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Yuan Z, Yu F, Zhang D, Wang H. Profiling of the assembly of RecA nucleofilaments implies a potential target for environmental factors to disturb DNA repair. J Environ Sci (China) 2021; 102:283-290. [PMID: 33637254 DOI: 10.1016/j.jes.2020.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/12/2023]
Abstract
Double-strand breaks (DSBs), one class of the most harmful DNA damage forms that bring elevated health risks, need to be repaired timely and effectively. However, an increasing number of environmental pollutants have been identified to impair DSB repair from various mechanisms. Our previous work indicated that the formation of unsaturated RecA nucleofilaments plays an essential role in homology recombination (HR) pathway which can accurately repair DSBs. In this study, by developing a benzonase cutting protection assay and combining it with traditional electrophoretic mobility shift assay (EMSA) analysis, we further investigated the assembly patterns of four RecA mutants that display differential DSB repair ability and ATPase activity. We observed that the mutants (G204S and S69G) possessing both ATP hydrolysis and DSB repair activities form unsaturated nucleofilaments similar to that formed by the wild type RecA, whereas the other two ATP hydrolysis-deficient mutants (K72R and E96D) that fail to mediate HR form more compacted nucleofilaments in the presence of ATP. These results establish a coupling of ATPase activity and effective DSB repair ability via the assembly status of RecA nucleofilaments. This linkage provides a potential target for environmental factors to disturb the essential HR pathway for DSB repair by suppressing the ATPase activity and altering the assembly pattern of nucleofilaments.
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Affiliation(s)
- Zheng Yuan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangzhi Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dapeng Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China; Institute of Environment and Health, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 430056, China.
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2
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Henry C, Loiseau L, Vergnes A, Vertommen D, Mérida-Floriano A, Chitteni-Pattu S, Wood EA, Casadesús J, Cox MM, Barras F, Ezraty B. Redox controls RecA protein activity via reversible oxidation of its methionine residues. eLife 2021; 10:63747. [PMID: 33605213 PMCID: PMC7943192 DOI: 10.7554/elife.63747] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
Reactive oxygen species (ROS) cause damage to DNA and proteins. Here, we report that the RecA recombinase is itself oxidized by ROS. Genetic and biochemical analyses revealed that oxidation of RecA altered its DNA repair and DNA recombination activities. Mass spectrometry analysis showed that exposure to ROS converted four out of nine Met residues of RecA to methionine sulfoxide. Mimicking oxidation of Met35 by changing it for Gln caused complete loss of function, whereas mimicking oxidation of Met164 resulted in constitutive SOS activation and loss of recombination activity. Yet, all ROS-induced alterations of RecA activity were suppressed by methionine sulfoxide reductases MsrA and MsrB. These findings indicate that under oxidative stress MsrA/B is needed for RecA homeostasis control. The implication is that, besides damaging DNA structure directly, ROS prevent repair of DNA damage by hampering RecA activity.
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Affiliation(s)
- Camille Henry
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin-Madison, United States
| | - Laurent Loiseau
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Alexandra Vergnes
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | | | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin-Madison, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin-Madison, United States
| | - Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin-Madison, United States
| | - Frédéric Barras
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France.,Institut Pasteur, Département de Microbiologie, SAMe Unit, Paris, France.,UMR CNRS-Institut Pasteur 2001 Integrated and Molecular Microbiology (IMM), Paris, France
| | - Benjamin Ezraty
- Aix-Marseille Univ, CNRS, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
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Leite WC, Penteado RF, Gomes F, Iulek J, Etto RM, Saab SC, Steffens MBR, Galvão CW. MAW point mutation impairs H. Seropedicae RecA ATP hydrolysis and DNA repair without inducing large conformational changes in its structure. PLoS One 2019; 14:e0214601. [PMID: 30998678 PMCID: PMC6472873 DOI: 10.1371/journal.pone.0214601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/17/2019] [Indexed: 11/18/2022] Open
Abstract
RecA is a multifunctional protein that plays a central role in DNA repair in bacteria. The structural Make ATP Work motif (MAW) is proposed to control the ATPase activity of RecA. In the present work, we report the biochemical activity and structural effects of the L53Q mutation at the MAW motif of the RecA protein from H. seropedicae (HsRecA L53Q). In vitro studies showed that HsRecA L53Q can bind ADP, ATP, and ssDNA, as does wild-type RecA. However, the ATPase and DNA-strand exchange activities were completely lost. In vivo studies showed that the expression of HsRecA L53Q in E. coli recA1 does not change its phenotype when cells were challenged with MMS and UV. Molecular dynamics simulations showed the L53Q point mutation did not cause large conformational changes in the HsRecA structure. However, there is a difference on dynamical cross-correlation movements of the residues involved in contacts within the ATP binding site and regions that hold the DNA binding sites. Additionally, a new hydrogen bond, formed between Q53 and T49, was hypothesized to allow an independent motion of the MAW motif from the hydrophobic core, what could explain the observed loss of activity of HsRecA L53Q.
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Affiliation(s)
- Wellington C. Leite
- Department of Physics, State University of Ponta Grossa (UEPG), Ponta Grossa,Paraná, Brazil
- * E-mail: (WCL); .(CWG)
| | - Renato F. Penteado
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Fernando Gomes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Rafael M. Etto
- Department of Chemistry, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Sérgio C. Saab
- Department of Physics, State University of Ponta Grossa (UEPG), Ponta Grossa,Paraná, Brazil
| | - Maria B. R. Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Carolina W. Galvão
- Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
- * E-mail: (WCL); .(CWG)
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Prasad D, Muniyappa K. The Anionic Phospholipids in the Plasma Membrane Play an Important Role in Regulating the Biochemical Properties and Biological Functions of RecA Proteins. Biochemistry 2019; 58:1295-1310. [PMID: 30726069 DOI: 10.1021/acs.biochem.8b01147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli RecA (EcRecA) forms discrete foci that cluster at cell poles during normal growth, which are redistributed along the filamented cell axis upon induction of the SOS response. The plasma membrane is thought to act as a scaffold for EcRecA foci, thereby playing an important role in RecA-dependent homologous recombination. In addition, in vivo and in vitro studies demonstrate that EcRecA binds strongly to the anionic phospholipids. However, there have been almost no data on the association of mycobacterial RecA proteins with the plasma membrane and the effects of membrane components on their function. Here, we show that mycobacterial RecA proteins specifically interact with phosphatidylinositol and cardiolipin among other anionic phospholipids; however, they had no effect on the ability of RecA proteins to bind single-stranded DNA. Interestingly, phosphatidylinositol and cardiolipin impede the DNA-dependent ATPase activity of RecA proteins, although ATP binding is not affected. Furthermore, the ability of RecA proteins to promote DNA strand exchange is not affected by anionic phospholipids. Strikingly, anionic phospholipids suppress the RecA-stimulated autocatalytic cleavage of the LexA repressor. The Mycobacterium smegmatis RecA foci localize to the cell poles during normal growth, and these structures disassemble and reassemble into several foci along the cell after the induction of DNA damage. Taken together, these data support the notion that the interaction of RecA with cardiolipin and phosphatidylinositol, the major anionic phospholipids of the mycobacterial plasma membrane, may be physiologically relevant, as they provide a scaffold for RecA storage and may regulate recombinational DNA repair and the SOS response.
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Affiliation(s)
- Deepika Prasad
- Department of Biochemistry , Indian Institute of Science , Bengaluru 560012 , India
| | - K Muniyappa
- Department of Biochemistry , Indian Institute of Science , Bengaluru 560012 , India
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Šimatović A, Mitrikeski PT, Vlašić I, Sopta M, Brčić-Kostić K. The Walker A motif mutation recA4159 abolishes the SOS response and recombination in a recA730 mutant of Escherichia coli. Res Microbiol 2016; 167:462-71. [PMID: 27130282 DOI: 10.1016/j.resmic.2016.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 12/20/2022]
Abstract
In bacteria, the RecA protein forms recombinogenic filaments required for the SOS response and DNA recombination. In order to form a recombinogenic filament, wild type RecA needs to bind ATP and to interact with mediator proteins. The RecA730 protein is a mutant version of RecA with superior catalytic abilities, allowing filament formation without the help of mediator proteins. The mechanism of RecA730 filament formation is not well understood, and the question remains as to whether the RecA730 protein requires ATP binding in order to become competent for filament formation. We examined two mutants, recA730,4159 (presumed to be defective for ATP binding) and recA730,2201 (defective for ATP hydrolysis), and show that they have different properties with respect to SOS induction, conjugational recombination and double-strand break repair. We show that ATP binding is essential for all RecA730 functions, while ATP hydrolysis is required only for double-strand break repair. Our results emphasize the similarity of the SOS response and conjugational recombination, neither of which requires ATP hydrolysis by RecA730.
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Affiliation(s)
- Ana Šimatović
- Laboratory of Evolutionary Genetics, Department of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Petar T Mitrikeski
- Laboratory of Evolutionary Genetics, Department of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Institute for Research and Development of Sustainable Ecosystems, Faculty of Veterinary Medicine, Heinzelova 55, 10000 Zagreb, Croatia.
| | - Ignacija Vlašić
- Laboratory of Evolutionary Genetics, Department of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Mary Sopta
- Laboratory of Evolutionary Genetics, Department of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Krunoslav Brčić-Kostić
- Laboratory of Evolutionary Genetics, Department of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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Rajendram M, Zhang L, Reynolds BJ, Auer GK, Tuson HH, Ngo KV, Cox MM, Yethiraj A, Cui Q, Weibel DB. Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli. Mol Cell 2015; 60:374-84. [PMID: 26481664 DOI: 10.1016/j.molcel.2015.09.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/14/2015] [Accepted: 09/09/2015] [Indexed: 10/22/2022]
Abstract
We characterize the interaction of RecA with membranes in vivo and in vitro and demonstrate that RecA binds tightly to the anionic phospholipids cardiolipin (CL) and phosphatidylglycerol (PG). Using computational models, we identify two regions of RecA that interact with PG and CL: (1) the N-terminal helix and (2) loop L2. Mutating these regions decreased the affinity of RecA to PG and CL in vitro. Using 3D super-resolution microscopy, we demonstrate that depleting Escherichia coli PG and CL altered the localization of RecA foci and hindered the formation of RecA filament bundles. Consequently, E. coli cells lacking aPLs fail to initiate a robust SOS response after DNA damage, indicating that the membrane acts as a scaffold for nucleating the formation of RecA filament bundles and plays an important role in the SOS response.
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Affiliation(s)
- Manohary Rajendram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Leili Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bradley J Reynolds
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - George K Auer
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hannah H Tuson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Khanh V Ngo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Ronayne EA, Cox MM. RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps. Nucleic Acids Res 2013; 42:3871-83. [PMID: 24371286 PMCID: PMC3973344 DOI: 10.1093/nar/gkt1342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The bacteriophage P1 recombination enhancement function (Ref) protein is a RecA-dependent programmable endonuclease. Ref targets displacement loops formed when an oligonucleotide is bound by a RecA filament and invades homologous double-stranded DNA sequences. Mechanistic details of this reaction have been explored, revealing that (i) Ref is nickase, cleaving the two target strands of a displacement loop sequentially, (ii) the two strands are cleaved in a prescribed order, with the paired strand cut first and (iii) the two cleavage events have different requirements. Cutting the paired strand is rapid, does not require RecA-mediated ATP hydrolysis and is promoted even by Ref active site variant H153A. The displaced strand is cleaved much more slowly, requires RecA-mediated ATP hydrolysis and does not occur with Ref H153A. The two cleavage events are also affected differently by solution conditions. We postulate that the second cleavage (displaced strand) is limited by some activity of RecA protein.
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Affiliation(s)
- Erin A Ronayne
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Fagerburg MV, Schauer GD, Thickman KR, Bianco PR, Khan SA, Leuba SH, Anand SP. PcrA-mediated disruption of RecA nucleoprotein filaments--essential role of the ATPase activity of RecA. Nucleic Acids Res 2012; 40:8416-24. [PMID: 22743269 PMCID: PMC3458574 DOI: 10.1093/nar/gks641] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The essential DNA helicase, PcrA, regulates recombination by displacing the recombinase RecA from the DNA. The nucleotide-bound state of RecA determines the stability of its nucleoprotein filaments. Using single-molecule fluorescence approaches, we demonstrate that RecA displacement by a translocating PcrA requires the ATPase activity of the recombinase. We also show that in a ‘head-on collision’ between a polymerizing RecA filament and a translocating PcrA, the RecA K72R ATPase mutant, but not wild-type RecA, arrests helicase translocation. Our findings demonstrate that translocation of PcrA is not sufficient to displace RecA from the DNA and assigns an essential role for the ATPase activity of RecA in helicase-mediated disruption of its filaments.
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Affiliation(s)
- Matt V Fagerburg
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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