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Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [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: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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Hughes-Games A, Roberts AP, Davis SA, Hill DJ. Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects. Microb Genom 2020; 6:e000372. [PMID: 32375974 PMCID: PMC7371117 DOI: 10.1099/mgen.0.000372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023] Open
Abstract
Mobile genetic elements (MGEs) are key factors responsible for dissemination of virulence determinants and antimicrobial-resistance genes amongst pathogenic bacteria. Conjugative MGEs are notable for their high gene loads donated per transfer event, broad host ranges and phylogenetic ubiquity amongst prokaryotes, with the subclass of chromosomally inserted integrative and conjugative elements (ICEs) being particularly abundant. The focus on a small number of model systems has biased the study of ICEs towards those conferring readily selectable phenotypes to host cells, whereas the identification and characterization of integrated cryptic elements remains challenging. Even though antimicrobial resistance and horizontally acquired virulence genes are major factors aggravating neisserial infection, conjugative MGEs of Neisseria gonorrhoeae and Neisseria meningitidis remain poorly characterized. Using a phenotype-independent approach based on atypical distributions of DNA uptake sequences (DUSs) in MGEs relative to the chromosomal background, we have identified two groups of chromosomally integrated conjugative elements in Neisseria: one found almost exclusively in pathogenic species possibly deriving from the genus Kingella, the other belonging to a group of Neisseria mucosa-like commensals. The former element appears to enable transfer of traditionally gonococcal-specific loci such as the virulence-associated toxin-antitoxin system fitAB to N. meningitidis chromosomes, whilst the circular form of the latter possesses a unique attachment site (attP) sequence seemingly adapted to exploit DUS motifs as chromosomal integration sites. In addition to validating the use of DUS distributions in Neisseriaceae MGE identification, the >170 identified ICE sequences provide a valuable resource for future studies of ICE evolution and host adaptation.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Adam P. Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sean A. Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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Briggs GS, Yu J, Mahdi AA, Lloyd RG. The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA. Nucleic Acids Res 2010; 38:6433-46. [PMID: 20525790 PMCID: PMC2965237 DOI: 10.1093/nar/gkq509] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The DNA-binding protein RdgC has been identified as an inhibitor of RecA-mediated homologous recombination in Escherichia coli. In Neisseria species, RdgC also has a role in virulence-associated antigenic variation. We have previously solved the crystal structure of the E. coli RdgC protein and shown it to form a toroidal dimer. In this study, we have conducted a mutational analysis of residues proposed to mediate interactions at the dimer interfaces. We demonstrate that destabilizing either interface has a serious effect on in vivo function, even though a stable complex with circular DNA was still observed. We conclude that tight binding is required for inhibition of RecA activity. We also investigated the role of the RdgC finger domain, and demonstrate that it plays a crucial role in the binding of circular DNA. Together, these data allow us to propose a model for how RdgC loads onto DNA. We discuss how RdgC might inhibit RecA-mediated strand exchange, and how RdgC might be displaced by other DNA metabolism enzymes such as polymerases and helicases.
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Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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Grove JI, Wood SR, Briggs GS, Oldham NJ, Lloyd RG. A soluble RecN homologue provides means for biochemical and genetic analysis of DNA double-strand break repair in Escherichia coli. DNA Repair (Amst) 2009; 8:1434-43. [PMID: 19846353 DOI: 10.1016/j.dnarep.2009.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/30/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
RecN is a highly conserved, SMC-like protein in bacteria. It plays an important role in the repair of DNA double-strand breaks and is therefore a key factor in maintaining genome integrity. The insolubility of Escherichia coli RecN has limited efforts to unravel its function. We overcame this limitation by replacing the resident coding sequence with that of Haemophilus influenzae RecN. The heterologous construct expresses Haemophilus RecN from the SOS-inducible E. coli promoter. The hybrid gene is fully functional, promoting survival after I-SceI induced DNA breakage, gamma irradiation or exposure to mitomycin C as effectively as the native gene, indicating that the repair activity is conserved between these two species. H. influenzae RecN is quite soluble, even when expressed at high levels, and is readily purified. Its analysis by ionisation-mass spectrometry, gel filtration and glutaraldehyde crosslinking indicates that it is probably a dimer under physiological conditions, although a higher multimer cannot be excluded. The purified protein displays a weak ATPase activity that is essential for its DNA repair function in vivo. However, no DNA-binding activity was detected, which contrasts with RecN from Bacillus subtilis. RecN proteins from Aquifex aeolicus and Bacteriodes fragilis also proved soluble. Neither binds DNA, but the Aquifex RecN has weak ATPase activity. Our findings support studies indicating that RecN, and the SOS response in general, behave differently in E. coli and B. subtilis. The hybrid recN reported provides new opportunities to study the genetics and biochemistry of how RecN operates in E. coli.
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Affiliation(s)
- Jane I Grove
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Ha JY, Kim HK, Kim DJ, Kim KH, Oh SJ, Lee HH, Yoon HJ, Song HK, Suh SW. The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding. Nucleic Acids Res 2007; 35:2671-81. [PMID: 17426134 PMCID: PMC1885664 DOI: 10.1093/nar/gkm144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface (‘interface A’) between tip/center domains is more nonpolar than the other (‘interface B’) between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of ∼30 Å diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.
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Affiliation(s)
- Jun Yong Ha
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Hye Kyong Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Do Jin Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Kyoung Hoon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Sung Jin Oh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Hyun Kyu Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea and Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
- *To whom correspondence should be addressed +82-2-880-6653+82-2-889-1568
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Briggs GS, McEwan PA, Yu J, Moore T, Emsley J, Lloyd RG. Ring structure of the Escherichia coli DNA-binding protein RdgC associated with recombination and replication fork repair. J Biol Chem 2007; 282:12353-7. [PMID: 17308310 DOI: 10.1074/jbc.c700023200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA-binding protein, RdgC, is associated with recombination and replication fork repair in Escherichia coli and with the virulence-associated, pilin antigenic variation mediated by RecA and other recombination proteins in Neisseria species. We solved the structure of the E. coli protein and refined it to 2.4A. RdgC crystallizes as a dimer with a head-to-head, tail-to-tail organization forming a ring with a 30 A diameter hole at the center. The protein fold is unique and reminiscent of a horseshoe with twin gates closing the open end. The central hole is lined with positively charged residues and provides a highly plausible DNA binding channel consistent with the nonspecific mode of binding detected in vitro and with the ability of RdgC to modulate RecA function in vivo.
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Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH
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Drees JC, Chitteni-Pattu S, McCaslin DR, Inman RB, Cox MM. Inhibition of RecA protein function by the RdgC protein from Escherichia coli. J Biol Chem 2005; 281:4708-17. [PMID: 16377615 DOI: 10.1074/jbc.m513592200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli RdgC protein is a potential negative regulator of RecA function. RdgC inhibits RecA protein-promoted DNA strand exchange, ATPase activity, and RecA-dependent LexA cleavage. The primary mechanism of RdgC inhibition appears to involve a simple competition for DNA binding sites, especially on duplex DNA. The capacity of RecA to compete with RdgC is improved by the DinI protein. RdgC protein can inhibit DNA strand exchange catalyzed by RecA nucleoprotein filaments formed on single-stranded DNA by binding to the homologous duplex DNA and thereby blocking access to that DNA by the RecA nucleoprotein filaments. RdgC protein binds to single-stranded and double-stranded DNA, and the protein can be visualized on DNA using electron microscopy. RdgC protein exists in solution as a mixture of oligomeric states in equilibrium, most likely as monomers, dimers, and tetramers. This concentration-dependent change of state appears to affect its mode of binding to DNA and its capacity to inhibit RecA. The various species differ in their capacity to inhibit RecA function.
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Affiliation(s)
- Julia C Drees
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, USA
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Tessmer I, Moore T, Lloyd RG, Wilson A, Erie DA, Allen S, Tendler SJB. AFM studies on the role of the protein RdgC in bacterial DNA recombination. J Mol Biol 2005; 350:254-62. [PMID: 15923011 DOI: 10.1016/j.jmb.2005.04.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 04/04/2005] [Accepted: 04/19/2005] [Indexed: 02/03/2023]
Abstract
Genetic studies of rdgC in different bacterial systems suggest that it may play a role in replication and recombination. However, the exact function of the corresponding protein, RdgC, is unknown. In this study, we have imaged complexes of RdgC with both linear and supercoiled circular plasmid DNA using atomic force microscopy. We confirm that RdgC does not target any specific sequences in double-stranded DNA, as has been suggested from biochemical data. However, we detect an increased affinity of the protein to DNA ends, and an ability to promote bending of DNA. Similar binding preferences have been reported for enzymes involved in recombination. Protein complexes with supercoiled plasmid DNA further enabled us to study the effect of RdgC on DNA superstructure. At high concentrations of protein we observed promotion of DNA condensation. Recombination is largely enhanced by close contacts of distant regions along the DNA strands, as can occur, for instance, through condensation. Our data thus support a possible function of RdgC as a midwife of recombination.
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MESH Headings
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Bacterial/ultrastructure
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/ultrastructure
- Microscopy, Atomic Force
- Nucleic Acid Conformation
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Plasmids/ultrastructure
- Protein Structure, Quaternary
- Recombination, Genetic
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Affiliation(s)
- Ingrid Tessmer
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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