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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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Sandler SJ, Bonde NJ, Wood EA, Cox MM, Keck JL. The intrinsically disordered linker in the single-stranded DNA-binding protein influences DNA replication restart and recombination pathways in Escherichia coli K-12. J Bacteriol 2024; 206:e0033023. [PMID: 38470036 PMCID: PMC11025327 DOI: 10.1128/jb.00330-23] [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: 10/05/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Tetrameric single-stranded (ss) DNA-binding proteins (SSBs) stabilize ssDNA intermediates formed during genome maintenance reactions in Bacteria. SSBs also recruit proteins important for these processes through direct SSB-protein interactions, including proteins involved in DNA replication restart and recombination processes. SSBs are composed of an N-terminal oligomerization and ssDNA-binding domain, a C-terminal acidic tip that mediates SSB-protein interactions, and an internal intrinsically disordered linker (IDL). Deletions and insertions into the IDL are well tolerated with few phenotypes, although the largest deletions and insertions exhibit some sensitivity to DNA-damaging agents. To define specific DNA metabolism processes dependent on IDL length, ssb mutants that lack 16, 26, 37, or 47 residues of the 57-residue IDL were tested for synthetic phenotypes with mutations in DNA replication restart or recombination genes. We also tested the impact of integrating a fluorescent domain within the SSB IDL using an ssb::mTur2 insertion mutation. Only the largest deletion tested or the insertion mutation causes sensitivity in any of the pathways. Mutations in two replication restart pathways (PriA-B1 and PriA-C) showed synthetic lethalities or small colony phenotypes with the largest deletion or insertion mutations. Recombination gene mutations del(recBCD) and del(ruvABC) show synthetic phenotypes only when combined with the largest ssb deletion. These results suggest that a minimum IDL length is important in some genome maintenance reactions in Escherichia coli. These include pathways involving PriA-PriB1, PriA-PriC, RecFOR, and RecG. The mTur2 insertion in the IDL may also affect SSB interactions in some processes, particularly the PriA-PriB1 and PriA-PriC replication restart pathways.IMPORTANCEssb is essential in Escherichia coli due to its roles in protecting ssDNA and coordinating genome maintenance events. While the DNA-binding core and acidic tip have well-characterized functions, the purpose of the intrinsically disordered linker (IDL) is poorly understood. In vitro studies have revealed that the IDL is important for cooperative ssDNA binding and phase separation. However, single-stranded (ss) DNA-binding protein (SSB) variants with large deletions and insertions in the IDL support normal cell growth. We find that the PriA-PriB1 and PriA-C replication restart, as well as the RecFOR- and RecG-dependent recombination, pathways are sensitive to IDL length. This suggests that cooperativity, phase separation, or a longer spacer between the core and acidic tip of SSB may be important for specific cellular functions.
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Affiliation(s)
- Steven J. Sandler
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, Massachusetts, USA
| | - Nina J. Bonde
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
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3
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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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4
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Morse M, Navarro Roby F, Kinare M, McIsaac J, Williams MC, Beuning PJ. DNA damage alters binding conformations of E. coli single-stranded DNA-binding protein. Biophys J 2023; 122:3950-3958. [PMID: 37632138 PMCID: PMC10560665 DOI: 10.1016/j.bpj.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/02/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are essential cellular components, binding to transiently exposed regions of single-stranded DNA (ssDNA) with high affinity and sequence non-specificity to coordinate DNA repair and replication. Escherichia coli SSB (EcSSB) is a homotetramer that wraps variable lengths of ssDNA in multiple conformations (typically occupying either 65 or 35 nt), which is well studied across experimental conditions of substrate length, salt, pH, temperature, etc. In this work, we use atomic force microscopy to investigate the binding of SSB to individual ssDNA molecules. We introduce non-canonical DNA bases that mimic naturally occurring DNA damage, synthetic abasic sites, as well as a non-DNA linker into our experimental constructs at sites predicted to interact with EcSSB. By measuring the fraction of DNA molecules with EcSSB bound as well as the volume of protein bound per DNA molecule, we determine the protein binding affinity, cooperativity, and conformation. We find that, with only one damaged nucleotide, the binding of EcSSB is unchanged relative to its binding to undamaged DNA. In the presence of either two tandem abasic sites or a non-DNA spacer, however, the binding affinity associated with a single EcSSB tetramer occupying the full substrate in the 65-nt mode is greatly reduced. In contrast, the binding of two EcSSB tetramers, each in the 35-nt mode, is preserved. Changes in the binding and cooperative behaviors of EcSSB across these constructs can inform how genomic repair and replication processes may change as environmental damage accumulates in DNA.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Francesco Navarro Roby
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Mansi Kinare
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - James McIsaac
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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5
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Perumal SK. A real-time fluorescent gp32 probe-based assay for monitoring single-stranded DNA-dependent DNA processing enzymes. Biochem Biophys Rep 2023; 35:101518. [PMID: 37534323 PMCID: PMC10391720 DOI: 10.1016/j.bbrep.2023.101518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
Single-stranded DNA (ssDNA) generated during DNA replication, recombination and damage repair reactions is an important intermediate and ssDNA-binding proteins that binds these intermediates coordinate various DNA metabolic processes. Mechanistic details of these ssDNA-dependent processes can be explored by monitoring the generation and consumption of ssDNA in real time. In this work, a fluorescein-labeled gp32-based sensor was employed to continuously monitor various aspects of ssDNA-dependent DNA replication and recombination processes in real time. The gp32 protein probe displayed high sensitivity and specificity to a variety of ssDNA-dependent processes of T4 phage. Several applications of the probe are illustrated here: the solution dynamics of ssDNA-binding protein, protein-protein and protein-DNA interactions involving gp32 protein and its mode of interaction, ssDNA translocation and protein displacement activities of helicases, primer extension activity of DNA polymerase holoenzyme and nucleoprotein filament formation during DNA recombination. The assay has identified new protein-protein interactions of gp32 during T4 replication and recombination. The fluorescent probe described here can thus be used as a universal probe for monitoring in real time various ssDNA-dependent processes, which is based on a well-characterized and easy-to-express bacteriophage T4 gene 32 protein, gp32.
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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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7
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Islam F, Purkait D, Mishra PP. Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective. J Phys Chem B 2023; 127:4351-4363. [PMID: 37163679 DOI: 10.1021/acs.jpcb.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase-DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.
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Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Debayan Purkait
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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8
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Bonde NJ, Henry C, Wood EA, Cox MM, Keck J. Interaction with the carboxy-terminal tip of SSB is critical for RecG function in E. coli. Nucleic Acids Res 2023; 51:3735-3753. [PMID: 36912097 PMCID: PMC10164576 DOI: 10.1093/nar/gkad162] [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: 12/21/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
In Escherichia coli, the single-stranded DNA-binding protein (SSB) acts as a genome maintenance organizational hub by interacting with multiple DNA metabolism proteins. Many SSB-interacting proteins (SIPs) form complexes with SSB by docking onto its carboxy-terminal tip (SSB-Ct). An alternative interaction mode in which SIPs bind to PxxP motifs within an intrinsically-disordered linker (IDL) in SSB has been proposed for the RecG DNA helicase and other SIPs. Here, RecG binding to SSB and SSB peptides was measured in vitro and the RecG/SSB interface was identified. The results show that RecG binds directly and specifically to the SSB-Ct, and not the IDL, through an evolutionarily conserved binding site in the RecG helicase domain. Mutations that block RecG binding to SSB sensitize E. coli to DNA damaging agents and induce the SOS DNA-damage response, indicating formation of the RecG/SSB complex is important in vivo. The broader role of the SSB IDL is also investigated. E. coli ssb mutant strains encoding SSB IDL deletion variants lacking all PxxP motifs retain wildtype growth and DNA repair properties, demonstrating that the SSB PxxP motifs are not major contributors to SSB cellular functions.
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Affiliation(s)
- Nina J Bonde
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elizabeth A Wood
- 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
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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9
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Osorio Garcia MA, Wood EA, Keck JL, Cox MM. Interaction with single-stranded DNA-binding protein (SSB) modulates Escherichia coli RadD DNA repair activities. J Biol Chem 2023; 299:104773. [PMID: 37142225 DOI: 10.1016/j.jbc.2023.104773] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
The bacterial RadD enzyme is important for multiple genome maintenance pathways, including RecA DNA strand exchange and RecA-independent suppression of DNA crossover template switching. However, much remains unknown about the precise roles of RadD. One potential clue into RadD mechanisms is its direct interaction with the single-stranded DNA binding protein (SSB), which coats single-stranded DNA exposed during genome maintenance reactions in cells. Interaction with SSB stimulates the ATPase activity of RadD. To probe the mechanism and importance of RadD:SSB complex formation, we identified a pocket on RadD that is essential for binding SSB. In a mechanism shared with many other SSB-interacting proteins, RadD uses a hydrophobic pocket framed by basic residues to bind the C-terminal end of SSB. We found that RadD variants that substitute acidic residues for basic residues in the SSB binding site impair RadD:SSB complex formation and eliminate SSB stimulation of RadD ATPase activity in vitro. Additionally, mutant E. coli strains carrying charge reversal radD changes display increased sensitivity to DNA damaging agents synergistically with deletions of radA and recG, although the phenotypes of the SSB-binding radD mutants are not as severe as a full radD deletion. This suggests that cellular RadD requires an intact the interaction with SSB for full RadD function.
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Affiliation(s)
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA.
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706.
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10
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Tököli A, Bodnár B, Bogár F, Paragi G, Hetényi A, Bartus É, Wéber E, Hegedüs Z, Szabó Z, Kecskeméti G, Szakonyi G, Martinek TA. Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design. Pharmaceutics 2023; 15:pharmaceutics15041032. [PMID: 37111518 PMCID: PMC10143822 DOI: 10.3390/pharmaceutics15041032] [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: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g., ExoI and RecO) is essential for designing high-affinity SSB mimetic inhibitors. Molecular dynamics simulations revealed the transient interactions of SSB-Ct with two hot spots on ExoI and RecO. The residual flexibility of the peptide-protein complexes allows adaptive molecular recognition. Scanning with non-canonical amino acids revealed that modifications at both termini of SSB-Ct could increase the affinity, supporting the two-hot-spot binding model. Combining unnatural amino acid substitutions on both segments of the peptide resulted in enthalpy-enhanced affinity, accompanied by enthalpy-entropy compensation, as determined by isothermal calorimetry. NMR data and molecular modeling confirmed the reduced flexibility of the improved affinity complexes. Our results highlight that the SSB-Ct mimetics bind to the DNA metabolizing targets through the hot spots, interacting with both of segments of the ligands.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Brigitta Bodnár
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Ferenc Bogár
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Gábor Paragi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- Institute of Physics, University of Pécs, H7624 Pécs, Hungary
- Department of Theoretical Physics, University of Szeged, H6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Zoltán Szabó
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gábor Kecskeméti
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged, H6720 Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
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11
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Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli. Int J Mol Sci 2023; 24:ijms24010741. [PMID: 36614183 PMCID: PMC9821108 DOI: 10.3390/ijms24010741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most perilous and harmful type of DNA damage and can cause tumorigenesis or cell death if left repaired with an error or unrepaired. RadD, a member of the SF2 family, is a recently discovered DNA repair protein involved in the repair of DSBs after radiation or chemical damage. However, the function of RadD in DNA repair remains unclear. Here, we determined the crystal structures of RadD/ATPγS and RadD/ATP complexes and revealed the novel mechanism of RadD binding to DNA and ATP hydrolysis with biochemical data. In the RadD catalytic center, the Gly34 and Gly36 on the P-loop are key residues for ATP binding besides the conserved amino acids Lys37 and Arg343 in the SF2 family. If any of them mutate, then RadD loses ATPase activity. Asp117 polarizes the attacking water molecule, which then starts a nucleophilic reaction toward γ-phosphate, forming the transition state. Lys68 acts as a pocket switch to regulate substrate entry and product release. We revealed that the C-terminal peptide of single-stranded DNA-binding protein (SSB) binds the RadD C-terminal domain (CTD) and promotes the RadD ATPase activity. Our mutagenesis studies confirmed that the residues Arg428 on the zinc finger domain (ZFD) and Lys488 on the CTD of RadD are the key sites for binding branched DNA. Using the Coot software combined with molecular docking, we propose a RadD-binding DNA model for the DNA damage repair process.
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12
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Newcomb ESP, Douma LG, Morris LA, Bloom LB. The Escherichia coli clamp loader rapidly remodels SSB on DNA to load clamps. Nucleic Acids Res 2022; 50:12872-12884. [PMID: 36511874 PMCID: PMC9825162 DOI: 10.1093/nar/gkac1169] [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: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Single-stranded DNA binding proteins (SSBs) avidly bind ssDNA and yet enzymes that need to act during DNA replication and repair are not generally impeded by SSB, and are often stimulated by SSB. Here, the effects of Escherichia coli SSB on the activities of the DNA polymerase processivity clamp loader were investigated. SSB enhances binding of the clamp loader to DNA by increasing the lifetime on DNA. Clamp loading was measured on DNA substrates that differed in length of ssDNA overhangs to permit SSB binding in different binding modes. Even though SSB binds DNA adjacent to single-stranded/double-stranded DNA junctions where clamps are loaded, the rate of clamp loading on DNA was not affected by SSB on any of the DNA substrates. Direct measurements of the relative timing of DNA-SSB remodeling and enzyme-DNA binding showed that the clamp loader rapidly remodels SSB on DNA such that SSB has little effect on DNA binding rates. However, when SSB was mutated to reduce protein-protein interactions with the clamp loader, clamp loading was inhibited by impeding binding of the clamp loader to DNA. Thus, protein-protein interactions between the clamp loader and SSB facilitate rapid DNA-SSB remodeling to allow rapid clamp loader-DNA binding and clamp loading.
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Affiliation(s)
- Elijah S P Newcomb
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Leslie A Morris
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Linda B Bloom
- To whom correspondence should be addressed. Tel: +1 352 294 8379; Fax: +1 352 392 2953;
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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
- * E-mail: (LL); (VP)
| | - 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
- * E-mail: (LL); (VP)
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14
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De Falco M, Porritiello A, Rota F, Scognamiglio V, Antonacci A, del Monaco G, De Felice M. The Finely Coordinated Action of SSB and NurA/HerA Complex Strictly Regulates the DNA End Resection Process in Saccharolobus solfataricus. Int J Mol Sci 2022; 23:ijms23052582. [PMID: 35269725 PMCID: PMC8910471 DOI: 10.3390/ijms23052582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
Generation of the 3' overhang is a critical step during homologous recombination (HR) and replication fork rescue processes. This event is usually performed by a series of DNA nucleases and/or helicases. The nuclease NurA and the ATPase HerA, together with the highly conserved MRE11/RAD50 proteins, play an important role in generating 3' single-stranded DNA during archaeal HR. Little is known, however, about HerA-NurA function and activation of this fundamental and complicated DNA repair process. Herein, we analyze the functional relationship among NurA, HerA and the single-strand binding protein SSB from Saccharolubus solfataricus. We demonstrate that SSB clearly inhibits NurA endonuclease activity and its exonuclease activities also when in combination with HerA. Moreover, we show that SSB binding to DNA is greatly stimulated by the presence of either NurA or NurA/HerA. In addition, if on the one hand NurA binding is not influenced, on the other hand, HerA binding is reduced when SSB is present in the reaction. In accordance with what has been observed, we have shown that HerA helicase activity is not stimulated by SSB. These data suggest that, in archaea, the DNA end resection process is governed by the strictly combined action of NurA, HerA and SSB.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
- Correspondence: (M.D.F.); (M.D.F.)
| | - Alessandra Porritiello
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Federica Rota
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Viviana Scognamiglio
- Department of Chemical Sciences and Materials Technologies, Institute of Crystallography, National Research Council, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (V.S.); (A.A.)
| | - Amina Antonacci
- Department of Chemical Sciences and Materials Technologies, Institute of Crystallography, National Research Council, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (V.S.); (A.A.)
| | - Giovanni del Monaco
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
| | - Mariarita De Felice
- Institute of Biosciences and BioResources, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (A.P.); (F.R.); (G.d.M.)
- Correspondence: (M.D.F.); (M.D.F.)
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15
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Sacquin-Mora S, Prévost C. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules 2021; 11:1529. [PMID: 34680162 PMCID: PMC8533853 DOI: 10.3390/biom11101529] [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: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.
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Affiliation(s)
- Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
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16
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Bianco PR. The mechanism of action of the SSB interactome reveals it is the first OB-fold family of genome guardians in prokaryotes. Protein Sci 2021; 30:1757-1775. [PMID: 34089559 PMCID: PMC8376408 DOI: 10.1002/pro.4140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/28/2022]
Abstract
The single-stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism in bacteria. This protein performs two distinct, but closely intertwined and indispensable functions in the cell. SSB binds to single-stranded DNA (ssDNA) and at least 20 partner proteins resulting in their regulation. These partners comprise a family of genome guardians known as the SSB interactome. Essential to interactome regulation is the linker/OB-fold network of interactions. This network of interactions forms when one or more PXXP motifs in the linker of SSB bind to an OB-fold in a partner, with interactome members involved in competitive binding between the linker and ssDNA to their OB-fold. Consequently, when linker-binding occurs to an OB-fold in an interactome partner, proteins are loaded onto the DNA. When linker/OB-fold interactions occur between SSB tetramers, cooperative ssDNA-binding results, producing a multi-tetrameric complex that rapidly protects the ssDNA. Within this SSB-ssDNA complex, there is an extensive and dynamic network of linker/OB-fold interactions that involves multiple tetramers bound contiguously along the ssDNA lattice. The dynamic behavior of these tetramers which includes binding mode changes, sliding as well as DNA wrapping/unwrapping events, are likely coupled to the formation and disruption of linker/OB-fold interactions. This behavior is essential to facilitating downstream DNA processing events. As OB-folds are critical to the essence of the linker/OB-fold network of interactions, and they are found in multiple interactome partners, the SSB interactome is classified as the first family of prokaryotic, oligosaccharide/oligonucleotide binding fold (OB-fold) genome guardians.
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MESH Headings
- Amino Acid Motifs
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding, Competitive
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Gene Regulatory Networks
- Genome, Bacterial
- Klebsiella pneumoniae/chemistry
- Klebsiella pneumoniae/genetics
- Klebsiella pneumoniae/metabolism
- Models, Molecular
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Oligosaccharides/chemistry
- Oligosaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Interaction Mapping
- Protein Multimerization
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Affiliation(s)
- Piero R. Bianco
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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17
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Magnetic Tweezers-Based Single-Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase. Methods Mol Biol 2021; 2281:93-115. [PMID: 33847954 DOI: 10.1007/978-1-0716-1290-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ability of magnetic tweezers to apply forces and measure molecular displacements has resulted in its extensive use to study the activity of enzymes involved in various aspects of nucleic acid metabolism. These studies have led to the discovery of key aspects of protein-protein and protein-nucleic acid interaction, uncovering dynamic heterogeneities that are lost to ensemble averaging in bulk experiments. The versatility of magnetic tweezers lies in the possibility and ease of tracking multiple parallel single-molecule events to yield statistically relevant single-molecule data. Moreover, they allow tracking both fast millisecond dynamics and slow processes (spanning several hours). In this chapter, we present the protocols used to study the interaction between E. coli SSB, single-stranded DNA (ssDNA), and E. coli RecQ helicase using magnetic tweezers. In particular, we propose constant force and force modulation assays to investigate SSB binding to DNA, as well as to characterize various facets of RecQ helicase activity stimulation by SSB.
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18
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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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19
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Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res 2020; 48:8445-8460. [PMID: 32644157 PMCID: PMC7470958 DOI: 10.1093/nar/gkaa579] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/31/2023] Open
Abstract
DNA lesions or other barriers frequently compromise replisome progress. The SF2 helicase RecG is a key enzyme in the processing of postreplication gaps or regressed forks in Escherichia coli. A deletion of the recG gene renders cells highly sensitive to a range of DNA damaging agents. Here, we demonstrate that RecG function is at least partially complemented by another SF2 helicase, RadD. A ΔrecGΔradD double mutant exhibits an almost complete growth defect, even in the absence of stress. Suppressors appear quickly, primarily mutations that compromise priA helicase function or recA promoter mutations that reduce recA expression. Deletions of uup (encoding the UvrA-like ABC system Uup), recO, or recF also suppress the ΔrecGΔradD growth phenotype. RadD and RecG appear to avoid toxic situations in DNA metabolism, either resolving or preventing the appearance of DNA repair intermediates produced by RecA or RecA-independent template switching at stalled forks or postreplication gaps. Barriers to replisome progress that require intervention by RadD or RecG occur in virtually every replication cycle. The results highlight the importance of the RadD protein for general chromosome maintenance and repair. They also implicate Uup as a new modulator of RecG function.
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Affiliation(s)
- Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Stefanie H Chen
- Biotechnology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Armstrong
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Antoine van Oijen
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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20
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Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions. Proc Natl Acad Sci U S A 2020; 117:26206-26217. [PMID: 33020264 PMCID: PMC7584906 DOI: 10.1073/pnas.2000761117] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells must rapidly and efficiently react to DNA damage to avoid its harmful consequences. Here we report a molecular mechanism that gives rise to a model of how bacterial cells mobilize DNA repair proteins for timely response to genomic stress and initiation of DNA repair upon exposure of single-stranded DNA. We found that bacterial single-stranded DNA binding protein (SSB), a central player in genome metabolism, can undergo dynamic phase separation under physiological conditions. SSB condensates can store a wide array of DNA repair proteins that specifically interact with SSB. However, elevated levels of single-stranded DNA during genomic stress can dissolve SSB condensates, enabling rapid mobilization of SSB and SSB-interacting proteins to sites of DNA damage. Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that the Escherichia coli SSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
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21
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Tököli A, Mag B, Bartus É, Wéber E, Szakonyi G, Simon MA, Czibula Á, Monostori É, Nyitray L, Martinek TA. Proteomimetic surface fragments distinguish targets by function. Chem Sci 2020; 11:10390-10398. [PMID: 34094300 PMCID: PMC8162404 DOI: 10.1039/d0sc03525d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 11/21/2022] Open
Abstract
The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Beáta Mag
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged Somogyi u. 4. H6720 Szeged Hungary
| | - Márton A Simon
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Ágnes Czibula
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - Éva Monostori
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
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22
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Dubiel K, Henry C, Spenkelink LM, Kozlov AG, Wood EA, Jergic S, Dixon NE, van Oijen AM, Cox MM, Lohman TM, Sandler SJ, Keck JL. Development of a single-stranded DNA-binding protein fluorescent fusion toolbox. Nucleic Acids Res 2020; 48:6053-6067. [PMID: 32374866 PMCID: PMC7293020 DOI: 10.1093/nar/gkaa320] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/15/2020] [Accepted: 05/04/2020] [Indexed: 01/13/2023] Open
Abstract
Bacterial single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA and help to recruit heterologous proteins to their sites of action. SSBs perform these essential functions through a modular structural architecture: the N-terminal domain comprises a DNA binding/tetramerization element whereas the C-terminus forms an intrinsically disordered linker (IDL) capped by a protein-interacting SSB-Ct motif. Here we examine the activities of SSB-IDL fusion proteins in which fluorescent domains are inserted within the IDL of Escherichia coli SSB. The SSB-IDL fusions maintain DNA and protein binding activities in vitro, although cooperative DNA binding is impaired. In contrast, an SSB variant with a fluorescent protein attached directly to the C-terminus that is similar to fusions used in previous studies displayed dysfunctional protein interaction activity. The SSB-IDL fusions are readily visualized in single-molecule DNA replication reactions. Escherichia coli strains in which wildtype SSB is replaced by SSB-IDL fusions are viable and display normal growth rates and fitness. The SSB-IDL fusions form detectible SSB foci in cells with frequencies mirroring previously examined fluorescent DNA replication fusion proteins. Cells expressing SSB-IDL fusions are sensitized to some DNA damaging agents. The results highlight the utility of SSB-IDL fusions for biochemical and cellular studies of genome maintenance reactions.
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Affiliation(s)
- Katarzyna Dubiel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Sandler
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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23
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Wang Y, Sun Z, Bianco PR, Lyubchenko YL. Atomic force microscopy-based characterization of the interaction of PriA helicase with stalled DNA replication forks. J Biol Chem 2020; 295:6043-6052. [PMID: 32209655 DOI: 10.1074/jbc.ra120.013013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/21/2020] [Indexed: 01/31/2023] Open
Abstract
In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3'-to-5' direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. Single-stranded DNA-binding protein (SSB) is typically present at the abandoned forks, but it is unclear how SSB and PriA interact, although it has been shown that the two proteins interact both physically and functionally. Here, we used atomic force microscopy to visualize the interaction of PriA with DNA substrates with or without SSB. These experiments were done in the absence of ATP to delineate the substrate recognition pattern of PriA before its ATP-catalyzed DNA-unwinding reaction. These analyses revealed that in the absence of SSB, PriA binds preferentially to a fork substrate with a gap in the leading strand. Such a preference has not been observed for 5'- and 3'-tailed duplexes, suggesting that it is the fork structure that plays an essential role in PriA's selection of DNA substrates. Furthermore, we found that in the absence of SSB, PriA binds exclusively to the fork regions of the DNA substrates. In contrast, fork-bound SSB loads PriA onto the duplex DNA arms of forks, suggesting a remodeling of PriA by SSB. We also demonstrate that the remodeling of PriA requires a functional C-terminal domain of SSB. In summary, our atomic force microscopy analyses reveal key details in the interactions between PriA and stalled DNA replication forks with or without SSB.
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Affiliation(s)
- Yaqing Wang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Piero R Bianco
- Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, New York 14214
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025.
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24
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Brosh RM, Matson SW. History of DNA Helicases. Genes (Basel) 2020; 11:genes11030255. [PMID: 32120966 PMCID: PMC7140857 DOI: 10.3390/genes11030255] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the DNA double helix, there has been a fascination in understanding the molecular mechanisms and cellular processes that account for: (i) the transmission of genetic information from one generation to the next and (ii) the remarkable stability of the genome. Nucleic acid biologists have endeavored to unravel the mysteries of DNA not only to understand the processes of DNA replication, repair, recombination, and transcription but to also characterize the underlying basis of genetic diseases characterized by chromosomal instability. Perhaps unexpectedly at first, DNA helicases have arisen as a key class of enzymes to study in this latter capacity. From the first discovery of ATP-dependent DNA unwinding enzymes in the mid 1970's to the burgeoning of helicase-dependent pathways found to be prevalent in all kingdoms of life, the story of scientific discovery in helicase research is rich and informative. Over four decades after their discovery, we take this opportunity to provide a history of DNA helicases. No doubt, many chapters are left to be written. Nonetheless, at this juncture we are privileged to share our perspective on the DNA helicase field - where it has been, its current state, and where it is headed.
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Affiliation(s)
- Robert M. Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| | - Steven W. Matson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
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25
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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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26
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Huang YH, Lin ES, Huang CY. Complexed crystal structure of SSB reveals a novel single-stranded DNA binding mode (SSB)3:1: Phe60 is not crucial for defining binding paths. Biochem Biophys Res Commun 2019; 520:353-358. [DOI: 10.1016/j.bbrc.2019.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 10/25/2022]
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27
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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] [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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28
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Bagchi D, Manosas M, Zhang W, Manthei KA, Hodeib S, Ducos B, Keck JL, Croquette V. Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interaction with SSB. Nucleic Acids Res 2019; 46:8500-8515. [PMID: 30053104 PMCID: PMC6144805 DOI: 10.1093/nar/gky647] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/15/2018] [Indexed: 12/16/2022] Open
Abstract
Most RecQ DNA helicases share a conserved domain arrangement that mediates their activities in genomic stability. This arrangement comprises a helicase motor domain, a RecQ C-terminal (RecQ-C) region including a winged-helix (WH) domain, and a ‘Helicase and RNase D C-terminal’ (HRDC) domain. Single-molecule real-time translocation and DNA unwinding by full-length Escherichia coli RecQ and variants lacking either the HRDC or both the WH and HRDC domains was analyzed. RecQ operated under two interconvertible kinetic modes, ‘slow’ and ‘normal’, as it unwound duplex DNA and translocated on single-stranded (ss) DNA. Consistent with a crystal structure of bacterial RecQ bound to ssDNA by base stacking, abasic sites blocked RecQ unwinding. Removal of the HRDC domain eliminates the slow mode while preserving the normal mode of activity. Unexpectedly, a RecQ variant lacking both the WH and HRDC domains retains weak helicase activity. The inclusion of E. coli ssDNA-binding protein (SSB) induces a third ‘fast’ unwinding mode four times faster than the normal RecQ mode and enhances the overall helicase activity (affinity, rate, and processivity). SSB stimulation was, furthermore, observed in the RecQ deletion variants, including the variant missing the WH domain. Our results support a model in which RecQ and SSB have multiple interacting modes.
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Affiliation(s)
- Debjani Bagchi
- Physics Department, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390002, India
| | - Maria Manosas
- Departament de Física de la Materia Condensada, Universitat de Barcelona, Barcelona 08028, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Weiting Zhang
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Kelly A Manthei
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Samar Hodeib
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Bertrand Ducos
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Vincent Croquette
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
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29
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Abstract
Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage. We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation.
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30
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Dubiel K, Myers AR, Kozlov AG, Yang O, Zhang J, Ha T, Lohman TM, Keck JL. Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins. J Mol Biol 2018; 431:178-195. [PMID: 30472092 DOI: 10.1016/j.jmb.2018.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 12/19/2022]
Abstract
Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA "bridge" and identifies an interface, termed the "bridge interface," that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells.
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Affiliation(s)
- Katarzyna Dubiel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Angela R Myers
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Jichuan Zhang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725 N. Wolfe Street, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University and Howard Hughes Medical Institute, 725 N. Wolfe Street, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University and Howard Hughes Medical Institute, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
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31
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Escherichia coli AlkB interacts with single-stranded DNA binding protein SSB by an intrinsically disordered region of SSB. Mol Biol Rep 2018; 45:865-870. [PMID: 29974396 DOI: 10.1007/s11033-018-4232-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Intrinsically disordered regions (IDRs) of proteins often regulate function through interactions with folded domains. Escherichia coli single-stranded DNA binding protein SSB binds and stabilizes single-stranded DNA (ssDNA). The N-terminal of SSB contains characteristic OB (oligonucleotide/oligosaccharide-binding) fold which binds ssDNA tightly but non-specifically. SSB also forms complexes with a large number proteins via the C-terminal interaction domain consisting mostly of acidic amino acid residues. The amino acid residues located between the OB-fold and C-terminal acidic domain are known to constitute an IDR and no functional significance has been attributed to this region. Although SSB is known to bind many DNA repair protein, it is not known whether it binds to DNA dealkylation repair protein AlkB. Here, we characterize AlkB SSB interaction and demonstrate that SSB binds to AlkB via the IDR. We have established that AlkB-SSB interaction by in vitro pull-down and yeast two-hybrid analysis. We mapped the site of contact to be the residues 152-169 of SSB. Unlike most of the SSB-binding proteins which utilize C-terminal acidic domain for interaction, IDR of SSB is necessary and sufficient for AlkB interaction.
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32
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Evans JJ, Gygli PE, McCaskill J, DeVeaux LC. Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage. Genes (Basel) 2018; 9:genes9040223. [PMID: 29677156 PMCID: PMC5924565 DOI: 10.3390/genes9040223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/08/2018] [Accepted: 04/12/2018] [Indexed: 01/23/2023] Open
Abstract
The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii, causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.
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Affiliation(s)
- Jessica J Evans
- South Dakota School of Mines and Technology, Biomedical Engineering Program, Rapid City, SD 57701, USA.
| | - Patrick E Gygli
- Idaho State University Department of Biological Sciences, Pocatello, ID 83209, USA.
| | - Julienne McCaskill
- Idaho State University Department of Biological Sciences, Pocatello, ID 83209, USA.
| | - Linda C DeVeaux
- New Mexico Institute of Mining and Technology, Department of Biology, Socorro, NM 87801, USA.
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33
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Mills M, Harami GM, Seol Y, Gyimesi M, Martina M, Kovács ZJ, Kovács M, Neuman KC. RecQ helicase triggers a binding mode change in the SSB-DNA complex to efficiently initiate DNA unwinding. Nucleic Acids Res 2017; 45:11878-11890. [PMID: 29059328 PMCID: PMC5714189 DOI: 10.1093/nar/gkx939] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/29/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
The single-stranded DNA binding protein (SSB) of Escherichia coli plays essential roles in maintaining genome integrity by sequestering ssDNA and mediating DNA processing pathways through interactions with DNA-processing enzymes. Despite its DNA-sequestering properties, SSB stimulates the DNA processing activities of some of its binding partners. One example is the genome maintenance protein RecQ helicase. Here, we determine the mechanistic details of the RecQ-SSB interaction using single-molecule magnetic tweezers and rapid kinetic experiments. Our results reveal that the SSB-RecQ interaction changes the binding mode of SSB, thereby allowing RecQ to gain access to ssDNA and facilitating DNA unwinding. Conversely, the interaction of RecQ with the SSB C-terminal tail increases the on-rate of RecQ-DNA binding and has a modest stimulatory effect on the unwinding rate of RecQ. We propose that this bidirectional communication promotes efficient DNA processing and explains how SSB stimulates rather than inhibits RecQ activity.
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Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gábor M. Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Máté Martina
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Zoltán J. Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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34
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Huang SH, Cozart MR, Hart MA, Kobryn K. The Borrelia burgdorferi telomere resolvase, ResT, possesses ATP-dependent DNA unwinding activity. Nucleic Acids Res 2017; 45:1319-1329. [PMID: 28180323 PMCID: PMC5388405 DOI: 10.1093/nar/gkw1243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 11/14/2022] Open
Abstract
Spirochetes of the genus Borrelia possess unusual genomes harboring multiple linear and circular replicons. The linear replicons are terminated by covalently closed hairpin (hp) telomeres. Hairpin telomeres are formed from replicated intermediates by the telomere resolvase, ResT, in a phosphoryl transfer reaction with mechanistic similarities to those promoted by type 1B topoisomerases and tyrosine recombinases. There is growing evidence that ResT is multifunctional. Upon ResT depletion DNA replication unexpectedly ceases. Additionally, ResT possesses RecO-like biochemical activities being able to promote single-strand annealing on both free ssDNA and ssDNA complexed with cognate single-stranded DNA binding protein. We report here that ResT possesses DNA-dependent ATPase activity that promotes DNA unwinding with a 3΄-5΄ polarity. ResT can unwind a variety of substrates including synthetic replication forks and D-loops. We demonstrate that ResT's twin activities of DNA unwinding and annealing can drive regression of a model replication fork. These properties are similar to those of the RecQ helicase of the RecF pathway involved in DNA gap repair. We propose that ResT's combination of activities implicates it in replication and recombination processes operating on the linear chromosome and plasmids of Borrelia burgdorferi.
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Affiliation(s)
- Shu Hui Huang
- Department of Microbiology & Immunology, College of Medicine, University of Saskatchewan Academic Health Sciences Building, 107 Wiggins Rd, Saskatoon, SK, Canada
| | - McKayla R Cozart
- Department of Microbiology & Immunology, College of Medicine, University of Saskatchewan Academic Health Sciences Building, 107 Wiggins Rd, Saskatoon, SK, Canada
| | - Madison A Hart
- Department of Microbiology & Immunology, College of Medicine, University of Saskatchewan Academic Health Sciences Building, 107 Wiggins Rd, Saskatoon, SK, Canada
| | - Kerri Kobryn
- Department of Microbiology & Immunology, College of Medicine, University of Saskatchewan Academic Health Sciences Building, 107 Wiggins Rd, Saskatoon, SK, Canada
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35
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Razi A, Britton RA, Ortega J. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly. Nucleic Acids Res 2017; 45:1027-1040. [PMID: 28180306 PMCID: PMC5388408 DOI: 10.1093/nar/gkw1231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 01/14/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process.
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Affiliation(s)
- Aida Razi
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology and Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
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36
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Bianco PR, Lyubchenko YL. SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork. Protein Sci 2017; 26:638-649. [PMID: 28078722 DOI: 10.1002/pro.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022]
Abstract
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.
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Affiliation(s)
- Piero R Bianco
- SUNY Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, 321 Cary Hall, 3435 Main St, Buffalo, New York 14214.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, 68198-6025
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37
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Tan HY, Wilczek LA, Pottinger S, Manosas M, Yu C, Nguyenduc T, Bianco PR. The intrinsically disordered linker of E. coli SSB is critical for the release from single-stranded DNA. Protein Sci 2017; 26:700-717. [PMID: 28078720 DOI: 10.1002/pro.3115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022]
Abstract
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, they have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target. In this study, they examine the role of the linker region in SSB function in a variety of DNA metabolic processes in vitro. Using the same linker mutants, the results show that in addition to association reactions (either DNA or protein), the IDL is critical for the release of SSB from DNA. This release can be under conditions of ssDNA competition or active displacement by a DNA helicase or recombinase. Consistent with their previous work these results indicate that SSB linker mutants are defective for SSB-SSB interactions, and when the IDL is removed a terminal SSB-DNA complex results. Formation of this complex inhibits downstream processing of DNA by helicases such as RecG or PriA as well as recombination, mediated by RecA. A model, based on the evidence herein, is presented to explain how the IDL acts in SSB function.
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Affiliation(s)
- Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Luke A Wilczek
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Maria Manosas
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028, Barcelona, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Cong Yu
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
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38
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Bianco PR, Pottinger S, Tan HY, Nguyenduc T, Rex K, Varshney U. The IDL of E. coli SSB links ssDNA and protein binding by mediating protein-protein interactions. Protein Sci 2017; 26:227-241. [PMID: 28127816 DOI: 10.1002/pro.3072] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022]
Abstract
The E. coli single strand DNA binding protein (SSB) is essential to viability where it functions in two seemingly disparate roles: it binds to single stranded DNA (ssDNA) and to target proteins that comprise the SSB interactome. The link between these roles resides in a previously under-appreciated region of the protein known as the intrinsically disordered linker (IDL). We present a model wherein the IDL is responsible for mediating protein-protein interactions critical to each role. When interactions occur between SSB tetramers, cooperative binding to ssDNA results. When binding occurs between SSB and an interactome partner, storage or loading of that protein onto the DNA takes place. The properties of the IDL that facilitate these interactions include the presence of repeats, a putative polyproline type II helix and, PXXP motifs that may facilitate direct binding to the OB-fold in a manner similar to that observed for SH3 domain binding of PXXP ligands in eukaryotic systems.
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Affiliation(s)
- Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Kervin Rex
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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39
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Bianco PR. The tale of SSB. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:111-118. [PMID: 27838363 DOI: 10.1016/j.pbiomolbio.2016.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/04/2016] [Indexed: 01/07/2023]
Abstract
The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions. It does this by binding, via PXXP motifs, to the OB-fold (aka SH3 domain) of a nearby protein. When the nearby protein is another SSB tetramer, this leads to a highly efficient ssDNA binding reaction that rapidly and cooperatively covers and protects the exposed nucleic acid from degradation. Alternatively, when the nearby protein is a member of the SSB interactome, loading of the enzyme onto the DNA takes places.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA; Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.
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40
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Chen SH, Byrne-Nash RT, Cox MM. Escherichia coli RadD Protein Functionally Interacts with the Single-stranded DNA-binding Protein. J Biol Chem 2016; 291:20779-86. [PMID: 27519413 DOI: 10.1074/jbc.m116.736223] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 11/06/2022] Open
Abstract
The bacterial single-stranded DNA binding protein (SSB) acts as an organizer of DNA repair complexes. The radD gene was recently identified as having an unspecified role in repair of radiation damage and, more specifically, DNA double-strand breaks. Purified RadD protein displays a DNA-independent ATPase activity. However, ATP hydrolytic rates are stimulated by SSB through its C terminus. The RadD and SSB proteins also directly interact in vivo in a yeast two-hybrid assay and in vitro through ammonium sulfate co-precipitation. Therefore, it is likely that the repair function of RadD is mediated through interaction with SSB at the site of damage.
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Affiliation(s)
- Stefanie H Chen
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Rose T Byrne-Nash
- 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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41
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Chemo-mechanical pushing of proteins along single-stranded DNA. Proc Natl Acad Sci U S A 2016; 113:6194-9. [PMID: 27185951 DOI: 10.1073/pnas.1602878113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-stranded (ss)DNA binding (SSB) proteins bind with high affinity to ssDNA generated during DNA replication, recombination, and repair; however, these SSBs must eventually be displaced from or reorganized along the ssDNA. One potential mechanism for reorganization is for an ssDNA translocase (ATP-dependent motor) to push the SSB along ssDNA. Here we use single molecule total internal reflection fluorescence microscopy to detect such pushing events. When Cy5-labeled Escherichia coli (Ec) SSB is bound to surface-immobilized 3'-Cy3-labeled ssDNA, a fluctuating FRET signal is observed, consistent with random diffusion of SSB along the ssDNA. Addition of Saccharomyces cerevisiae Pif1, a 5' to 3' ssDNA translocase, results in the appearance of isolated, irregularly spaced saw-tooth FRET spikes only in the presence of ATP. These FRET spikes result from translocase-induced directional (5' to 3') pushing of the SSB toward the 3' ssDNA end, followed by displacement of the SSB from the DNA end. Similar ATP-dependent pushing events, but in the opposite (3' to 5') direction, are observed with EcRep and EcUvrD (both 3' to 5' ssDNA translocases). Simulations indicate that these events reflect active pushing by the translocase. The ability of translocases to chemo-mechanically push heterologous SSB proteins along ssDNA provides a potential mechanism for reorganization and clearance of tightly bound SSBs from ssDNA.
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42
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Yu C, Tan HY, Choi M, Stanenas AJ, Byrd AK, D Raney K, Cohan CS, Bianco PR. SSB binds to the RecG and PriA helicases in vivo in the absence of DNA. Genes Cells 2016; 21:163-84. [PMID: 26766785 DOI: 10.1111/gtc.12334] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
The E. coli single-stranded DNA-binding protein (SSB) binds to the fork DNA helicases RecG and PriA in vitro. Typically for binding to occur, 1.3 m ammonium sulfate must be present, bringing into question the validity of these results as these are nonphysiological conditions. To determine whether SSB can bind to these helicases, we examined binding in vivo. First, using fluorescence microscopy, we show that SSB localizes PriA and RecG to the vicinity of the inner membrane in the absence of DNA damage. Localization requires that SSB be in excess over the DNA helicases and the SSB C-terminus and both PriA and RecG be present. Second, using the purification of tagged complexes, our results show that SSB binds to PriA and RecG in vivo, in the absence of DNA. We propose that this may be the 'storage form' of RecG and PriA. We further propose that when forks stall, RecG and PriA are targeted to the fork by SSB, which, by virtue of its high affinity for single-stranded DNA, allows these helicases to outcompete other proteins. This ensures their actions in the early stages of the rescue of stalled replication forks.
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Affiliation(s)
- Cong Yu
- Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA
| | - Hui Yin Tan
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Meerim Choi
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Adam J Stanenas
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, slot 516, Little Rock, AR, 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, slot 516, Little Rock, AR, 72205, USA
| | - Christopher S Cohan
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, 14214, USA
| | - Piero R Bianco
- Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
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43
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Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding. Proc Natl Acad Sci U S A 2015; 112:E6852-61. [PMID: 26540728 DOI: 10.1073/pnas.1518028112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40-60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.
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44
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Bell JC, Liu B, Kowalczykowski SC. Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. eLife 2015; 4:e08646. [PMID: 26381353 PMCID: PMC4652220 DOI: 10.7554/elife.08646] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/18/2015] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ∼30-70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TIRF) microscopy and observed intramolecular condensation of nucleoprotein complexes exceeding expectations based on simple wrapping transitions. We further examined this unexpected property by single-molecule force spectroscopy using magnetic tweezers. In conditions favoring complete wrapping, SSB engages in long-range reversible intramolecular interactions resulting in condensation of the SSB-ssDNA complex. RecO and RecOR, which interact with SSB, further condensed the complex. Our data support the idea that RecOR--and possibly other SSB-interacting proteins-function(s) in part to alter long-range, macroscopic interactions between or throughout nucleoprotein complexes by microscopically altering wrapping and bridging distant sites.
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Affiliation(s)
- Jason C Bell
- Graduate Group in Biochemistry and Molecular Biology, University of California, Davis, Davis, United States
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Bian Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
- Graduate Group in Biophysics, University of California, Davis, Davis, United States
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
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45
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Petzold C, Marceau AH, Miller KH, Marqusee S, Keck JL. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity. J Biol Chem 2015; 290:14626-36. [PMID: 25903123 PMCID: PMC4505529 DOI: 10.1074/jbc.m115.655134] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/16/2015] [Indexed: 12/21/2022] Open
Abstract
Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome.
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Affiliation(s)
- Christine Petzold
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Aimee H Marceau
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Katherine H Miller
- California Institute for Quantitative Biosciences, QB3 and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, QB3 and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - James L Keck
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
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46
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Bhat KP, Bétous R, Cortez D. High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling. J Biol Chem 2014; 290:4110-7. [PMID: 25552480 DOI: 10.1074/jbc.m114.627083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity.
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Affiliation(s)
- Kamakoti P Bhat
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Rémy Bétous
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - David Cortez
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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47
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RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination. Proc Natl Acad Sci U S A 2014; 111:E5133-42. [PMID: 25411316 DOI: 10.1073/pnas.1420009111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinational DNA repair by the RecF pathway of Escherichia coli requires the coordinated activities of RecA, RecFOR, RecQ, RecJ, and single-strand DNA binding (SSB) proteins. These proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsDNA) and supercoiled DNA. Repair starts with resection of the broken dsDNA by RecQ, a 3'→5' helicase, RecJ, a 5'→3' exonuclease, and SSB protein. The ends of a dsDNA break can be blunt-ended, or they may possess either 5'- or 3'-single-stranded DNA (ssDNA) overhangs of undefined length. Here we show that RecJ nuclease alone can initiate nucleolytic resection of DNA with 5'-ssDNA overhangs, and that RecQ helicase can initiate resection of DNA with blunt-ends or 3'-ssDNA overhangs by DNA unwinding. We establish that in addition to its well-known ssDNA exonuclease activity, RecJ can display dsDNA exonuclease activity, degrading 100-200 nucleotides of the strand terminating with a 5'-ssDNA overhang. The dsDNA product, with a 3'-ssDNA overhang, is an optimal substrate for RecQ, which unwinds this intermediate to reveal the complementary DNA strand with a 5'-end that is degraded iteratively by RecJ. On the other hand, RecJ cannot resect duplex DNA that is either blunt-ended or terminated with 3'-ssDNA; however, such DNA is unwound by RecQ to create ssDNA for RecJ exonuclease. RecJ requires interaction with SSB for exonucleolytic degradation of ssDNA but not dsDNA. Thus, complementary action by RecJ and RecQ permits initiation of recombinational repair from all dsDNA ends: 5'-overhangs, blunt, or 3'-overhangs. Such helicase-nuclease coordination is a common mechanism underlying resection in all organisms.
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48
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Regulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein. DNA Repair (Amst) 2014; 25:41-53. [PMID: 25481875 DOI: 10.1016/j.dnarep.2014.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/26/2014] [Accepted: 10/01/2014] [Indexed: 11/20/2022]
Abstract
Dda, one of three helicases encoded by bacteriophage T4, has been well-characterized biochemically but its biological role remains unclear. It is thought to be involved in origin dependent DNA replication, recombination-dependent replication, anti-recombination, and recombination repair. The Gp32 protein of bacteriophage T4 plays critical roles in DNA replication, recombination, and repair by coordinating protein components of the replication fork and by stabilizing ssDNA. Previous work demonstrated that stimulation of DNA synthesis by Dda helicase appears to require direct Gp32-Dda protein-protein interactions and that Gp32 and Dda form a tight complex in the absence of ssDNA. Here we characterize the effects of Gp32-Dda physical and functional interactions through changes in the duplex DNA unwinding and ATPase activities of Dda helicase in the presence of different variants of Gp32 and different DNA repair and replication intermediate structures. Results show that Gp32-Dda interactions can be enhancing or inhibitory, depending on the Gp32 domain seen by Dda. Protein-protein interactions with Gp32 stimulate the unwinding activity of Dda, an effect associated with increased turnover of ATP, suggesting a higher rate of ATPase-driven translocation. Dda-Gp32 interactions also promote the unwinding of DNA substrates at higher salt concentrations and in the presence of substrate-bound DNA polymerase. Conversely, the formation of Gp32 clusters on ssDNA can inhibit unwinding, suggesting that Gp32-ssDNA formation sterically regulates which portions of replication and recombination intermediates are accessible for processing by Dda helicase. The data suggest a mechanism of replication fork restart in which Gp32 promotes Dda activity in template switching while preventing premature fork progression.
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49
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Characterization of biochemical properties of Bacillus subtilis RecQ helicase. J Bacteriol 2014; 196:4216-28. [PMID: 25246477 DOI: 10.1128/jb.06367-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RecQ family helicases function as safeguards of the genome. Unlike Escherichia coli, the Gram-positive Bacillus subtilis bacterium possesses two RecQ-like homologues, RecQ[Bs] and RecS, which are required for the repair of DNA double-strand breaks. RecQ[Bs] also binds to the forked DNA to ensure a smooth progression of the cell cycle. Here we present the first biochemical analysis of recombinant RecQ[Bs]. RecQ[Bs] binds weakly to single-stranded DNA (ssDNA) and blunt-ended double-stranded DNA (dsDNA) but strongly to forked dsDNA. The protein exhibits a DNA-stimulated ATPase activity and ATP- and Mg(2+)-dependent DNA helicase activity with a 3' → 5' polarity. Molecular modeling shows that RecQ[Bs] shares high sequence and structure similarity with E. coli RecQ. Surprisingly, RecQ[Bs] resembles the truncated Saccharomyces cerevisiae Sgs1 and human RecQ helicases more than RecQ[Ec] with regard to its enzymatic activities. Specifically, RecQ[Bs] unwinds forked dsDNA and DNA duplexes with a 3'-overhang but is inactive on blunt-ended dsDNA and 5'-overhung duplexes. Interestingly, RecQ[Bs] unwinds blunt-ended DNA with structural features, including nicks, gaps, 5'-flaps, Kappa joints, synthetic replication forks, and Holliday junctions. We discuss these findings in the context of RecQ[Bs]'s possible functions in preserving genomic stability.
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Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. BIOMED RESEARCH INTERNATIONAL 2014; 2014:195162. [PMID: 25136561 PMCID: PMC4129139 DOI: 10.1155/2014/195162] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/20/2014] [Accepted: 07/01/2014] [Indexed: 01/31/2023]
Abstract
Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome in Escherichia coli is composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.
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