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Zakharova K, Liu M, Greenwald JR, Caldwell BC, Qi Z, Wysocki VH, Bell CE. Structural Basis for the Interaction of Redβ Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein. J Mol Biol 2024; 436:168590. [PMID: 38663547 DOI: 10.1016/j.jmb.2024.168590] [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: 02/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
Redβ is a protein from bacteriophage λ that binds to single-stranded DNA (ssDNA) to promote the annealing of complementary strands. Together with λ-exonuclease (λ-exo), Redβ is part of a two-component DNA recombination system involved in multiple aspects of genome maintenance. The proteins have been exploited in powerful methods for bacterial genome engineering in which Redβ can anneal an electroporated oligonucleotide to a complementary target site at the lagging strand of a replication fork. Successful annealing in vivo requires the interaction of Redβ with E. coli single-stranded DNA-binding protein (SSB), which coats the ssDNA at the lagging strand to coordinate access of numerous replication proteins. Previous mutational analysis revealed that the interaction between Redβ and SSB involves the C-terminal domain (CTD) of Redβ and the C-terminal tail of SSB (SSB-Ct), the site for binding of numerous host proteins. Here, we have determined the x-ray crystal structure of Redβ CTD in complex with a peptide corresponding to the last nine residues of SSB (MDFDDDIPF). Formation of the complex is predominantly mediated by hydrophobic interactions between two phenylalanine side chains of SSB (Phe-171 and Phe-177) and an apolar groove on the CTD, combined with electrostatic interactions between the C-terminal carboxylate of SSB and Lys-214 of the CTD. Mutation of any of these residues to alanine significantly disrupts the interaction of full-length Redβ and SSB proteins. Structural knowledge of this interaction will help to expand the utility of Redβ-mediated recombination to a wider range of bacterial hosts for applications in synthetic biology.
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Affiliation(s)
- Katerina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Mengqi Liu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Jacelyn R Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Brian C Caldwell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Zihao Qi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Vicki H Wysocki
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Charles E Bell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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2
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Newing TP, Brewster JL, Fitschen LJ, Bouwer JC, Johnston NP, Yu H, Tolun G. Redβ 177 annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination. Nat Commun 2022; 13:5649. [PMID: 36163171 PMCID: PMC9512822 DOI: 10.1038/s41467-022-33090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
The Redβ protein of the bacteriophage λ red recombination system is a model annealase which catalyzes single-strand annealing homologous DNA recombination. Here we present the structure of a helical oligomeric annealing intermediate of Redβ, consisting of N-terminal residues 1-177 bound to two complementary 27mer oligonucleotides, determined via cryogenic electron microscopy (cryo-EM) to a final resolution of 3.3 Å. The structure reveals a continuous binding groove which positions and stabilizes complementary DNA strands in a planar orientation to facilitate base pairing via a network of hydrogen bonding. Definition of the inter-subunit interface provides a structural basis for the propensity of Redβ to oligomerize into functionally significant long helical filaments, a trait shared by most annealases. Our cryo-EM structure and molecular dynamics simulations suggest that residues 133-138 form a flexible loop which modulates access to the binding groove. More than half a century after its discovery, this combination of structural and computational observations has allowed us to propose molecular mechanisms for the actions of the model annealase Redβ, a defining member of the Redβ/RecT protein family. Redβ annealase catalyses single-strand annealing homologous DNA recombination. Here, the authors present a cryo-EM structure of a Redβ annealing intermediate bound to two complementary 27mer oligonucleotides.
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Affiliation(s)
- Timothy P Newing
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Jodi L Brewster
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia
| | - Lucy J Fitschen
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia
| | - James C Bouwer
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia
| | - Nikolas P Johnston
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Gökhan Tolun
- School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia. .,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia.
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3
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Zakharova K, Caldwell BJ, Ta S, Wheat CT, Bell CE. Mutational Analysis of Redβ Single Strand Annealing Protein: Roles of the 14 Lysine Residues in DNA Binding and Recombination In Vivo. Int J Mol Sci 2021; 22:ijms22147758. [PMID: 34299376 PMCID: PMC8303780 DOI: 10.3390/ijms22147758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 01/05/2023] Open
Abstract
Redβ is a 261 amino acid protein from bacteriophage λ that promotes a single-strand annealing (SSA) reaction for repair of double-stranded DNA (dsDNA) breaks. While there is currently no high-resolution structure available for Redβ, models of its DNA binding domain (residues 1-188) have been proposed based on homology with human Rad52, and a crystal structure of its C-terminal domain (CTD, residues 193-261), which binds to λ exonuclease and E. coli single-stranded DNA binding protein (SSB), has been determined. To evaluate these models, the 14 lysine residues of Redβ were mutated to alanine, and the variants tested for recombination in vivo and DNA binding and annealing in vitro. Most of the lysines within the DNA binding domain, including K36, K61, K111, K132, K148, K154, and K172, were found to be critical for DNA binding in vitro and recombination in vivo. By contrast, none of the lysines within the CTD, including K214, K245, K251, K253, and K258 were required for DNA binding in vitro, but two, K214 and K253, were critical for recombination in vivo, likely due to their involvement in binding to SSB. K61 was identified as a residue that is critical for DNA annealing, but not for initial ssDNA binding, suggesting a role in binding to the second strand of DNA incorporated into the complex. The K148A variant, which has previously been shown to be defective in oligomer formation, had the lowest affinity for ssDNA, and was the only variant that was completely non-cooperative, suggesting that ssDNA binding is coupled to oligomerization.
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Affiliation(s)
- Katerina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; (K.Z.); (B.J.C.); (S.T.); (C.T.W.)
| | - Brian J. Caldwell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; (K.Z.); (B.J.C.); (S.T.); (C.T.W.)
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Shalya Ta
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; (K.Z.); (B.J.C.); (S.T.); (C.T.W.)
| | - Carter T. Wheat
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; (K.Z.); (B.J.C.); (S.T.); (C.T.W.)
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E. Bell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; (K.Z.); (B.J.C.); (S.T.); (C.T.W.)
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
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4
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Caldwell BJ, Norris A, Zakharova E, Smith CE, Wheat CT, Choudhary D, Sotomayor M, Wysocki VH, Bell CE. Oligomeric complexes formed by Redβ single strand annealing protein in its different DNA bound states. Nucleic Acids Res 2021; 49:3441-3460. [PMID: 33693865 PMCID: PMC8034648 DOI: 10.1093/nar/gkab125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Redβ is a single strand annealing protein from bacteriophage λ that binds loosely to ssDNA, not at all to pre-formed dsDNA, but tightly to a duplex intermediate of annealing. As viewed by electron microscopy, Redβ forms oligomeric rings on ssDNA substrate, and helical filaments on the annealed duplex intermediate. However, it is not clear if these are the functional forms of the protein in vivo. We have used size-exclusion chromatography coupled with multi-angle light scattering, analytical ultracentrifugation and native mass spectrometry (nMS) to characterize the size of the oligomers formed by Redβ in its different DNA-bound states. The nMS data, which resolve species with the highest resolution, reveal that Redβ forms an oligomer of 12 subunits in the absence of DNA, complexes ranging from 4 to 14 subunits on 38-mer ssDNA, and a much more distinct and stable complex of 11 subunits on 38-mer annealed duplex. We also measure the concentration of Redβ in cells active for recombination and find it to range from 7 to 27 μM. Collectively, these data provide new insights into the dynamic nature of the complex on ssDNA, and the more stable and defined complex on annealed duplex.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ekaterina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Christopher E Smith
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Carter T Wheat
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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5
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A simple and rapid pipeline for identification of receptor-binding sites on the surface proteins of pathogens. Sci Rep 2020; 10:1163. [PMID: 31980725 PMCID: PMC6981161 DOI: 10.1038/s41598-020-58305-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Ligand-receptor interactions play a crucial role in the plethora of biological processes. Several methods have been established to reveal ligand-receptor interface, however, the majority of methods are time-consuming, laborious and expensive. Here we present a straightforward and simple pipeline to identify putative receptor-binding sites on the pathogen ligands. Two model ligands (bait proteins), domain III of protein E of West Nile virus and NadA of Neisseria meningitidis, were incubated with the proteins of human brain microvascular endothelial cells immobilized on nitrocellulose or PVDF membrane, the complex was trypsinized on-membrane, bound peptides of the bait proteins were recovered and detected on MALDI-TOF. Two peptides of DIII (~916 Da and ~2003 Da) and four peptides of NadA (~1453 Da, ~1810 Da, ~2051 Da and ~2433 Da) were identified as plausible receptor-binders. Further, binding of the identified peptides to the proteins of endothelial cells was corroborated using biotinylated synthetic analogues in ELISA and immunocytochemistry. Experimental pipeline presented here can be upscaled easily to map receptor-binding sites on several ligands simultaneously. The approach is rapid, cost-effective and less laborious. The proposed experimental pipeline could be a simpler alternative or complementary method to the existing techniques used to reveal amino-acids involved in the ligand-receptor interface.
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6
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Caldwell BJ, Bell CE. Structure and mechanism of the Red recombination system of bacteriophage λ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:33-46. [PMID: 30904699 DOI: 10.1016/j.pbiomolbio.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA; Department of Chemistry and Biochemistry, 484 West 12th Avenue, 1060 Carmack Road, Columbus, OH, 43210, USA.
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7
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Caldwell BJ, Zakharova E, Filsinger GT, Wannier TM, Hempfling JP, Chun-Der L, Pei D, Church GM, Bell CE. Crystal structure of the Redβ C-terminal domain in complex with λ Exonuclease reveals an unexpected homology with λ Orf and an interaction with Escherichia coli single stranded DNA binding protein. Nucleic Acids Res 2019; 47:1950-1963. [PMID: 30624736 PMCID: PMC6393309 DOI: 10.1093/nar/gky1309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 02/06/2023] Open
Abstract
Bacteriophage λ encodes a DNA recombination system that includes a 5'-3' exonuclease (λ Exo) and a single strand annealing protein (Redβ). The two proteins form a complex that is thought to mediate loading of Redβ directly onto the single-stranded 3'-overhang generated by λ Exo. Here, we present a 2.3 Å crystal structure of the λ Exo trimer bound to three copies of the Redβ C-terminal domain (CTD). Mutation of residues at the hydrophobic core of the interface disrupts complex formation in vitro and impairs recombination in vivo. The Redβ CTD forms a three-helix bundle with unexpected structural homology to phage λ Orf, a protein that binds to E. coli single-stranded DNA binding protein (SSB) to function as a recombination mediator. Based on this relationship, we found that Redβ binds to full-length SSB, and to a peptide corresponding to its nine C-terminal residues, in an interaction that requires the CTD. These results suggest a dual role of the CTD, first in binding to λ Exo to facilitate loading of Redβ directly onto the initial single-stranded DNA (ssDNA) at a 3'-overhang, and second in binding to SSB to facilitate annealing of the overhang to SSB-coated ssDNA at the replication fork.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
| | - Ekaterina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
| | - Gabriel T Filsinger
- Department of Systems Biology, Harvard Medical School, Cambridge, MA 02138, USA
| | - Timothy M Wannier
- Department of Genetics, Harvard Medical School, Cambridge, MA 02138, USA
| | - Jordan P Hempfling
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Lee Chun-Der
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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8
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Subramaniam S, Erler A, Fu J, Kranz A, Tang J, Gopalswamy M, Ramakrishnan S, Keller A, Grundmeier G, Müller D, Sattler M, Stewart AF. DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions. Sci Rep 2016; 6:34525. [PMID: 27708411 PMCID: PMC5052646 DOI: 10.1038/srep34525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/15/2016] [Indexed: 01/09/2023] Open
Abstract
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. Mutations of the C-terminal domain were evaluated using both single- and double stranded (ss and ds) substrates in recombination assays. Mutations of critical amino acids affected either dsDNA recombination or both ssDNA and dsDNA recombination indicating two separable functions, one of which is critical for dsDNA recombination and the second for recombination per se. As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. Because the nucleoprotein filament formed with C-terminally truncated Redβ has altered properties, the second C-terminal function could be due to an interaction required for functional filaments. Alternatively the second C-terminal function could indicate a requirement for a Redβ-host factor interaction. These data further advance the model for Red recombination and the proposition that Redβ and RAD52 SSAPs share ancestral and mechanistic roots.
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Affiliation(s)
| | - Axel Erler
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Andrea Kranz
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jing Tang
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mohanraj Gopalswamy
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Daniel Müller
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstraße 26, 4058 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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9
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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10
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Smith CE, Bell CE. Domain Structure of the Redβ Single-Strand Annealing Protein: the C-terminal Domain is Required for Fine-Tuning DNA-binding Properties, Interaction with the Exonuclease Partner, and Recombination in vivo. J Mol Biol 2016; 428:561-578. [PMID: 26780547 DOI: 10.1016/j.jmb.2016.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/19/2015] [Accepted: 01/12/2016] [Indexed: 11/28/2022]
Abstract
Redβ is a component of the Red recombination system of bacteriophage λ that promotes a single strand annealing (SSA) reaction to generate end-to-end concatemers of the phage genome for packaging. Redβ interacts with λ exonuclease (λexo), the other component of the Red system, to form a "synaptosome" complex that somehow integrates the end resection and annealing steps of the reaction. Previous work using limited proteolysis and chemical modification revealed that Redβ consists of an N-terminal DNA binding domain, residues 1-177, and a flexible C-terminal "tail", residues 178-261. Here, we quantitatively compare the binding of the full-length protein (Redβ(FL)) and the N-terminal domain (Redβ(177)) to different lengths of ssDNA substrate and annealed duplex product. We find that in general, Redβ(FL) binds more tightly to annealed duplex product than to ssDNA substrate, while Redβ(177) binds more tightly to ssDNA. In addition, the C-terminal region of Redβ corresponding to residues 182-261 was purified and found to fold into an α-helical domain that is required for the interaction with λexo to form the synaptosome complex. Deletion analysis of Redβ revealed that removal of just eleven residues from the C-terminus disrupts the interaction with λexo as well as ssDNA and dsDNA recombination in vivo. By contrast, the determinants for self-oligomerization of Redβ appear to reside solely within the N-terminal domain. The subtle but significant differences in the relative binding of Redβ(FL) and Redβ(177) to ssDNA substrate and annealed duplex product may be important for Redβ to function as a SSA protein in vivo.
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Affiliation(s)
- Christopher E Smith
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210.
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11
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Matsubara K, Malay AD, Curtis FA, Sharples GJ, Heddle JG. Structural and functional characterization of the Redβ recombinase from bacteriophage λ. PLoS One 2013; 8:e78869. [PMID: 24244379 PMCID: PMC3823998 DOI: 10.1371/journal.pone.0078869] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022] Open
Abstract
The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure.
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Affiliation(s)
| | - Ali D. Malay
- Heddle Initiative Research Unit, RIKEN, Wako, Saitama, Japan
| | - Fiona A. Curtis
- School of Biological and Biomedical Sciences, Department of Chemistry, Durham University, Durham, United Kingdom
| | - Gary J. Sharples
- School of Biological and Biomedical Sciences, Department of Chemistry, Durham University, Durham, United Kingdom
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Abstract
The homologous recombination systems of linear double-stranded (ds)DNA bacteriophages are required for the generation of genetic diversity, the repair of dsDNA breaks, and the formation of concatemeric chromosomes, the immediate precursor to packaging. These systems have been studied for decades as a means to understand the basic principles of homologous recombination. From the beginning, it was recognized that these recombinases are linked intimately to the mechanisms of phage DNA replication. In the last decade, however, investigators have exploited these recombination systems as tools for genetic engineering of bacterial chromosomes, bacterial artificial chromosomes, and plasmids. This recombinational engineering technology has been termed "recombineering" and offers a new paradigm for the genetic manipulation of bacterial chromosomes, which is far more efficient than the classical use of nonreplicating integration vectors for gene replacement. The phage λ Red recombination system, in particular, has been used to construct gene replacements, deletions, insertions, inversions, duplications, and single base pair changes in the Escherichia coli chromosome. This chapter discusses the components of the recombination systems of λ, rac prophage, and phage P22 and properties of single-stranded DNA annealing proteins from these and other phage that have been instrumental for the development of this technology. The types of genetic manipulations that can be made are described, along with proposed mechanisms for both double-stranded DNA- and oligonucleotide-mediated recombineering events. Finally, the impact of this technology to such diverse fields as bacterial pathogenesis, metabolic engineering, and mouse genomics is discussed.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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13
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Viral bacterial artificial chromosomes: generation, mutagenesis, and removal of mini-F sequences. J Biomed Biotechnol 2012; 2012:472537. [PMID: 22496607 PMCID: PMC3303620 DOI: 10.1155/2012/472537] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/21/2011] [Accepted: 10/27/2011] [Indexed: 12/29/2022] Open
Abstract
Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.
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Bird AW, Erler A, Fu J, Hériché JK, Maresca M, Zhang Y, Hyman AA, Stewart AF. High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes. Nat Methods 2011; 9:103-9. [PMID: 22138824 DOI: 10.1038/nmeth.1803] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 10/19/2011] [Indexed: 01/08/2023]
Abstract
Whereas bacterial artificial chromosomes (BACs) offer many advantages in studies of gene and protein function, generation of seamless, precisely mutated BACs has been difficult. Here we describe a counterselection-based recombineering method and its accompanying reagents. After identifying intramolecular recombination as the major problem in counterselection, we built a strategy to reduce these unwanted events by expressing Redβ alone at the crucial step. We enhanced this method by using phosphothioated oligonucleotides, using a sequence-altered rpsL counterselection gene and developing online software for oligonucleotide design. We illustrated this method by generating transgenic mammalian cell lines carrying small interfering RNA-resistant and point-mutated BAC transgenes. Using this approach, we generated mutated TACC3 transgenes to identify phosphorylation-specific spindle defects after knockdown of endogenous TACC3 expression. Our results highlight the complementary use of precisely mutated BAC transgenes and RNA interference in the study of cell biology at physiological expression levels and regulation.
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Affiliation(s)
- Alexander W Bird
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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15
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Tischer BK, Smith GA, Osterrieder N. En passant mutagenesis: a two step markerless red recombination system. Methods Mol Biol 2010; 634:421-30. [PMID: 20677001 DOI: 10.1007/978-1-60761-652-8_30] [Citation(s) in RCA: 445] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial artificial chromosomes are used to maintain and modify large sequences of different origins in Escherichia coli. In addition to RecA-based shuttle mutagenesis, Red recombination is commonly used for sequence modification. Since foreign sequences, such as antibiotic resistance genes as well as frt- or loxP-sites are often unwanted in mutant BAC clones, we developed a Red-based technique that allows for the scarless generation of point mutations, deletions, and insertion of smaller and larger sequences. The method employs a sequence duplication that is inserted into the target sequence in the first recombination step and the excision of the selection marker by in vivo I-SceI cleavage and the second Red recombination. To allow for convenient and highly efficient mutagenesis without the use of additional plasmids, the E. coli strain GS1783 with a chromosomal encoded inducible Red- and I-SceI-expression was created.
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Maresca M, Erler A, Fu J, Friedrich A, Zhang Y, Stewart AF. Single-stranded heteroduplex intermediates in lambda Red homologous recombination. BMC Mol Biol 2010; 11:54. [PMID: 20670401 PMCID: PMC2918612 DOI: 10.1186/1471-2199-11-54] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/29/2010] [Indexed: 11/28/2022] Open
Abstract
Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Redα exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed 'beta' recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i) an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii) the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s) appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.
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Affiliation(s)
- Marcello Maresca
- Technische Universität Dresden, BioInnovationsZentrum, Dresden, Germany
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Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, Seidel R, Habermann B, Muller DJ, Stewart AF. Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52. J Mol Biol 2009; 391:586-98. [PMID: 19527729 DOI: 10.1016/j.jmb.2009.06.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 06/09/2009] [Accepted: 06/10/2009] [Indexed: 11/26/2022]
Abstract
Single-strand annealing proteins, such as Redbeta from lambda phage or eukaryotic Rad52, play roles in homologous recombination. Here, we use atomic force microscopy to examine Redbeta quaternary structure and Redbeta-DNA complexes. In the absence of DNA, Redbeta forms a shallow right-handed helix. The presence of single-stranded DNA (ssDNA) disrupts this structure. Upon addition of a second complementary ssDNA, annealing generates a left-handed helix that incorporates 14 Redbeta monomers per helical turn, with each Redbeta monomer annealing approximately 11 bp of DNA. The smallest stable annealing intermediate requires 20 bp DNA and two Redbeta monomers. Hence, we propose that Redbeta promotes base pairing by first increasing the number of transient interactions between ssDNAs. Then, annealing is promoted by the binding of a second Redbeta monomer, which nucleates the formation of a stable annealing intermediate. Using threading, we identify sequence similarities between the RecT/Redbeta and the Rad52 families, which strengthens previous suggestions, based on similarities of their quaternary structures, that they share a common mode of action. Hence, our findings have implications for a common mechanism of DNA annealing mediated by single-strand annealing proteins including Rad52.
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Affiliation(s)
- Axel Erler
- Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
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