JA, Johnsen PJ, Harms K. The recombination initiation functions DprA and RecFOR suppress microindel mutations in Acinetobacter baylyi ADP1. Mol Microbiol 2024; 122:1-10. [PMID: 38760330 DOI: 10.1111/mmi.15277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Short-Patch Double Illegitimate Recombination (SPDIR) has been recently identified as a rare mutation mechanism. During SPDIR, ectopic DNA single-strands anneal with genomic DNA at microhomologies and get integrated during DNA replication, presumably acting as primers for Okazaki fragments. The resulting microindel mutations are highly variable in size and sequence. In the soil bacterium Acinetobacter baylyi, SPDIR is tightly controlled by genome maintenance functions including RecA. It is thought that RecA scavenges DNA single-strands and renders them unable to anneal. To further elucidate the role of RecA in this process, we investigate the roles of the upstream functions DprA, RecFOR, and RecBCD, all of which load DNA single-strands with RecA. Here we show that all three functions suppress SPDIR mutations in the wildtype to levels below the detection limit. While SPDIR mutations are slightly elevated in the absence of DprA, they are strongly increased in the absence of both DprA and RecA. This SPDIR-avoiding function of DprA is not related to its role in natural transformation. These results suggest a function for DprA in combination with RecA to avoid potentially harmful microindel mutations, and offer an explanation for the ubiquity of dprA in the genomes of naturally non-transformable bacteria.
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Affiliation(s)
- Mikkel M Liljegren
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - João A Gama
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Pål J Johnsen
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Klaus Harms
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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2
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Gómez‐Campo CL, Abdelmoteleb A, Pulido V, Gost M, Sánchez‐Hevia DL, Berenguer J, Mencía M. Differential requirement for RecFOR pathway components in Thermus thermophilus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13269. [PMID: 38822640 PMCID: PMC11143384 DOI: 10.1111/1758-2229.13269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/06/2024] [Indexed: 06/03/2024]
Abstract
Recombinational repair is an important mechanism that allows DNA replication to overcome damaged templates, so the DNA is duplicated timely and correctly. The RecFOR pathway is one of the common ways to load RecA, while the RuvABC complex operates in the resolution of DNA intermediates. We have generated deletions of recO, recR and ruvB genes in Thermus thermophilus, while a recF null mutant could not be obtained. The recO deletion was in all cases accompanied by spontaneous loss of function mutations in addA or addB genes, which encode a helicase-exonuclease also key for recombination. The mutants were moderately affected in viability and chromosome segregation. When we generated these mutations in a Δppol/addAB strain, we observed that the transformation efficiency was maintained at the typical level of Δppol/addAB, which is 100-fold higher than that of the wild type. Most mutants showed increased filamentation phenotypes, especially ruvB, which also had DNA repair defects. These results suggest that in T. thermophilus (i) the components of the RecFOR pathway have differential roles, (ii) there is an epistatic relationship of the AddAB complex over the RecFOR pathway and (iii) that neither of the two pathways or their combination is strictly required for viability although they are necessary for normal DNA repair and chromosome segregation.
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Affiliation(s)
- Cristina L. Gómez‐Campo
- Center for Plant Biotechnology and Genomics (CBGP)Polytechnic University of MadridMadridSpain
| | - Ali Abdelmoteleb
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
- Department of Botany, Faculty of AgricultureMenoufia UniversityShebin El‐KomEgypt
| | - Verónica Pulido
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Marc Gost
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | | | - José Berenguer
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Mario Mencía
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
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3
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Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A. RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res 2024; 52:5195-5208. [PMID: 38567730 PMCID: PMC11109961 DOI: 10.1093/nar/gkae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria Yanovskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Olga Musharova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Piscataway, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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4
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Nautiyal A, Thakur M. Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution. ACS OMEGA 2024; 9:12515-12538. [PMID: 38524412 PMCID: PMC10956419 DOI: 10.1021/acsomega.3c09866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.
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Affiliation(s)
- Astha Nautiyal
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manoj Thakur
- Sri
Venkateswara College, Benito Juarez Road, University of Delhi, New Delhi 110021, India
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5
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Bonde NJ, Kozlov AG, Cox MM, Lohman TM, Keck JL. Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. Crit Rev Biochem Mol Biol 2024; 59:99-127. [PMID: 38770626 PMCID: PMC11209772 DOI: 10.1080/10409238.2024.2330372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 05/22/2024]
Abstract
The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ssDNA and transfers rapidly between different segments of ssDNA. SSB interacts with many other proteins involved in DNA metabolism, with 22 such SSB-interacting proteins, or SIPs, defined to date. These interactions chiefly involve the disordered and conserved C-terminal residues of SSB. When not bound to ssDNA, SSB can aggregate to form a phase-separated biomolecular condensate. Current understanding of the properties of SSB and the functional significance of its many intermolecular interactions are summarized in this review.
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Affiliation(s)
- Nina J. Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander G. Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Lee SJ, Ahn SY, Oh HB, Kim SY, Song WS, Yoon SI. Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni. Int J Mol Sci 2023; 24:12947. [PMID: 37629127 PMCID: PMC10454854 DOI: 10.3390/ijms241612947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The recombination mediator complex RecFOR, consisting of the RecF, RecO, and RecR proteins, is needed to initiate homologous recombination in bacteria by positioning the recombinase protein RecA on damaged DNA. Bacteria from the phylum Campylobacterota, such as the pathogen Campylobacter jejuni, lack the recF gene and trigger homologous recombination using only RecR and RecO. To elucidate the functional properties of C. jejuni RecR (cjRecR) in recombination initiation that differ from or are similar to those in RecF-expressing bacteria, we determined the crystal structure of cjRecR and performed structure-based binding analyses. cjRecR forms a rectangular ring-like tetrameric structure and coordinates a zinc ion using four cysteine residues, as observed for RecR proteins from RecF-expressing bacteria. However, the loop of RecR that has been shown to recognize RecO and RecF in RecF-expressing bacteria is substantially shorter in cjRecR as a canonical feature of Campylobacterota RecR proteins, indicating that cjRecR lost a part of the loop in evolution due to the lack of RecF and has a low RecO-binding affinity. Furthermore, cjRecR features a larger positive patch and exhibits substantially higher ssDNA-binding affinity than RecR from RecF-expressing bacteria. Our study provides a framework for a deeper understanding of the RecOR-mediated recombination pathway.
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Affiliation(s)
- Su-jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Si Yeon Ahn
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seung Yeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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7
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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: 5] [Impact Index Per Article: 5.0] [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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8
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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: 0] [Impact Index Per Article: 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
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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9
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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: 3] [Impact Index Per Article: 3.0] [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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10
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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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11
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Yahya AH, Harston SR, Colton WL, Cabeen MT. Distinct Screening Approaches Uncover PA14_36820 and RecA as Negative Regulators of Biofilm Phenotypes in Pseudomonas aeruginosa PA14. Microbiol Spectr 2023; 11:e0377422. [PMID: 36971546 PMCID: PMC10100956 DOI: 10.1128/spectrum.03774-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Pseudomonas aeruginosa commonly infects hospitalized patients and the lungs of individuals with cystic fibrosis. This species is known for forming biofilms, which are communities of bacterial cells held together and encapsulated by a self-produced extracellular matrix. The matrix provides extra protection to the constituent cells, making P. aeruginosa infections challenging to treat. We previously identified a gene, PA14_16550, which encodes a DNA-binding TetR-type repressor and whose deletion reduced biofilm formation. Here, we assessed the transcriptional impact of the 16550 deletion and found six differentially regulated genes. Among them, our results implicated PA14_36820 as a negative regulator of biofilm matrix production, while the remaining 5 had modest effects on swarming motility. We also screened a transposon library in a biofilm-impaired ΔamrZ Δ16550 strain for restoration of matrix production. Surprisingly, we found that disruption or deletion of recA increased biofilm matrix production, both in biofilm-impaired and wild-type strains. Because RecA functions both in recombination and in the DNA damage response, we asked which function of RecA is important with respect to biofilm formation by using point mutations in recA and lexA to specifically disable each function. Our results implied that loss of either function of RecA impacts biofilm formation, suggesting that enhanced biofilm formation may be one physiological response of P. aeruginosa cells to loss of either RecA function. IMPORTANCE Pseudomonas aeruginosa is a notorious human pathogen well known for forming biofilms, communities of bacteria that protect themselves within a self-secreted matrix. Here, we sought to find genetic determinants that impacted biofilm matrix production in P. aeruginosa strains. We identified a largely uncharacterized protein (PA14_36820) and, surprisingly, RecA, a widely conserved bacterial DNA recombination and repair protein, as negatively regulating biofilm matrix production. Because RecA has two main functions, we used specific mutations to isolate each function and found that both functions influenced matrix production. Identifying negative regulators of biofilm production may suggest future strategies to reduce the formation of treatment-resistant biofilms.
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Affiliation(s)
- Amal H. Yahya
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sophie R. Harston
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - William L. Colton
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Matthew T. Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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12
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Shinn MK, Chaturvedi SK, Kozlov AG, Lohman T. Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA. Nucleic Acids Res 2023; 51:2284-2297. [PMID: 36808259 PMCID: PMC10018359 DOI: 10.1093/nar/gkad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
Escherichia coli single stranded (ss) DNA binding protein (SSB) plays essential roles in DNA maintenance. It binds ssDNA with high affinity through its N-terminal DNA binding core and recruits at least 17 different SSB interacting proteins (SIPs) that are involved in DNA replication, recombination, and repair via its nine amino acid acidic tip (SSB-Ct). E. coli RecO, a SIP, is an essential recombination mediator protein in the RecF pathway of DNA repair that binds ssDNA and forms a complex with E. coli RecR protein. Here, we report ssDNA binding studies of RecO and the effects of a 15 amino acid peptide containing the SSB-Ct monitored by light scattering, confocal microscope imaging, and analytical ultracentrifugation (AUC). We find that one RecO monomer can bind the oligodeoxythymidylate, (dT)15, while two RecO monomers can bind (dT)35 in the presence of the SSB-Ct peptide. When RecO is in molar excess over ssDNA, large RecO-ssDNA aggregates occur that form with higher propensity on ssDNA of increasing length. Binding of RecO to the SSB-Ct peptide inhibits RecO-ssDNA aggregation. RecOR complexes can bind ssDNA via RecO, but aggregation is suppressed even in the absence of the SSB-Ct peptide, demonstrating an allosteric effect of RecR on RecO binding to ssDNA. Under conditions where RecO binds ssDNA but does not form aggregates, SSB-Ct binding enhances the affinity of RecO for ssDNA. For RecOR complexes bound to ssDNA, we also observe a shift in RecOR complex equilibrium towards a RecR4O complex upon binding SSB-Ct. These results suggest a mechanism by which SSB recruits RecOR to facilitate loading of RecA onto ssDNA gaps.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sumit K Chaturvedi
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy M Lohman
- To whom correspondence should be addressed. Tel: +1 314 362 4393; Fax: +1 314 362 7183;
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13
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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14
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Bonde NJ, Romero ZJ, Chitteni-Pattu S, Cox MM. RadD is a RecA-dependent accessory protein that accelerates DNA strand exchange. Nucleic Acids Res 2022; 50:2201-2210. [PMID: 35150260 PMCID: PMC8887467 DOI: 10.1093/nar/gkac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
In rapidly growing cells, with recombinational DNA repair required often and a new replication fork passing every 20 min, the pace of RecA-mediated DNA strand exchange is potentially much too slow for bacterial DNA metabolism. The enigmatic RadD protein, a putative SF2 family helicase, exhibits no independent helicase activity on branched DNAs. Instead, RadD greatly accelerates RecA-mediated DNA strand exchange, functioning only when RecA protein is present. The RadD reaction requires the RadD ATPase activity, does not require an interaction with SSB, and may disassemble RecA filaments as it functions. We present RadD as a new class of enzyme, an accessory protein that accelerates DNA strand exchange, possibly with a helicase-like action, in a reaction that is entirely RecA-dependent. RadD is thus a DNA strand exchange (recombination) synergist whose primary function is to coordinate closely with and accelerate the DNA strand exchange reactions promoted by the RecA recombinase. Multiple observations indicate a uniquely close coordination of RadD with RecA function.
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Affiliation(s)
- Nina J Bonde
- 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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15
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The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ. PLoS Genet 2021; 17:e1009972. [PMID: 34936656 PMCID: PMC8735627 DOI: 10.1371/journal.pgen.1009972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/06/2022] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.
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16
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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: 0] [Impact Index Per Article: 0] [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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17
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Shinn MK, Kozlov AG, Lohman TM. Allosteric effects of SSB C-terminal tail on assembly of E. coli RecOR proteins. Nucleic Acids Res 2021; 49:1987-2004. [PMID: 33450019 PMCID: PMC7913777 DOI: 10.1093/nar/gkaa1291] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli RecO is a recombination mediator protein that functions in the RecF pathway of homologous recombination, in concert with RecR, and interacts with E. coli single stranded (ss) DNA binding (SSB) protein via the last 9 amino acids of the C-terminal tails (SSB-Ct). Structures of the E. coli RecR and RecOR complexes are unavailable; however, crystal structures from other organisms show differences in RecR oligomeric state and RecO stoichiometry. We report analytical ultracentrifugation studies of E. coli RecR assembly and its interaction with RecO for a range of solution conditions using both sedimentation velocity and equilibrium approaches. We find that RecR exists in a pH-dependent dimer-tetramer equilibrium that explains the different assembly states reported in previous studies. RecO binds with positive cooperativity to a RecR tetramer, forming both RecR4O and RecR4O2 complexes. We find no evidence of a stable RecO complex with RecR dimers. However, binding of RecO to SSB-Ct peptides elicits an allosteric effect, eliminating the positive cooperativity and shifting the equilibrium to favor a RecR4O complex. These studies suggest a mechanism for how SSB binding to RecO influences the distribution of RecOR complexes to facilitate loading of RecA onto SSB coated ssDNA to initiate homologous recombination.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.,Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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18
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Kloos J, Johnsen PJ, Harms K. Tn 1 transposition in the course of natural transformation enables horizontal antibiotic resistance spread in Acinetobacter baylyi. MICROBIOLOGY-SGM 2020; 167. [PMID: 33270000 PMCID: PMC8116780 DOI: 10.1099/mic.0.001003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transposons are genetic elements that change their intracellular genomic position by transposition and are spread horizontally between bacteria when located on plasmids. It was recently discovered that transposition from fully heterologous DNA also occurs in the course of natural transformation. Here, we characterize the molecular details and constraints of this process using the replicative transposon Tn1 and the naturally competent bacterium Acinetobacter baylyi. We find that chromosomal insertion of Tn1 by transposition occurs at low but detectable frequencies and preferably around the A. baylyi terminus of replication. We show that Tn1 transposition is facilitated by transient expression of the transposase and resolvase encoded by the donor DNA. RecA protein is essential for the formation of a circular, double-stranded cytoplasmic intermediate from incoming donor DNA, and RecO is beneficial but not essential in this process. Absence of the recipient RecBCD nuclease stabilizes the double-stranded intermediate. Based on these results, we suggest a mechanistic model for transposition during natural transformation.
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Affiliation(s)
- Julia Kloos
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Pål J Johnsen
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Klaus Harms
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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19
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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: 5] [Impact Index Per Article: 1.3] [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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20
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Serment-Guerrero J, Dominguez-Monroy V, Davila-Becerril J, Morales-Avila E, Fuentes-Lorenzo JL. Induction of the SOS response of Escherichia coli in repair-defective strains by several genotoxic agents. Mutat Res 2020; 854-855:503196. [PMID: 32660820 DOI: 10.1016/j.mrgentox.2020.503196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022]
Abstract
DNA is exposed to the attack of several exogenous agents that modify its chemical structure, so cells must repair those changes in order to survive. Alkylating agents introduce methyl or ethyl groups in most of the cyclic or exocyclic nitrogen atoms of the ring and exocyclic oxygen available in DNA bases producing damage that can induce the SOS response in Escherichia coli and many other bacteria. Likewise, ultraviolet light produces mainly cyclobutane pyrimidine dimers that arrest the progression of the replication fork and triggers such response. The need of some enzymes (such as RecO, ExoI and RecJ) in processing injuries produced by gamma radiation prior the induction of the SOS response has been reported before. In the present work, several repair-defective strains of E. coli were treated with methyl methanesulfonate, ethyl methanesulfonate, mitomycin C or ultraviolet light. Both survival and SOS induction (by means of the Chromotest) were tested. Our results indicate that the participation of these genes depends on the type of injury caused by a genotoxin on DNA.
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Affiliation(s)
- Jorge Serment-Guerrero
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico.
| | - Viridiana Dominguez-Monroy
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico
| | - Jenny Davila-Becerril
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, La Marquesa, Estado de México, Mexico
| | - Enrique Morales-Avila
- Facultad de Química, Universidad Autónoma del Estado de México, Toluca, Estado de México, Mexico
| | - Jorge Luis Fuentes-Lorenzo
- Laboratorio de Microbiología y Mutagénesis Ambiental, Grupo de Investigación en Microbiología y Genética, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
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21
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Hwang J, Kim JY, Kim C, Park S, Joo S, Kim SK, Lee NK. Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans. eLife 2020; 9:50945. [PMID: 32297860 PMCID: PMC7200156 DOI: 10.7554/elife.50945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, a protein that is essential for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA-binding protein (drSSB) for binding to the freely exposed ssDNA, and efficiently displaces drSSB from ssDNA without consuming ATP. drRecO replaces drSSB and dissociates it completely from ssDNA even though drSSB binds to ssDNA approximately 300 times more strongly than drRecO does. We suggest that drRecO facilitates the loading of RecA onto drSSB-coated ssDNA by utilizing a small drSSB-free space on ssDNA that is generated by the fast diffusion of drSSB on ssDNA.
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Affiliation(s)
- Jihee Hwang
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, United States
| | - Cheolhee Kim
- Daegu National Science Museum, Daegu, Republic of Korea
| | - Soojin Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
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22
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Shinn MK, Kozlov AG, Nguyen B, Bujalowski WM, Lohman TM. Are the intrinsically disordered linkers involved in SSB binding to accessory proteins? Nucleic Acids Res 2019; 47:8581-8594. [PMID: 31329947 PMCID: PMC7145534 DOI: 10.1093/nar/gkz606] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
Escherichia coli single strand (ss) DNA binding (SSB) protein protects ssDNA intermediates and recruits at least 17 SSB interacting proteins (SIPs) during genome maintenance. The SSB C-termini contain a 9 residue acidic tip and a 56 residue intrinsically disordered linker (IDL). The acidic tip interacts with SIPs; however a recent proposal suggests that the IDL may also interact with SIPs. Here we examine the binding to four SIPs (RecO, PriC, PriA and χ subunit of DNA polymerase III) of three peptides containing the acidic tip and varying amounts of the IDL. Independent of IDL length, we find no differences in peptide binding to each individual SIP indicating that binding is due solely to the acidic tip. However, the tip shows specificity, with affinity decreasing in the order: RecO > PriA ∼ χ > PriC. Yet, RecO binding to the SSB tetramer and an SSB–ssDNA complex show significant thermodynamic differences compared to the peptides alone, suggesting that RecO interacts with another region of SSB, although not the IDL. SSB containing varying IDL deletions show different binding behavior, with the larger linker deletions inhibiting RecO binding, likely due to increased competition between the acidic tip interacting with DNA binding sites within SSB.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biochemistry and Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.,Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Binh Nguyen
- Department of Biochemistry and Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Wlodek M Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Timothy M Lohman
- Department of Biochemistry and Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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23
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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: 26] [Impact Index Per Article: 5.2] [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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24
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Deveryshetty J, Peterlini T, Ryzhikov M, Brahiti N, Dellaire G, Masson JY, Korolev S. Novel RNA and DNA strand exchange activity of the PALB2 DNA binding domain and its critical role for DNA repair in cells. eLife 2019; 8:44063. [PMID: 31017574 PMCID: PMC6533086 DOI: 10.7554/elife.44063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
BReast Cancer Associated proteins 1 and 2 (BRCA1, -2) and Partner and Localizer of BRCA2 (PALB2) protein are tumour suppressors linked to a spectrum of malignancies, including breast cancer and Fanconi anemia. PALB2 coordinates functions of BRCA1 and BRCA2 during homology-directed repair (HDR) and interacts with several chromatin proteins. In addition to protein scaffold function, PALB2 binds DNA. The functional role of this interaction is poorly understood. We identified a major DNA-binding site of PALB2, mutations in which reduce RAD51 foci formation and the overall HDR efficiency in cells by 50%. PALB2 N-terminal DNA-binding domain (N-DBD) stimulates the function of RAD51 recombinase. Surprisingly, it possesses the strand exchange activity without RAD51. Moreover, N-DBD stimulates the inverse strand exchange and can use DNA and RNA substrates. Our data reveal a versatile DNA interaction property of PALB2 and demonstrate a critical role of PALB2 DNA binding for chromosome repair in cells.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
| | - Thibaut Peterlini
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | - Mikhail Ryzhikov
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
| | - Nadine Brahiti
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | | | - Jean-Yves Masson
- Genome Stability LaboratoryCHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research CenterQuébec CityCanada
| | - Sergey Korolev
- Edward A Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSaint LouisUnited States
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25
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Xia J, Mei Q, Rosenberg SM. Tools To Live By: Bacterial DNA Structures Illuminate Cancer. Trends Genet 2019; 35:383-395. [PMID: 30962000 DOI: 10.1016/j.tig.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022]
Abstract
Holliday junctions (HJs) are DNA intermediates in homology-directed DNA repair and replication stalling, but until recently were undetectable in living cells. We review how an engineered protein that traps and labels HJs in Escherichia coli illuminates the biology of DNA and cancer. HJ chromatin immunoprecipitation with deep sequencing (ChIP-seq) analysis showed the directionality of double-strand break (DSB) repair in the E. coli genome. Quantification of HJs as fluorescent foci in live cells revealed that the commonest spontaneous problem repaired via HJs is replication-dependent single-stranded DNA gaps, not DSBs. Focus quantification also indicates that RecQ DNA helicase plays dual roles in promoting repair HJs and preventing replication-stall HJs in an E. coli model of RAD51-overexpressing (most) cancers. Moreover, cancer transcriptomes imply that most cancers suffer frequent fork stalls that are reduced by the HJ removers EME1 and GEN1, as well as by the human RecQ orthologs BLM and RECQL4-surprising potential procancer roles for these known cancer-preventing proteins.
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Affiliation(s)
- Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Mei
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA.
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26
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Lu CH, Chang TT, Cho CC, Lin HC, Li HW. Stable Nuclei of Nucleoprotein Filament and High ssDNA Binding Affinity Contribute to Enhanced RecA E38K Recombinase Activity. Sci Rep 2017; 7:14964. [PMID: 29097773 PMCID: PMC5668366 DOI: 10.1038/s41598-017-15088-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/20/2017] [Indexed: 11/10/2022] Open
Abstract
RecA plays central roles in the homologous recombination to repair double-stranded DNA break damage in E. coli. A previously identified recA strain surviving high doses of UV radiation includes a dominant RecA E38K mutation. Using single-molecule experiments, we showed that the RecA E38K variant protein assembles nucleoprotein filaments more rapidly than the wild-type RecA. We also used a single-molecule fluorescence resonance energy transfer (smFRET) experiment to compare the nucleation cluster dynamics of wild-type RecA and RecA E38K mutants on various short ssDNA substrates. At shorter ssDNA, nucleation clusters of RecA E38K form dynamically, while only few were seen in wild-type RecA. RecA E38K also forms stable nuclei by specifically lowering the dissociation rate constant, kd. These observations provide evidence that greater nuclei stability and higher ssDNA binding affinity contribute to the observed enhanced recombination activity of the RecA E38K mutant. Given that assembly of RecA nucleoprotein filaments is the first committed step in recombinational repair processes, enhancement at this step gives rise to a more efficient recombinase.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Ting-Tzu Chang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chia-Chuan Cho
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hui-Cin Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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27
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Gourley CR, Negretti NM, Konkel ME. The food-borne pathogen Campylobacter jejuni depends on the AddAB DNA repair system to defend against bile in the intestinal environment. Sci Rep 2017; 7:14777. [PMID: 29089630 PMCID: PMC5665897 DOI: 10.1038/s41598-017-14646-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Accurate repair of DNA damage is crucial to ensure genome stability and cell survival of all organisms. Bile functions as a defensive barrier against intestinal colonization by pathogenic microbes. Campylobacter jejuni, a leading bacterial cause of foodborne illness, possess strategies to mitigate the toxic components of bile. We recently found that growth of C. jejuni in medium with deoxycholate, a component of bile, caused DNA damage consistent with the exposure to reactive oxygen species. We hypothesized that C. jejuni must repair DNA damage caused by reactive oxygen species to restore chromosomal integrity. Our efforts focused on determining the importance of the putative AddAB DNA repair proteins. A C. jejuni addAB mutant demonstrated enhanced sensitivity to deoxycholate and was impaired in DNA double strand break repair. Complementation of the addAB mutant restored resistance to deoxycholate, as well as function of the DNA double strand break repair system. The importance of these findings translated to the natural host, where the AddAB system was found to be required for efficient C. jejuni colonization of the chicken intestine. This research provides new insight into the molecular mechanism utilized by C. jejuni, and possibly other intestinal pathogens, to survive in the presence of bile.
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Affiliation(s)
- Christopher R Gourley
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, 99164-7520, WA, USA
| | - Nicholas M Negretti
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, 99164-7520, WA, USA
| | - Michael E Konkel
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, 99164-7520, WA, USA.
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28
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Le S, Serrano E, Kawamura R, Carrasco B, Yan J, Alonso JC. Bacillus subtilis RecA with DprA-SsbA antagonizes RecX function during natural transformation. Nucleic Acids Res 2017; 45:8873-8885. [PMID: 28911099 PMCID: PMC5587729 DOI: 10.1093/nar/gkx583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/29/2017] [Indexed: 01/07/2023] Open
Abstract
Bacillus subtilis DprA and RecX proteins, which interact with RecA, are crucial for efficient chromosomal and plasmid transformation. We showed that RecA, in the rATP·Mg2+ bound form (RecA·ATP), could not compete with RecX, SsbA or SsbB for assembly onto single-stranded (ss)DNA, but RecA·dATP partially displaced these proteins from ssDNA. RecX promoted reversible depolymerization of preformed RecA·ATP filaments. The two-component DprA–SsbA mediator reversed the RecX negative effect on RecA filament extension, but not DprA or DprA and SsbB. In the presence of DprA–SsbA, RecX added prior to RecA·ATP inhibited DNA strand exchange, but this inhibition was reversed when RecX was added after RecA. We propose that RecA nucleation is more sensitive to RecX action than is RecA filament growth. DprA–SsbA facilitates formation of an active RecA filament that directly antagonizes the inhibitory effects of RecX. RecX and DprA enable chromosomal transformation by altering RecA filament dynamics. DprA–SsbA and RecX proteins constitute a new regulatory network of RecA function. DprA–SsbA contributes to the formation of an active RecA filament and directly antagonizes the inhibitory effects of RecX during natural transformation.
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Affiliation(s)
- Shimin Le
- Department of Physics, National University of Singapore, 117551, Singapore.,Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Ryo Kawamura
- Department of Physics, National University of Singapore, 117551, Singapore.,Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Jie Yan
- Department of Physics, National University of Singapore, 117551, Singapore.,Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
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29
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Cheng K, Xu G, Xu H, Zhao Y, Hua Y. Deinococcus radiodurans
DR1088 is a novel RecF-interacting protein that stimulates single-stranded DNA annealing. Mol Microbiol 2017; 106:518-529. [DOI: 10.1111/mmi.13828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences; Zhejiang University; Hangzhou 310029 China
| | - Guangzhi Xu
- Agriculture and Food Science School; Zhejiang Agriculture and Forestry University, Zhejiang; Lin'an 311300 China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences; Zhejiang University; Hangzhou 310029 China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences; Zhejiang University; Hangzhou 310029 China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences; Zhejiang University; Hangzhou 310029 China
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30
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Laureti L, Lee L, Philippin G, Pagès V. A non-catalytic role of RecBCD in homology directed gap repair and translesion synthesis. Nucleic Acids Res 2017; 45:5877-5886. [PMID: 28369478 PMCID: PMC5449595 DOI: 10.1093/nar/gkx217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/23/2017] [Indexed: 11/14/2022] Open
Abstract
The RecBCD complex is a key factor in DNA metabolism. This protein complex harbors a processive nuclease and two helicases activities that give it the ability to process duplex DNA ends. These enzymatic activities make RecBCD a major player in double strand break repair, conjugational recombination and degradation of linear DNA. In this work, we unravel a new role of the RecBCD complex in the processing of DNA single-strand gaps that are generated at DNA replication-blocking lesions. We show that independently of its nuclease or helicase activities, the entire RecBCD complex is required for recombinational repair of the gap and efficient translesion synthesis. Since none of the catalytic functions of RecBCD are required for those processes, we surmise that the complex acts as a structural element that stabilizes the blocked replication fork, allowing efficient DNA damage tolerance.
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Affiliation(s)
- Luisa Laureti
- Team DNA Damage Tolerance, Cancer Research Center of Marseille, CRCM, Aix Marseille univ, CNRS, inserm, institut Paoli-Calmettes, 13009 Marseille, France
| | - Lara Lee
- Team DNA Damage Tolerance, Cancer Research Center of Marseille, CRCM, Aix Marseille univ, CNRS, inserm, institut Paoli-Calmettes, 13009 Marseille, France
| | - Gaëlle Philippin
- Team DNA Damage Tolerance, Cancer Research Center of Marseille, CRCM, Aix Marseille univ, CNRS, inserm, institut Paoli-Calmettes, 13009 Marseille, France
| | - Vincent Pagès
- Team DNA Damage Tolerance, Cancer Research Center of Marseille, CRCM, Aix Marseille univ, CNRS, inserm, institut Paoli-Calmettes, 13009 Marseille, France
- To whom correspondence should be addressed. Tel: + 33 486 97 73 84; Fax: +33 486 97 74 99;
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31
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Wardell K, Haldenby S, Jones N, Liddell S, Ngo GHP, Allers T. RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator. DNA Repair (Amst) 2017; 55:7-16. [PMID: 28501701 PMCID: PMC5480776 DOI: 10.1016/j.dnarep.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/23/2017] [Accepted: 04/25/2017] [Indexed: 11/20/2022]
Abstract
Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination - it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination mediator, which it does by inducing a conformational change in RadA and thereby promoting its polymerisation on DNA.
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Affiliation(s)
- Kayleigh Wardell
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Sam Haldenby
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Nathan Jones
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Susan Liddell
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Greg H P Ngo
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
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32
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Hülter N, Sørum V, Borch-Pedersen K, Liljegren MM, Utnes ALG, Primicerio R, Harms K, Johnsen PJ. Costs and benefits of natural transformation in Acinetobacter baylyi. BMC Microbiol 2017; 17:34. [PMID: 28202049 PMCID: PMC5312590 DOI: 10.1186/s12866-017-0953-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. Results We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation. Conclusions Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0953-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Hülter
- Genomic Microbiology, Institute of Microbiology, Christian-Albrechts-University Kiel, Am Botanischen Garten 11, 24118, Kiel, Germany.,Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Kristina Borch-Pedersen
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep, 0033, Oslo, Norway
| | - Mikkel M Liljegren
- Centre for Ecolgical and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Ane L G Utnes
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway. .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway.
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33
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Korolev S. Advances in structural studies of recombination mediator proteins. Biophys Chem 2016; 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] [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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34
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Xia J, Chen LT, Mei Q, Ma CH, Halliday JA, Lin HY, Magnan D, Pribis JP, Fitzgerald DM, Hamilton HM, Richters M, Nehring RB, Shen X, Li L, Bates D, Hastings PJ, Herman C, Jayaram M, Rosenberg SM. Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. SCIENCE ADVANCES 2016; 2:e1601605. [PMID: 28090586 PMCID: PMC5222578 DOI: 10.1126/sciadv.1601605] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/05/2016] [Indexed: 05/05/2023]
Abstract
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E. coli and demonstrate genome-scale directionality of double-strand break (DSB) repair along the chromosome. Unexpectedly, most spontaneous HR-HJ foci are instigated, not by DSBs, but rather by single-stranded DNA damage generated by replication. We show that RecQ, the E. coli ortholog of five human cancer proteins, nonredundantly promotes HR-HJ formation in single cells and, in a novel junction-guardian role, also prevents apparent non-HR-HJs promoted by RecA overproduction. We propose that one or more human RecQ orthologs may act similarly in human cancers overexpressing the RecA ortholog RAD51 and find that cancer genome expression data implicate the orthologs BLM and RECQL4 in conjunction with EME1 and GEN1 as probable HJ reducers in such cancers. Our results support RecA-overproducing E. coli as a model of the many human tumors with up-regulated RAD51 and provide the first glimpses of important, previously elusive reaction intermediates in DNA replication and repair in single living cells.
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Affiliation(s)
- Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li-Tzu Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Institute of Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Jennifer A. Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hsin-Yu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Magnan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - John P. Pribis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Devon M. Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Holly M. Hamilton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan Richters
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ralf B. Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Institute of Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Susan M. Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry, Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77030, USA
- Corresponding author.
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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: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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36
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Kim T, Chitteni-Pattu S, Cox BL, Wood EA, Sandler SJ, Cox MM. Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination. PLoS Genet 2015; 11:e1005278. [PMID: 26047498 PMCID: PMC4457935 DOI: 10.1371/journal.pgen.1005278] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
The recombination activity of Escherichia coli (E. coli) RecA protein reflects an evolutionary balance between the positive and potentially deleterious effects of recombination. We have perturbed that balance, generating RecA variants exhibiting improved recombination functionality via random mutagenesis followed by directed evolution for enhanced function in conjugation. A recA gene segment encoding a 59 residue segment of the protein (Val79-Ala137), encompassing an extensive subunit-subunit interface region, was subjected to degenerate oligonucleotide-mediated mutagenesis. An iterative selection process generated at least 18 recA gene variants capable of producing a higher yield of transconjugants. Three of the variant proteins, RecA I102L, RecA V79L and RecA E86G/C90G were characterized based on their prominence. Relative to wild type RecA, the selected RecA variants exhibited faster rates of ATP hydrolysis, more rapid displacement of SSB, decreased inhibition by the RecX regulator protein, and in general displayed a greater persistence on DNA. The enhancement in conjugational function comes at the price of a measurable RecA-mediated cellular growth deficiency. Persistent DNA binding represents a barrier to other processes of DNA metabolism in vivo. The growth deficiency is alleviated by expression of the functionally robust RecX protein from Neisseria gonorrhoeae. RecA filaments can be a barrier to processes like replication and transcription. RecA regulation by RecX protein is important in maintaining an optimal balance between recombination and other aspects of DNA metabolism. The genetic recombination systems of bacteria have not evolved for optimal enzymatic function. As recombination and recombination systems can have deleterious effects, these systems have evolved sufficient function to repair a level of DNA double strand breaks typically encountered during replication and cell division. However, maintenance of genome stability requires a proper balance between all aspects of DNA metabolism. A substantial increase in recombinase function is possible, but it comes with a cellular cost. Here, we use a kind of directed evolution to generate variants of the Escherichia coli RecA protein with an enhanced capacity to promote conjugational recombination. The mutations all occur within a targeted 59 amino acid segment of the protein, encompassing a significant part of the subunit-subunit interface. The RecA variants exhibit a range of altered activities. In general, the mutations appear to increase RecA protein persistence as filaments formed on DNA creating barriers to DNA replication and/or transcription. The barriers can be eliminated via expression of more robust forms of a RecA regulator, the RecX protein. The results elucidate an evolutionary compromise between the beneficial and deleterious effects of recombination.
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Affiliation(s)
- Taejin Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Benjamin L. Cox
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Steven J. Sandler
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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37
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Carrasco B, Yadav T, Serrano E, Alonso JC. Bacillus subtilis RecO and SsbA are crucial for RecA-mediated recombinational DNA repair. Nucleic Acids Res 2015; 43:5984-97. [PMID: 26001966 PMCID: PMC4499154 DOI: 10.1093/nar/gkv545] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/12/2015] [Indexed: 11/13/2022] Open
Abstract
Genetic data have revealed that the absence of Bacillus subtilis RecO and one of the end-processing avenues (AddAB or RecJ) renders cells as sensitive to DNA damaging agents as the null recA, suggesting that both end-resection pathways require RecO for recombination. RecA, in the rATP·Mg(2+) bound form (RecA·ATP), is inactive to catalyze DNA recombination between linear double-stranded (ds) DNA and naked complementary circular single-stranded (ss) DNA. We showed that RecA·ATP could not nucleate and/or polymerize on SsbA·ssDNA or SsbB·ssDNA complexes. RecA·ATP nucleates and polymerizes on RecO·ssDNA·SsbA complexes more efficiently than on RecO·ssDNA·SsbB complexes. Limiting SsbA concentrations were sufficient to stimulate RecA·ATP assembly on the RecO·ssDNA·SsbB complexes. RecO and SsbA are necessary and sufficient to 'activate' RecA·ATP to catalyze DNA strand exchange, whereas the AddAB complex, RecO alone or in concert with SsbB was not sufficient. In presence of AddAB, RecO and SsbA are still necessary for efficient RecA·ATP-mediated three-strand exchange recombination. Based on genetic and biochemical data, we proposed that SsbA and RecO (or SsbA, RecO and RecR in vivo) are crucial for RecA activation for both, AddAB and RecJ-RecQ (RecS) recombinational repair pathways.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Tribhuwan Yadav
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
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38
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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: 1.2] [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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39
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Curtis FA, Malay AD, Trotter AJ, Wilson LA, Barradell-Black MMH, Bowers LY, Reed P, Hillyar CRT, Yeo RP, Sanderson JM, Heddle JG, Sharples GJ. Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding. PLoS One 2014; 9:e102454. [PMID: 25083707 PMCID: PMC4118853 DOI: 10.1371/journal.pone.0102454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/17/2014] [Indexed: 01/05/2023] Open
Abstract
Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination.
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Affiliation(s)
- Fiona A. Curtis
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Ali D. Malay
- Heddle Initiative Research Unit, RIKEN, Wako, Saitama, Japan
| | - Alexander J. Trotter
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Lindsay A. Wilson
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Michael M. H. Barradell-Black
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Laura Y. Bowers
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Patricia Reed
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Christopher R. T. Hillyar
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Robert P. Yeo
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - John M. Sanderson
- Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | | | - Gary J. Sharples
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- * E-mail:
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40
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Cheng K, Xu X, Zhao Y, Wang L, Xu G, Hua Y. The key residue for SSB-RecO interaction is dispensable for Deinococcus radiodurans DNA repair in vivo. Acta Biochim Biophys Sin (Shanghai) 2014; 46:368-76. [PMID: 24681881 DOI: 10.1093/abbs/gmu013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The RecFOR DNA repair pathway is one of the major RecA-dependent recombinatorial repair pathways in bacteria and plays an important role in double-strand breaks repair. RecO, one of the major recombination mediator proteins in the RecFOR pathway, has been shown to assist RecA loading onto single-stranded binding protein (SSB) coated single-stranded DNA (ssDNA). However, it has not been characterized whether the protein-protein interaction between RecO and SSB contributes to that process in vivo. Here, we identified the residue arginine-121 of Deinococcus radiodurans RecO (drRecO-R121) as the key residue for RecO-SSB interaction. The substitution of drRecO-R121 with alanine greatly abolished the binding of RecO to SSB but not the binding to RecR. Meanwhile, SSB-coated ssDNA annealing activity was also compromised by the mutation of the residue of drRecO. However, the drRecO-R121A strain showed only modest sensitivity to DNA damaging agents. Taking these data together, arginine-121 of drRecO is the key residue for SSB-RecO interaction, which may not play a vital role in the SSB displacement and RecA loading process of RecFOR DNA repair pathway in vivo.
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Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
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41
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Vlašić I, Mertens R, Seco EM, Carrasco B, Ayora S, Reitz G, Commichau FM, Alonso JC, Moeller R. Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break. Nucleic Acids Res 2013; 42:2295-307. [PMID: 24285298 PMCID: PMC3936729 DOI: 10.1093/nar/gkt1194] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacillus subtilis RecA is important for spore resistance to DNA damage, even though spores contain a single non-replicating genome. We report that inactivation of RecA or its accessory factors, RecF, RecO, RecR and RecX, drastically reduce survival of mature dormant spores to ultrahigh vacuum desiccation and ionizing radiation that induce single strand (ss) DNA nicks and double-strand breaks (DSBs). The presence of non-cleavable LexA renders spores less sensitive to DSBs, and spores impaired in DSB recognition or end-processing show sensitivities to X-rays similar to wild-type. In vitro RecA cannot compete with SsbA for nucleation onto ssDNA in the presence of ATP. RecO is sufficient, at least in vitro, to overcome SsbA inhibition and stimulate RecA polymerization on SsbA-coated ssDNA. In the presence of SsbA, RecA slightly affects DNA replication in vitro, but addition of RecO facilitates RecA-mediated inhibition of DNA synthesis. We propose that repairing of the DNA lesions generates a replication stress to germinating spores, and the RecA·ssDNA filament might act by preventing potentially dangerous forms of DNA repair occurring during replication. RecA might stabilize a stalled fork or prevent or promote dissolution of reversed forks rather than its cleavage that should require end-processing.
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Affiliation(s)
- Ignacija Vlašić
- Radiation Biology Department, German Aerospace Center, Institute of Aerospace Medicine, Linder Höhe, D-51147 Cologne (Köln), Germany, Division of Molecular Biology, Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain and Department of General Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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42
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Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair. J Mol Biol 2013; 425:4802-19. [PMID: 24021816 DOI: 10.1016/j.jmb.2013.08.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/01/2013] [Accepted: 08/16/2013] [Indexed: 11/21/2022]
Abstract
Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold "tetramer". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance.
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43
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Alves JMP, Serrano MG, Maia da Silva F, Voegtly LJ, Matveyev AV, Teixeira MMG, Camargo EP, Buck GA. Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. Genome Biol Evol 2013; 5:338-50. [PMID: 23345457 PMCID: PMC3590767 DOI: 10.1093/gbe/evt012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.
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Affiliation(s)
- João M P Alves
- Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, VA, USA.
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44
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Ngo KV, Molzberger ET, Chitteni-Pattu S, Cox MM. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem 2013; 288:21351-21366. [PMID: 23729671 DOI: 10.1074/jbc.m113.459230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RecA protein of Deinococcus radiodurans (DrRecA) has a central role in genome reconstitution after exposure to extreme levels of ionizing radiation. When bound to DNA, filaments of DrRecA protein exhibit active and inactive states that are readily interconverted in response to several sets of stimuli and conditions. At 30 °C, the optimal growth temperature, and at physiological pH 7.5, DrRecA protein binds to double-stranded DNA (dsDNA) and forms extended helical filaments in the presence of ATP. However, the ATP is not hydrolyzed. ATP hydrolysis of the DrRecA-dsDNA filament is activated by addition of single-stranded DNA, with or without the single-stranded DNA-binding protein. The ATPase function of DrRecA nucleoprotein filaments thus exists in an inactive default state under some conditions. ATPase activity is thus not a reliable indicator of DNA binding for all bacterial RecA proteins. Activation is effected by situations in which the DNA substrates needed to initiate recombinational DNA repair are present. The inactive state can also be activated by decreasing the pH (protonation of multiple ionizable groups is required) or by addition of volume exclusion agents. Single-stranded DNA-binding protein plays a much more central role in DNA pairing and strand exchange catalyzed by DrRecA than is the case for the cognate proteins in Escherichia coli. The data suggest a mechanism to enhance the efficiency of recombinational DNA repair in the context of severe genomic degradation in D. radiodurans.
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Affiliation(s)
- Khanh V Ngo
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eileen T Molzberger
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
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45
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RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Proc Natl Acad Sci U S A 2013; 110:5410-5. [PMID: 23509251 DOI: 10.1073/pnas.1303301110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This report discovers a role of Escherichia coli RecA, the cellular recombinase, in directing the action of several DNA polymerases at the replication fork. Bulk chromosome replication is performed by DNA polymerase (Pol) III. However, E. coli contains translesion synthesis (TLS) Pols II, IV, and V that also function with the helicase, primase, and sliding clamp in the replisome. Surprisingly, we find that RecA specifically activates replisomes that contain TLS Pols. In sharp contrast, RecA severely inhibits the Pol III replisome. Given the opposite effects of RecA on Pol III and TLS replisomes, we propose that RecA acts as a switch to regulate the occupancy of polymerases within a moving replisome.
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46
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Early steps of double-strand break repair in Bacillus subtilis. DNA Repair (Amst) 2013; 12:162-76. [PMID: 23380520 DOI: 10.1016/j.dnarep.2012.12.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/04/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
Abstract
All organisms rely on integrated networks to repair DNA double-strand breaks (DSBs) in order to preserve the integrity of the genetic information, to re-establish replication, and to ensure proper chromosomal segregation. Genetic, cytological, biochemical and structural approaches have been used to analyze how Bacillus subtilis senses DNA damage and responds to DSBs. RecN, which is among the first responders to DNA DSBs, promotes the ordered recruitment of repair proteins to the site of a lesion. Cells have evolved different mechanisms for efficient end processing to create a 3'-tailed duplex DNA, the substrate for RecA binding, in the repair of one- and two-ended DSBs. Strand continuity is re-established via homologous recombination (HR), utilizing an intact homologous DNA molecule as a template. In the absence of transient diploidy or of HR, however, two-ended DSBs can be directly re-ligated via error-prone non-homologous end-joining. Here we review recent findings that shed light on the early stages of DSB repair in Firmicutes.
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Structural studies of SSB interaction with RecO. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 922:123-31. [PMID: 22976180 DOI: 10.1007/978-1-62703-032-8_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Interaction of recombination protein RecO with single-stranded (ss) DNA-binding protein (SSB) is essential for DNA damage repair and restart of stalled replication (Cox, Crit Rev Biochem Mol Biol 42(1):41-63, 2007). To understand mechanism of this interaction and its role in DNA repair, we deciphered a high-resolution structure of RecO complex with C-terminal tail of SSB (SSB-Ct). The structure revealed a key role of hydrophobic interactions between two proteins and suggests the mechanism of RecO recruitment to DNA during homologous recombination and strand annealing.
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Gupta R, Ryzhikov M, Koroleva O, Unciuleac M, Shuman S, Korolev S, Glickman MS. A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing. Nucleic Acids Res 2013; 41:2284-95. [PMID: 23295671 PMCID: PMC3575820 DOI: 10.1093/nar/gks1298] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mycobacteria have two genetically distinct pathways for the homology-directed repair of DNA double-strand breaks: homologous recombination (HR) and single-strand annealing (SSA). HR is abolished by deletion of RecA and reduced in the absence of the AdnAB helicase/nuclease. By contrast, SSA is RecA-independent and requires RecBCD. Here we examine the function of RecO in mycobacterial DNA recombination and repair. Loss of RecO elicits hypersensitivity to DNA damaging agents similar to that caused by deletion of RecA. We show that RecO participates in RecA-dependent HR in a pathway parallel to the AdnAB pathway. We also find that RecO plays a role in the RecA-independent SSA pathway. The mycobacterial RecO protein displays a zinc-dependent DNA binding activity in vitro and accelerates the annealing of SSB-coated single-stranded DNA. These findings establish a role for RecO in two pathways of mycobacterial DNA double-strand break repair and suggest an in vivo function for the DNA annealing activity of RecO proteins, thereby underscoring their similarity to eukaryal Rad52.
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Affiliation(s)
- Richa Gupta
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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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: 51] [Impact Index Per Article: 4.3] [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: 3.3] [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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