1
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Gaydar V, Zananiri R, Saied L, Dvir O, Kaplan A, Henn A. Communication between DNA and nucleotide binding sites facilitates stepping by the RecBCD helicase. Nucleic Acids Res 2024; 52:3911-3923. [PMID: 38364872 DOI: 10.1093/nar/gkae108] [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: 05/22/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Double-strand DNA breaks are the severest type of genomic damage, requiring rapid response to ensure survival. RecBCD helicase in prokaryotes initiates processive and rapid DNA unzipping, essential for break repair. The energetics of RecBCD during translocation along the DNA track are quantitatively not defined. Specifically, it's essential to understand the mechanism by which RecBCD switches between its binding states to enable its translocation. Here, we determine, by systematic affinity measurements, the degree of coupling between DNA and nucleotide binding to RecBCD. In the presence of ADP, RecBCD binds weakly to DNA that harbors a double overhang mimicking an unwinding intermediate. Consistently, RecBCD binds weakly to ADP in the presence of the same DNA. We did not observe coupling between DNA and nucleotide binding for DNA molecules having only a single overhang, suggesting that RecBCD subunits must both bind DNA to 'sense' the nucleotide state. On the contrary, AMPpNp shows weak coupling as RecBCD remains strongly bound to DNA in its presence. Detailed thermodynamic analysis of the RecBCD reaction mechanism suggests an 'energetic compensation' between RecB and RecD, which may be essential for rapid unwinding. Our findings provide the basis for a plausible stepping mechanism' during the processive translocation of RecBCD.
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Affiliation(s)
- Vera Gaydar
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Rani Zananiri
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Or Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Arnon Henn
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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2
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Fazio NT, Mersch KN, Hao L, Lohman TM. E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity. J Mol Biol 2024; 436:168381. [PMID: 38081382 PMCID: PMC11131135 DOI: 10.1016/j.jmb.2023.168381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as occurring by the ATPase motors mechanically pulling the DNA duplex across a wedge domain in the helicase, biochemical data show that processive DNA unwinding by E. coli RecBCD helicase can occur in the absence of ssDNA translocation by the canonical RecB and RecD motors. Here we show that DNA unwinding is not a simple consequence of ssDNA translocation by the motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecBΔNucCD) unwinds dsDNA at significantly slower rates than RecBCD, while the ssDNA translocation rate is unaffected. This effect is primarily due to the absence of the nuclease domain since a nuclease-dead mutant (RecBD1080ACD), which retains the nuclease domain, showed no change in ssDNA translocation or dsDNA unwinding rates relative to RecBCD on short DNA substrates (≤60 base pairs). Hence, ssDNA translocation is not rate-limiting for DNA unwinding. RecBΔNucCD also initiates unwinding much slower than RecBCD from a blunt-ended DNA. RecBΔNucCD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecBD1080ACD unwinding are intermediate between RecBCD and RecBΔNucCD. Surprisingly, significant pauses in DNA unwinding occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, possibly allosterically and that RecBΔNucCD may mimic a post-chi state of RecBCD.
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Affiliation(s)
- Nicole T Fazio
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Kacey N Mersch
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
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3
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [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: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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4
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Fazio N, Mersch KN, Hao L, Lohman TM. E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.561901. [PMID: 37905078 PMCID: PMC10614803 DOI: 10.1101/2023.10.13.561901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as a consequence of mechanically pulling the DNA duplex across a wedge domain in the helicase by the single stranded (ss)DNA translocase activity of the ATPase motors, biochemical data indicate that processive DNA unwinding by the E. coli RecBCD helicase can occur in the absence of ssDNA translocation of the canonical RecB and RecD motors. Here, we present evidence that dsDNA unwinding is not a simple consequence of ssDNA translocation by the RecBCD motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecB ΔNuc CD) unwinds dsDNA at significantly slower rates than RecBCD, while the rate of ssDNA translocation is unaffected. This effect is primarily due to the absence of the nuclease domain and not the absence of the nuclease activity, since a nuclease-dead mutant (RecB D1080A CD), which retains the nuclease domain, showed no significant change in rates of ssDNA translocation or dsDNA unwinding relative to RecBCD on short DNA substrates (≤ 60 base pairs). This indicates that ssDNA translocation is not rate-limiting for DNA unwinding. RecB ΔNuc CD also initiates unwinding much slower than RecBCD from a blunt-ended DNA, although it binds with higher affinity than RecBCD. RecB ΔNuc CD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecB D1080A CD unwinding are intermediate between RecBCD and RecB ΔNuc CD. Surprisingly, significant pauses occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, rather than DNA translocation, possibly allosterically. Since the rate of DNA unwinding by RecBCD also slows after it recognizes a chi sequence, RecB ΔNuc CD may mimic a post- chi state of RecBCD.
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5
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CRISPR-Cas adaptation in Escherichia coli. Biosci Rep 2023; 43:232582. [PMID: 36809461 PMCID: PMC10011333 DOI: 10.1042/bsr20221198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/23/2023] Open
Abstract
Prokaryotes use the adaptive immunity mediated via the Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated (CRISPR-Cas) system for protection against invading elements such as phages and plasmids. The immunity is achieved by capturing small DNA fragments or spacers from foreign nucleic acids (protospacers) and integrating them into the host CRISPR locus. This step of CRISPR-Cas immunity called 'naïve CRISPR adaptation' requires the conserved Cas1-Cas2 complex and is often supported by variable host proteins that assist in spacer processing and integration. Bacteria that have acquired new spacers become immune to the same invading elements when reinfected. CRISPR-Cas immunity can also be updated by integrating new spacers from the same invading elements, a process called 'primed adaptation'. Only properly selected and integrated spacers are functional in the next steps of CRISPR immunity when their processed transcripts are used for RNA-guided target recognition and interference (target degradation). Capturing, trimming, and integrating new spacers in the correct orientation are universal steps of adaptation to all CRISPR-Cas systems, but some details are CRISPR-Cas type-specific and species-specific. In this review, we provide an overview of the mechanisms of CRISPR-Cas class 1 type I-E adaptation in Escherichia coli as a general model for adaptation processes (DNA capture and integration) that have been studied in detail. We focus on the role of host non-Cas proteins involved in adaptation, particularly on the role of homologous recombination.
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Fochtman TJ, Oza JP. Established and Emerging Methods for Protecting Linear DNA in Cell-Free Expression Systems. Methods Protoc 2023; 6:mps6020036. [PMID: 37104018 PMCID: PMC10146267 DOI: 10.3390/mps6020036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a method utilized for producing proteins without the limits of cell viability. The plug-and-play utility of CFPS is a key advantage over traditional plasmid-based expression systems and is foundational to the potential of this biotechnology. A key limitation of CFPS is the varying stability of DNA types, limiting the effectiveness of cell-free protein synthesis reactions. Researchers generally rely on plasmid DNA for its ability to support robust protein expression in vitro. However, the overhead required to clone, propagate, and purify plasmids reduces the potential of CFPS for rapid prototyping. While linear templates overcome the limits of plasmid DNA preparation, linear expression templates (LETs) were under-utilized due to their rapid degradation in extract based CFPS systems, limiting protein synthesis. To reach the potential of CFPS using LETs, researchers have made notable progress toward protection and stabilization of linear templates throughout the reaction. The current advancements range from modular solutions, such as supplementing nuclease inhibitors and genome engineering to produce strains lacking nuclease activity. Effective application of LET protection techniques improves expression yields of target proteins to match that of plasmid-based expression. The outcome of LET utilization in CFPS is rapid design–build–test–learn cycles to support synthetic biology applications. This review describes the various protection mechanisms for linear expression templates, methodological insights for implementation, and proposals for continued efforts that may further advance the field.
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7
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Soniat MM, Nguyen G, Kuo HC, Finkelstein IJ. The MRN complex and topoisomerase IIIa-RMI1/2 synchronize DNA resection motor proteins. J Biol Chem 2023; 299:102802. [PMID: 36529288 PMCID: PMC9971906 DOI: 10.1016/j.jbc.2022.102802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
DNA resection-the nucleolytic processing of broken DNA ends-is the first step of homologous recombination. Resection is catalyzed by the resectosome, a multienzyme complex that includes bloom syndrome helicase (BLM), DNA2 or exonuclease 1 nucleases, and additional DNA-binding proteins. Although the molecular players have been known for over a decade, how the individual proteins work together to regulate DNA resection remains unknown. Using single-molecule imaging, we characterized the roles of the MRE11-RAD50-NBS1 complex (MRN) and topoisomerase IIIa (TOP3A)-RMI1/2 during long-range DNA resection. BLM partners with TOP3A-RMI1/2 to form the BTRR (BLM-TOP3A-RMI1/2) complex (or BLM dissolvasome). We determined that TOP3A-RMI1/2 aids BLM in initiating DNA unwinding, and along with MRN, stimulates DNA2-mediated resection. Furthermore, we found that MRN promotes the association between BTRR and DNA and synchronizes BLM and DNA2 translocation to prevent BLM from pausing during resection. Together, this work provides direct observation of how MRN and DNA2 harness the BTRR complex to resect DNA efficiently and how TOP3A-RMI1/2 regulates the helicase activity of BLM to promote efficient DNA repair.
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Affiliation(s)
- Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
| | - Giaochau Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
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8
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Wang BB, Xu JZ, Zhang F, Liu S, Liu J, Zhang WG. Review of DNA repair enzymes in bacteria: With a major focus on AddAB and RecBCD. DNA Repair (Amst) 2022; 118:103389. [PMID: 36030574 DOI: 10.1016/j.dnarep.2022.103389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
DNA recombination repair systems are essential for organisms to maintain genomic stability. In recent years, we have improved our understanding of the mechanisms of RecBCD/AddAB family-mediated DNA double-strand break repair. In E. coli, it is RecBCD that plays a central role, and in Firmicute Bacillus subtilis it is the AddAB complex that functions. However, there are open questions about the mechanism of DNA repair in bacteria. For example, how bacteria containing crossover hotspot instigator (Chi) sites regulate the activity of proteins. In addition, we still do not know the exact process by which the RecB nuclease or AddA nuclease structural domains load RecA onto DNA. We also know little about the mechanism of DNA repair in the industrially important production bacterium Corynebacterium glutamicum (C. glutamicum). Therefore, exploring DNA repair mechanisms in bacteria may not only deepen our understanding of the DNA repair process in this species but also guide us in the targeted treatment of diseases associated with recombination defects, such as cancer. In this paper, we firstly review the classical proteins RecBCD and AddAB involved in DNA recombination repair, secondly focus on the novel helical nuclease AdnAB found in the genus Mycobacterium.
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Affiliation(s)
- Bing-Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China.
| | - Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China.
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9
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Xue C, Salunkhe SJ, Tomimatsu N, Kawale AS, Kwon Y, Burma S, Sung P, Greene EC. Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing. Nat Commun 2022; 13:2248. [PMID: 35473934 PMCID: PMC9042962 DOI: 10.1038/s41467-022-29937-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Sameer J Salunkhe
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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Bianco PR. Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays. Methods 2021; 204:348-360. [PMID: 34896247 PMCID: PMC9534331 DOI: 10.1016/j.ymeth.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
There are multiple assays available that can provide insight into the biochemical mechanism of DNA helicases. For the first 22 years since their discovery, bulk-phase assays were used. These include gel-based, spectrophotometric, and spectrofluorometric assays that revealed many facets of these enzymes. From 2001, single-molecule studies have contributed additional insight into these DNA nanomachines to reveal details on energy coupling, step size, processivity as well as unique aspects of individual enzyme behavior that were masked in the averaging inherent in ensemble studies. In this review, important aspects of the study of helicases are discussed including beginning with active, nuclease-free enzyme, followed by several bulk-phase approaches that have been developed and still find widespread use today. Finally, two single-molecule approaches are discussed, and the resulting findings are related to the results obtained in bulk-phase studies.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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11
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Kong M, Greene EC. Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks. Front Cell Dev Biol 2021; 9:745311. [PMID: 34869333 PMCID: PMC8636147 DOI: 10.3389/fcell.2021.745311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
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12
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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13
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Yasmin T, Azeroglu B, Cockram CA, Leach DRF. Distribution of Holliday junctions and repair forks during Escherichia coli DNA double-strand break repair. PLoS Genet 2021; 17:e1009717. [PMID: 34432790 PMCID: PMC8386832 DOI: 10.1371/journal.pgen.1009717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022] Open
Abstract
Accurate repair of DNA double-strand breaks (DSBs) is crucial for cell survival and genome integrity. In Escherichia coli, DSBs are repaired by homologous recombination (HR), using an undamaged sister chromosome as template. The DNA intermediates of this pathway are expected to be branched molecules that may include 4-way structures termed Holliday junctions (HJs), and 3-way structures such as D-loops and repair forks. Using a tool creating a site-specific, repairable DSB on only one of a pair of replicating sister chromosomes, we have determined how these branched DNA intermediates are distributed across a DNA region that is undergoing DSB repair. In cells, where branch migration and cleavage of HJs are limited by inactivation of the RuvABC complex, HJs and repair forks are principally accumulated within a distance of 12 kb from sites of recombination initiation, known as Chi, on each side of the engineered DSB. These branched DNA structures can even be detected in the region of DNA between the Chi sites flanking the DSB, a DNA segment not expected to be engaged in recombination initiation, and potentially degraded by RecBCD nuclease action. This is observed even in the absence of the branch migration and helicase activities of RuvAB, RadA, RecG, RecQ and PriA. The detection of full-length DNA fragments containing HJs in this central region implies that DSB repair can restore the two intact chromosomes, into which HJs can relocate prior to their resolution. The distribution of recombination intermediates across the 12kb region beyond Chi is altered in xonA, recJ and recQ mutants suggesting that, in the RecBCD pathway of DSB repair, exonuclease I stimulates the formation of repair forks and that RecJQ promotes strand-invasion at a distance from the recombination initiation sites.
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Affiliation(s)
- Tahirah Yasmin
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Charlotte A. Cockram
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
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14
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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15
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Hao L, Zhang R, Lohman TM. Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting. J Mol Biol 2021; 433:167147. [PMID: 34246654 DOI: 10.1016/j.jmb.2021.167147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/14/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022]
Abstract
E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17-18 nucleotides and can melt at least 10-11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecBNuc) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecBNuc, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecBNuc. This suggests that the RecBNuc domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecBNuc is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecBNuc is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.
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Affiliation(s)
- Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States.
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16
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Bianco PR, Lu Y. Single-molecule insight into stalled replication fork rescue in Escherichia coli. Nucleic Acids Res 2021; 49:4220-4238. [PMID: 33744948 PMCID: PMC8096234 DOI: 10.1093/nar/gkab142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 01/05/2023] Open
Abstract
DNA replication forks stall at least once per cell cycle in Escherichia coli. DNA replication must be restarted if the cell is to survive. Restart is a multi-step process requiring the sequential action of several proteins whose actions are dictated by the nature of the impediment to fork progression. When fork progress is impeded, the sequential actions of SSB, RecG and the RuvABC complex are required for rescue. In contrast, when a template discontinuity results in the forked DNA breaking apart, the actions of the RecBCD pathway enzymes are required to resurrect the fork so that replication can resume. In this review, we focus primarily on the significant insight gained from single-molecule studies of individual proteins, protein complexes, and also, partially reconstituted regression and RecBCD pathways. This insight is related to the bulk-phase biochemical data to provide a comprehensive review of each protein or protein complex as it relates to stalled DNA replication fork rescue.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yue Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
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17
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Singh R, Chandel S, Ghosh A, Dey D, Chakravarti R, Roy S, Ravichandiran V, Ghosh D. Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules. Mol Biotechnol 2021; 63:459-476. [PMID: 33774733 DOI: 10.1007/s12033-021-00310-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/14/2021] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas protein technology area is rapidly growing technique for genome editing and modulation of transcription of several microbes. Successful engineering in microbes requires an emphasis on the aspect of efficiency and targeted aiming, which can be employed using CRISPR/Cas system. Hence, this type of system is used to modify the genome of several microbes such as yeast and bacteria. In recent years, CRISPR/Cas systems have been chosen for metabolic engineering in microbes due to their specificity, orthogonality, and efficacy. Therefore, we need to review the scheme which was acquired for the execution of the CRISPR/Cas system for the modification and metabolic engineering in yeast and bacteria. In this review, we highlighted the application of the CRISPR/Cas system which has been used for the production of small molecules in the microbial system that is chemically and biologically important.
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Affiliation(s)
- Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Arijit Ghosh
- Department of Chemistry, University of Calcutta, Kolkata, 700009, India
| | - Dhritiman Dey
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Syamal Roy
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - V Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India.
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18
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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: 54] [Impact Index Per Article: 13.5] [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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19
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Xie P. Non-tight and tight chemomechanical couplings of biomolecular motors under hindering loads. J Theor Biol 2020; 490:110173. [PMID: 31982418 DOI: 10.1016/j.jtbi.2020.110173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 10/25/2022]
Abstract
Biomolecular motors make use of free energy released from chemical reaction (typically ATP hydrolysis) to perform mechanical motion or work. An important issue is whether a molecular motor exhibits tight or non-tight chemomechanical (CM) coupling. The tight CM coupling refers to that each ATPase activity is coupled with a mechanical step, while the non-tight CM coupling refers to that an ATPase activity is not necessarily coupled with a mechanical step. Here, we take kinesin, monomeric DNA helicase, ring-shaped hexameric DNA helicase and ribosome as examples to study this issue. Our studies indicate that some motors such as kinesin, monomeric helicase and ribosome exhibit non-tight CM coupling under hindering forces, while others such as the ring-shaped hexameric helicase exhibit tight or nearly tight CM coupling under any force. For the former, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the CM coupling efficiency, while the ATPase rate is independent or nearly independent of the force. For the latter, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the ATPase rate, while the CM coupling efficiency is independent or nearly independent of the force.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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20
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A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair. Nat Struct Mol Biol 2020; 27:71-77. [PMID: 31907455 PMCID: PMC7000243 DOI: 10.1038/s41594-019-0355-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/21/2019] [Indexed: 12/04/2022]
Abstract
The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognised and others in which it is not. The Chi-recognised structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognised and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair.
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21
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Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection. Proc Natl Acad Sci U S A 2019; 116:24507-24516. [PMID: 31740608 DOI: 10.1073/pnas.1913546116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain. Here we report cryoelectron microscopy (cryo-EM) structures of AdnAB in three functional states: in the absence of DNA and in complex with forked duplex DNAs before and after cleavage of the 5' single-strand DNA (ssDNA) tail by the AdnA nuclease. The structures reveal the path of the 5' ssDNA through the AdnA nuclease domain and the mechanism of 5' strand cleavage; the path of the 3' tracking strand through the AdnB motor and the DNA contacts that couple ATP hydrolysis to mechanical work; the position of the AdnA iron-sulfur cluster subdomain at the Y junction and its likely role in maintaining the split trajectories of the unwound 5' and 3' strands. Single-molecule DNA curtain analysis of DSB resection reveals that AdnAB is highly processive but prone to spontaneous pausing at random sites on duplex DNA. A striking property of AdnAB is that the velocity of DSB resection slows after the enzyme experiences a spontaneous pause. Our results highlight shared as well as distinctive properties of AdnAB vis-à-vis the RecBCD and AddAB clades of bacterial DSB-resecting motor nucleases.
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22
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Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J. Structural insights into DNA degradation by human mitochondrial nuclease MGME1. Nucleic Acids Res 2019; 46:11075-11088. [PMID: 30247721 PMCID: PMC6237815 DOI: 10.1093/nar/gky855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/11/2018] [Indexed: 01/16/2023] Open
Abstract
Mitochondrial nucleases play important roles in accurate maintenance and correct metabolism of mtDNA, the own genetic materials of mitochondria that are passed exclusively from mother to child. MGME1 is a highly conserved DNase that was discovered recently. Mutations in MGME1-coding gene lead to severe mitochondrial syndromes characterized by external ophthalmoplegia, emaciation, and respiratory failure in humans. Unlike many other nucleases that are distributed in multiple cellular organelles, human MGME1 is a mitochondria-specific nuclease; therefore, it can serve as an ideal target for treating related syndromes. Here, we report one HsMGME1-Mn2+ complex and three different HsMGME1-DNA complex structures. In combination with in vitro cleavage assays, our structures reveal the detailed molecular basis for substrate DNA binding and/or unwinding by HsMGME1. Besides the conserved two-cation-assisted catalytic mechanism, structural analysis of HsMGME1 and comparison with homologous proteins also clarified substrate binding and cleavage directionalities of the DNA double-strand break repair complexes RecBCD and AddAB.
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Affiliation(s)
- Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ruiqi Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yangyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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23
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Kasaciunaite K, Fettes F, Levikova M, Daldrop P, Anand R, Cejka P, Seidel R. Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection. EMBO J 2019; 38:e101516. [PMID: 31268598 PMCID: PMC6601037 DOI: 10.15252/embj.2019101516] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/24/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
DNA double-strand break repair by homologous recombination employs long-range resection of the 5' DNA ends at the break points. In Saccharomyces cerevisiae, this process can be performed by the RecQ helicase Sgs1 and the helicase-nuclease Dna2. Though functional interplay between them has been shown, it remains unclear whether and how these proteins cooperate on the molecular level. Here, we resolved the dynamics of DNA unwinding by Sgs1 at the single-molecule level and investigated Sgs1 regulation by Dna2, the single-stranded DNA-binding protein RPA, and the Top3-Rmi1 complex. We found that Dna2 modulates the velocity of Sgs1, indicating that during end resection both proteins form a functional complex and couple their activities. Sgs1 drives DNA unwinding and feeds single-stranded DNA to Dna2 for degradation. RPA was found to regulate the processivity and the affinity of Sgs1 to the DNA fork, while Top3-Rmi1 modulated the velocity of Sgs1. We hypothesize that the differential regulation of Sgs1 activity by its protein partners is important to support diverse cellular functions of Sgs1 during the maintenance of genome stability.
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Affiliation(s)
- Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Maryna Levikova
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Peter Daldrop
- Institute for Molecular Cell Biology, University of Münster, Münster, Germany
| | - Roopesh Anand
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
- Institute for Molecular Cell Biology, University of Münster, Münster, Germany
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24
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Regulatory control of Sgs1 and Dna2 during eukaryotic DNA end resection. Proc Natl Acad Sci U S A 2019; 116:6091-6100. [PMID: 30850524 DOI: 10.1073/pnas.1819276116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the repair of DNA double-strand breaks by homologous recombination, the DNA break ends must first be processed into 3' single-strand DNA overhangs. In budding yeast, end processing requires the helicase Sgs1 (BLM in humans), the nuclease/helicase Dna2, Top3-Rmi1, and replication protein A (RPA). Here, we use single-molecule imaging to visualize Sgs1-dependent end processing in real-time. We show that Sgs1 is recruited to DNA ends through Top3-Rmi1-dependent or -independent means, and in both cases Sgs1 is maintained in an immoble state at the DNA ends. Importantly, the addition of Dna2 triggers processive Sgs1 translocation, but DNA resection only occurs when RPA is also present. We also demonstrate that the Sgs1-Dna2-Top3-Rmi1-RPA ensemble can efficiently disrupt nucleosomes, and that Sgs1 itself possesses nucleosome remodeling activity. Together, these results shed light on the regulatory interplay among conserved protein factors that mediate the nucleolytic processing of DNA ends in preparation for homologous recombination-mediated chromosome damage repair.
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25
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Zananiri R, Malik O, Rudnizky S, Gaydar V, Kreiserman R, Henn A, Kaplan A. Synergy between RecBCD subunits is essential for efficient DNA unwinding. eLife 2019; 8:e40836. [PMID: 30601118 PMCID: PMC6338465 DOI: 10.7554/elife.40836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/01/2019] [Indexed: 12/12/2022] Open
Abstract
The subunits of the bacterial RecBCD act in coordination, rapidly and processively unwinding DNA at the site of a double strand break. RecBCD is able to displace DNA-binding proteins, suggesting that it generates high forces, but the specific role of each subunit in the force generation is unclear. Here, we present a novel optical tweezers assay that allows monitoring the activity of RecBCD's individual subunits, when they are part of an intact full complex. We show that RecBCD and its subunits are able to generate forces up to 25-40 pN without a significant effect on their velocity. Moreover, the isolated RecD translocates fast but is a weak helicase with limited processivity. Experiments at a broad range of [ATP] and forces suggest that RecD unwinds DNA as a Brownian ratchet, rectified by ATP binding, and that the presence of the other subunits shifts the ratchet equilibrium towards the post-translocation state.
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Affiliation(s)
- Rani Zananiri
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Omri Malik
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Russell Berrie Nanotechnology InstituteTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Sergei Rudnizky
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Vera Gaydar
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Roman Kreiserman
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Faculty of PhysicsTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Arnon Henn
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Ariel Kaplan
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
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26
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Xie P. Modeling DNA Unwinding by AddAB Helicase-Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD. Cell Mol Bioeng 2018; 12:179-191. [PMID: 31719908 DOI: 10.1007/s12195-018-00563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/29/2018] [Indexed: 01/28/2023] Open
Abstract
Introduction AddAB enzyme is a helicase-nuclease complex that initiates recombinational repair of double-stranded DNA breaks. It catalyzes processive DNA unwinding and concomitant resection of the unwound strands, which are modulated by the recognition of a recombination hotspot called Chi in the 3'-terminated strand. Despite extensive structural, biochemical and single molecule studies, the detailed molecular mechanism of DNA unwinding by the complex and modulation by Chi sequence remains unclear. Methods A model of DNA unwinding by the AddAB complex and modulation by Chi recognition was presented, based on which the dynamics of AddAB complex was studied analytically. Results The theoretical results explain well the available experimental data on effect of DNA sequence on velocity, effect of Chi recognition on velocity, static disorder peculiar to the AddAB complex, and dynamics of pausing of wild-type and mutant AddAB complexes occurring at Chi or Chi-like sequence. Predictions were provided. Comparisons of AddAB complex with other helicase-nuclease complexes such as RecBCD and AdnAB were made. Conclusions The study has strong implications for the molecular mechanism of DNA unwinding by the AddAB complex. The intriguing issues are addressed of why Chi recognition is an inefficient process, how AddAB complex pauses upon recognizing Chi sequence, how the paused state transits to the translocating state, why the mutant AddAB with a stronger affinity to Chi sequence has a shorter pausing lifetime, why the pausing lifetime is sensitive to the solution temperature, and so on.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190 China
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27
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Xie P. A model of DNA unwinding dynamics by the RecBCD complex and its regulation by Chi recognition. J Theor Biol 2018; 448:142-156. [DOI: 10.1016/j.jtbi.2018.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/12/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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28
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Pavankumar TL, Sinha AK, Ray MK. Biochemical characterization of RecBCD enzyme from an Antarctic Pseudomonas species and identification of its cognate Chi (χ) sequence. PLoS One 2018; 13:e0197476. [PMID: 29775464 PMCID: PMC5959072 DOI: 10.1371/journal.pone.0197476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae Lz4W RecBCD enzyme, RecBCDPs, is a trimeric protein complex comprised of RecC, RecB, and RecD subunits. RecBCD enzyme is essential for P. syringae growth at low temperature, and it protects cells from low temperature induced replication arrest. In this study, we show that the RecBCDPs enzyme displays distinct biochemical behaviors. Unlike E. coli RecBCD enzyme, the RecD subunit is indispensable for RecBCDPs function. The RecD motor activity is essential for the Chi-like fragments production in P. syringae, highlighting a distinct role for P. syringae RecD subunit in DNA repair and recombination process. Here, we demonstrate that the RecBCDPs enzyme recognizes a unique octameric DNA sequence, 5′-GCTGGCGC-3′ (ChiPs) that attenuates nuclease activity of the enzyme when it enters dsDNA from the 3′-end. We propose that the reduced translocation activities manifested by motor-defective mutants cause cold sensitivity in P. syrinage; emphasizing the importance of DNA processing and recombination functions in rescuing low temperature induced replication fork arrest.
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Affiliation(s)
- Theetha L. Pavankumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail: (TLP); (MKR)
| | - Anurag K. Sinha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay K. Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail: (TLP); (MKR)
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29
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Che S, Chen Y, Liang Y, Zhang Q, Bartlam M. Crystal structure of RecR, a member of the RecFOR DNA-repair pathway, from Pseudomonas aeruginosa PAO1. Acta Crystallogr F Struct Biol Commun 2018; 74:222-230. [PMID: 29633970 PMCID: PMC5894107 DOI: 10.1107/s2053230x18003503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination in Pseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway in P. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR from P. aeruginosa PAO1 (PaRecR) is reported. PaRecR crystallizes in space group P6122, with two monomers per asymmetric unit. Analytical ultracentrifugation data show that PaRecR forms a stable dimer, but can exist as a tetramer in solution. The crystal structure shows that dimeric PaRecR forms a ring-like tetramer architecture via crystal symmetry. The presence of a ligand in the Walker B motif of one RecR subunit suggests a putative nucleotide-binding site.
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Affiliation(s)
- Shiyou Che
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yujing Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yakun Liang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Qionglin Zhang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Mark Bartlam
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
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30
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Sinha AK, Possoz C, Durand A, Desfontaines JM, Barre FX, Leach DRF, Michel B. Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome. PLoS Genet 2018. [PMID: 29522563 PMCID: PMC5862497 DOI: 10.1371/journal.pgen.1007256] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
It was recently reported that the recBC mutants of Escherichia coli, deficient for DNA double-strand break (DSB) repair, have a decreased copy number of their terminus region. We previously showed that this deficit resulted from DNA loss after post-replicative breakage of one of the two sister-chromosome termini at cell division. A viable cell and a dead cell devoid of terminus region were thus produced and, intriguingly, the reaction was transmitted to the following generations. Using genome marker frequency profiling and observation by microscopy of specific DNA loci within the terminus, we reveal here the origin of this phenomenon. We observed that terminus DNA loss was reduced in a recA mutant by the double-strand DNA degradation activity of RecBCD. The terminus-less cell produced at the first cell division was less prone to divide than the one produced at the next generation. DNA loss was not heritable if the chromosome was linearized in the terminus and occurred at chromosome termini that were unable to segregate after replication. We propose that in a recB mutant replication fork breakage results in the persistence of a linear DNA tail attached to a circular chromosome. Segregation of the linear and circular parts of this "σ-replicating chromosome" causes terminus DNA breakage during cell division. One daughter cell inherits a truncated linear chromosome and is not viable. The other inherits a circular chromosome attached to a linear tail ending in the chromosome terminus. Replication extends this tail, while degradation of its extremity results in terminus DNA loss. Repeated generation and segregation of new σ-replicating chromosomes explains the heritability of post-replicative breakage. Our results allow us to determine that in E. coli at each generation, 18% of cells are subject to replication fork breakage at dispersed, potentially random, chromosomal locations.
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Affiliation(s)
- Anurag Kumar Sinha
- Bacterial DNA stability, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail: (AKS); (BM)
| | - Christophe Possoz
- Evolution and maintenance of circular chromosomes, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Adeline Durand
- Bacterial DNA stability, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Michel Desfontaines
- Evolution and maintenance of circular chromosomes, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François-Xavier Barre
- Evolution and maintenance of circular chromosomes, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bénédicte Michel
- Bacterial DNA stability, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail: (AKS); (BM)
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31
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Cho CC, Chung C, Li HW. How Chi Sequence Modifies RecBCD Single-Stranded DNA Translocase Activity. Chemphyschem 2017; 19:243-247. [PMID: 29032606 DOI: 10.1002/cphc.201700840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/12/2017] [Indexed: 11/12/2022]
Abstract
E. coli RecBCD initiates homologous repair as well as degrades foreign DNA. Recognition of chi sequence (5'-GCTGGTGG-3') switches RecBCD from a destructive, nucleolytic mode into a repair-active one that promotes RecA-mediated recombination. RecBCD includes a 3'-to-5' single-stranded DNA (ssDNA) translocase in RecB subunit, a 5'-to-3' translocase in RecD, and a secondary translocase activity associated with RecBC. To understand how chi specifically affects each translocase activity, we directly visualized individual RecBCD translocating along DNA substrates containing a ssDNA gap of different polarities, with or without chi. Disappearance of RecBCD from the ssDNA signals the loss of the ssDNA translocase activity. For substrates containing a ssDNA gap that RecBCD encounters in the 3'-to-5' polarity (3'-to-5' ssDNA), wild-type RecBCD disappears from the DNA substrates with similarly high percentage, either with chi or without. This suggests that (1) the 3'-to-5' translocase in RecB is unaffected by chi and (2) it is low in processivity. With substrates containing a ssDNA gap that RecBCD encounters in the 5'-to-3' polarity (5'-to-3' ssDNA), we found that the leaving percentage increases significantly with chi, implying inactivation of the 5'-to-3' translocase of RecD upon chi recognition. Surprisingly, the RecD defective mutant RecBCDK177Q showed only ≈50 % leaving on 5'-to-3' ssDNA, directly revealing the presence of RecBC secondary translocase and its activity is unaffected by chi. Multiple ssDNA translocases within the RecBCD complex both before and after chi ensures processive unwinding of DNA substrates required for efficient recombination events.
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Affiliation(s)
- Chia-Chuan Cho
- Department of Chemistry, National (Taiwan) University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Cinya Chung
- Department of Chemistry, National (Taiwan) University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National (Taiwan) University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
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32
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Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor. Proc Natl Acad Sci U S A 2017; 114:E6322-E6331. [PMID: 28716908 DOI: 10.1073/pnas.1701368114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In physiological settings, all nucleic acids motor proteins must travel along substrates that are crowded with other proteins. However, the physical basis for how motor proteins behave in these highly crowded environments remains unknown. Here, we use real-time single-molecule imaging to determine how the ATP-dependent translocase RecBCD travels along DNA occupied by tandem arrays of high-affinity DNA binding proteins. We show that RecBCD forces each protein into its nearest adjacent neighbor, causing rapid disruption of the protein-nucleic acid interaction. This mechanism is not the same way that RecBCD disrupts isolated nucleoprotein complexes on otherwise naked DNA. Instead, molecular crowding itself completely alters the mechanism by which RecBCD removes tightly bound protein obstacles from DNA.
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33
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Marshall R, Maxwell CS, Collins SP, Beisel CL, Noireaux V. Short DNA containing χ sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems. Biotechnol Bioeng 2017; 114:2137-2141. [PMID: 28475211 DOI: 10.1002/bit.26333] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/14/2017] [Accepted: 04/30/2017] [Indexed: 12/12/2022]
Abstract
Escherichia coli cell-free transcription-translation (TXTL) systems offer versatile platforms for advanced biomanufacturing and for prototyping synthetic biological parts and devices. Production and testing could be accelerated with the use of linear DNA, which can be rapidly and cheaply synthesized. However, linear DNA is efficiently degraded in TXTL preparations from E. coli. Here, we show that double-stranded DNA encoding χ sites-eight base-pair sequences preferentially bound by the RecBCD recombination machinery-stabilizes linear DNA and greatly enhances the TXTL-based expression and activity of a fluorescent reporter gene, simple regulatory cascades, and T7 bacteriophage particles. The χ-site DNA and the DNA-binding λ protein Gam yielded similar enhancements, and DNA with as few as four χ sites was sufficient to ensure robust gene expression in TXTL. Given the affordability and scalability of producing the short χ-site DNA, this generalized strategy is expected to advance the broad use of TXTL systems across its many applications. Biotechnol. Bioeng. 2017;114: 2137-2141. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455
| | - Colin S Maxwell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455
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34
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Badrinarayanan A, Le TBK, Spille JH, Cisse II, Laub MT. Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB. PLoS Genet 2017; 13:e1006783. [PMID: 28489851 PMCID: PMC5443536 DOI: 10.1371/journal.pgen.1006783] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 05/24/2017] [Accepted: 04/26/2017] [Indexed: 12/03/2022] Open
Abstract
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400–2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair–the attenuation of DNA-end processing and the initiation of homology search by RecA–thereby helping to ensure that genomic integrity is maintained during DSB repair. Double-strand breaks (DSBs) are a threat to genome integrity and are faithfully repaired via homologous recombination. The initial processing of DSB ends that prepares them for recombination has been well-studied in vitro, but is less well characterized in vivo. We describe a deep sequencing-based assay for assessing the early steps of DSB processing in bacterial cells by the helicase-nuclease complex AddAB. We find that a combination of chi site recognition and RecA loading is required to attenuate AddAB activity. In the absence of RecA, the chromosome is excessively degraded with a concomitant loss in transcription. Our results, along with prior studies, support a model for how chi recognition and RecA together regulate AddAB to maintain genome integrity and facilitate recombination.
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Affiliation(s)
- Anjana Badrinarayanan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bangalore, India
| | - Tung B. K. Le
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Ibrahim I. Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
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35
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Abstract
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways. Furthermore, unexpected discoveries have resulted from capabilities to resolve molecular heterogeneity and cell subpopulations, provoking new questions about the role of stochastic processes in DNA repair and mutagenesis. These studies are leading to new technologies that will find widespread use in basic research, biotechnology, and medicine.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
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36
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Pavankumar TL, Exell JC, Kowalczykowski SC. Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases. Methods Enzymol 2016; 581:1-32. [PMID: 27793277 DOI: 10.1016/bs.mie.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The unique translocation and DNA unwinding properties of DNA helicases can be concealed by the stochastic behavior of enzyme molecules within the necessarily large populations used in ensemble experiments. With recent technological advances, the direct visualization of helicases acting on individual DNA molecules has contributed significantly to the current understanding of their mechanisms of action and biological functions. The combination of single-molecule techniques that enable both manipulation of individual protein or DNA molecules and visualization of their actions has made it possible to literally see novel and unique biochemical characteristics that were previously masked. Here, we describe the execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, these methods allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.
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Affiliation(s)
| | - J C Exell
- University of California, Davis, CA, United States
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37
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The excluded DNA strand is SEW important for hexameric helicase unwinding. Methods 2016; 108:79-91. [DOI: 10.1016/j.ymeth.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/04/2023] Open
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38
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Wilkinson M, Chaban Y, Wigley DB. Mechanism for nuclease regulation in RecBCD. eLife 2016; 5. [PMID: 27644322 PMCID: PMC5030088 DOI: 10.7554/elife.18227] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/29/2016] [Indexed: 11/30/2022] Open
Abstract
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5’-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves a SH3 domain that binds to a region of the RecB subunit in a binding mode that is distinct from others observed previously in SH3 domains and, to our knowledge, this is the first example of peptide-binding of an SH3 domain in a bacterial system. DOI:http://dx.doi.org/10.7554/eLife.18227.001
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yuriy Chaban
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
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39
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Pinto C, Kasaciunaite K, Seidel R, Cejka P. Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases. eLife 2016; 5. [PMID: 27612385 PMCID: PMC5030094 DOI: 10.7554/elife.18574] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022] Open
Abstract
Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA. DOI:http://dx.doi.org/10.7554/eLife.18574.001
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Affiliation(s)
- Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Ralf Seidel
- Institute of Experimental Physics I, University of Leipzig, Leipzig, Germany
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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40
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Simon MJ, Sokoloski JE, Hao L, Weiland E, Lohman TM. Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation. J Mol Biol 2016; 428:2997-3012. [PMID: 27422010 DOI: 10.1016/j.jmb.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/13/2016] [Accepted: 07/06/2016] [Indexed: 11/25/2022]
Abstract
Escherichia coli RecBCD is a DNA helicase/nuclease that functions in double-stranded DNA break repair. RecBCD possesses two motors (RecB, a 3' to 5' translocase, and RecD, a 5' to 3' translocase). Current DNA unwinding models propose that motor translocation is tightly coupled to base pair melting. However, some biochemical evidence suggests that DNA melting of multiple base pairs may occur separately from single-stranded DNA translocation. To test this hypothesis, we designed DNA substrates containing reverse backbone polarity linkages that prevent ssDNA translocation of the canonical RecB and RecD motors. Surprisingly, we find that RecBCD can processively unwind DNA for at least 80bp beyond the reverse polarity linkages. This ability requires an ATPase active RecB motor, the RecB "arm" domain, and also the RecB nuclease domain, but not its nuclease activity. These results indicate that RecBCD can unwind duplex DNA processively in the absence of ssDNA translocation by the canonical motors and that the nuclease domain regulates the helicase activity of RecBCD.
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Affiliation(s)
- Michael J Simon
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Joshua E Sokoloski
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA.
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41
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Abstract
The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine genomic integrity and cause the accumulation of gross chromosomal abnormalities-including rearrangements, deletions, and aneuploidy-that contribute to cancer formation. Recombination proceeds through the formation of joint DNA molecules-homologously paired but metastable DNA intermediates that are processed by several alternative subpathways-making recombination a versatile and robust mechanism to repair damaged chromosomes. Modern biophysical methods make it possible to visualize, probe, and manipulate the individual molecules participating in the intermediate steps of recombination, revealing new details about the mechanics of genetic recombination. We review and discuss the individual stages of homologous recombination, focusing on common pathways in bacteria, yeast, and humans, and place particular emphasis on the molecular mechanisms illuminated by single-molecule methods.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
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42
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Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT. Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes. Nucleic Acids Res 2016; 44:5849-60. [PMID: 27220465 PMCID: PMC4937329 DOI: 10.1093/nar/gkw445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 05/09/2016] [Indexed: 01/02/2023] Open
Abstract
RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2-4 μM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (∼4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD-DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex. Five observations support this interpretation. First, these dynamics were present in the absence of ATP. Second, the onset of the dynamics was coupled to RecBCD entering into an unwinding-competent state that required a sufficiently long 5' strand to engage the RecD helicase. Third, the dynamics were modulated by the GC-content of the dsDNA. Fourth, the dynamics were suppressed by an engineered interstrand cross-link in the dsDNA that prevented unwinding. Finally, these dynamics were suppressed by binding of a specific non-hydrolyzable ATP analog. Collectively, these observations show that during unwinding, RecBCD binds to DNA in a dynamic mode that is modulated by the nucleotide state of the ATP-binding pocket.
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Affiliation(s)
- Ashley R Carter
- Department of Physics, Amherst College, Amherst, MA 01002, USA
| | - Maasa H Seaberg
- Department of Physics, University of Colorado, Boulder, CO 80309, USA JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B1R6, Canada
| | - Gang Sun
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | | | - Hung-Wen Li
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec H4B1R6, Canada
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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43
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Gyimesi M, Harami GM, Kocsis ZS, Kovács M. Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases. Methods 2016; 108:24-39. [PMID: 27133766 DOI: 10.1016/j.ymeth.2016.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 01/11/2023] Open
Abstract
Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins. We outline practically useful analysis procedures for equilibrium, steady-state and transient kinetic data. This analysis can be used to quantitatively characterize the enzymatic steps of the NTP hydrolytic cycle, the binding site size, stoichiometry and energetics of protein-NA interactions, the rate and processivity of translocation along and unwinding of NA strands, and the mechanochemical coupling between these processes. The described methods yield insights into the functional role of the enzymes, and also greatly aid the design and interpretation of single-molecule experiments as well as the engineering of enzymatic properties for biotechnological applications.
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Affiliation(s)
- Máté Gyimesi
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Zsuzsa S Kocsis
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
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Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. J Biol Chem 2016; 291:12467-12480. [PMID: 27044751 DOI: 10.1074/jbc.m116.719591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/06/2022] Open
Abstract
The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.
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Affiliation(s)
- Brian W Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Katie L Dodge
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Carly T Thaxton
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Danae Olaso
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798.
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Gilhooly NS, Carrasco C, Gollnick B, Wilkinson M, Wigley DB, Moreno-Herrero F, Dillingham MS. Chi hotspots trigger a conformational change in the helicase-like domain of AddAB to activate homologous recombination. Nucleic Acids Res 2016; 44:2727-41. [PMID: 26762979 PMCID: PMC4824097 DOI: 10.1093/nar/gkv1543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/27/2015] [Indexed: 11/29/2022] Open
Abstract
In bacteria, the repair of double-stranded DNA breaks is modulated by Chi sequences. These are recognised by helicase-nuclease complexes that process DNA ends for homologous recombination. Chi activates recombination by changing the biochemical properties of the helicase-nuclease, transforming it from a destructive exonuclease into a recombination-promoting repair enzyme. This transition is thought to be controlled by the Chi-dependent opening of a molecular latch, which enables part of the DNA substrate to evade degradation beyond Chi. Here, we show that disruption of the latch improves Chi recognition efficiency and stabilizes the interaction of AddAB with Chi, even in mutants that are impaired for Chi binding. Chi recognition elicits a structural change in AddAB that maps to a region of AddB which resembles a helicase domain, and which harbours both the Chi recognition locus and the latch. Mutation of the latch potentiates the change and moderately reduces the duration of a translocation pause at Chi. However, this mutant displays properties of Chi-modified AddAB even in the complete absence of bona fide hotspot sequences. The results are used to develop a model for AddAB regulation in which allosteric communication between Chi binding and latch opening ensures quality control during recombination hotspot recognition.
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Affiliation(s)
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
| | - Benjamin Gollnick
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
| | - Martin Wilkinson
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Dale B Wigley
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
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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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47
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Kowalczykowski SC. An Overview of the Molecular Mechanisms of Recombinational DNA Repair. Cold Spring Harb Perspect Biol 2015; 7:a016410. [PMID: 26525148 PMCID: PMC4632670 DOI: 10.1101/cshperspect.a016410] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for genomic integrity. It is a template-directed process that uses a second chromosomal copy (sister, daughter, or homolog) to ensure proper repair of broken chromosomes. The key steps of recombination are conserved from phage through human, and an overview of those steps is provided in this review. The first step is resection by helicases and nucleases to produce single-stranded DNA (ssDNA) that defines the homologous locus. The ssDNA is a scaffold for assembly of the RecA/RAD51 filament, which promotes the homology search. On finding homology, the nucleoprotein filament catalyzes exchange of DNA strands to form a joint molecule. Recombination is controlled by regulating the fate of both RecA/RAD51 filaments and DNA pairing intermediates. Finally, intermediates that mature into Holliday structures are disjoined by either nucleolytic resolution or topological dissolution.
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Affiliation(s)
- Stephen C Kowalczykowski
- Department of Microbiology & Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616
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48
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Abstract
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
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49
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Abstract
AddAB and RecBCD-type helicase-nuclease complexes control the first stage of bacterial homologous recombination (HR) – the resection of double strand DNA breaks. A switch in the activities of the complexes to initiate repair by HR is regulated by a short, species-specific DNA sequence known as a Crossover Hotspot Instigator (Chi) site. It has been shown that, upon encountering Chi, AddAB and RecBCD pause translocation before resuming at a reduced rate. Recently, the structure of B.subtilis AddAB in complex with its regulatory Chi sequence revealed the nature of Chi binding and the paused translocation state. Here the structural features associated with Chi binding are described in greater detail and discussed in relation to the related E.coli RecBCD system.
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Affiliation(s)
- Martin Wilkinson
- a Division of Structural Biology; Institute of Cancer Research; Chester Beatty Laboratories ; London , UK
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50
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Cejka P. DNA End Resection: Nucleases Team Up with the Right Partners to Initiate Homologous Recombination. J Biol Chem 2015; 290:22931-8. [PMID: 26231213 DOI: 10.1074/jbc.r115.675942] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The repair of DNA double-strand breaks by homologous recombination commences by nucleolytic degradation of the 5'-terminated strand of the DNA break. This leads to the formation of 3'-tailed DNA, which serves as a substrate for the strand exchange protein Rad51. The nucleoprotein filament then invades homologous DNA to drive template-directed repair. In this review, I discuss mainly the mechanisms of DNA end resection in Saccharomyces cerevisiae, which includes short-range resection by Mre11-Rad50-Xrs2 and Sae2, as well as processive long-range resection by Sgs1-Dna2 or Exo1 pathways. Resection mechanisms are highly conserved between yeast and humans, and analogous machineries are found in prokaryotes as well.
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Affiliation(s)
- Petr Cejka
- From the Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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