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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Qian J, Cartee A, Xu W, Yan Y, Wang B, Artsimovitch I, Dunlap D, Finzi L. Reciprocating RNA Polymerase batters through roadblocks. Nat Commun 2024; 15:3193. [PMID: 38609371 PMCID: PMC11014978 DOI: 10.1038/s41467-024-47531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.
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Affiliation(s)
- Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | - Bing Wang
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Irina Artsimovitch
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA.
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3
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Amundsen SK, Smith GR. RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiol Mol Biol Rev 2023; 87:e0004123. [PMID: 38047637 PMCID: PMC10732027 DOI: 10.1128/mmbr.00041-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYRecBCD enzyme is a multi-functional protein that initiates the major pathway of homologous genetic recombination and DNA double-strand break repair in Escherichia coli. It is also required for high cell viability and aids proper DNA replication. This 330-kDa, three-subunit enzyme is one of the fastest, most processive helicases known and contains a potent nuclease controlled by Chi sites, hotspots of recombination, in DNA. RecBCD undergoes major changes in activity and conformation when, during DNA unwinding, it encounters Chi (5'-GCTGGTGG-3') and nicks DNA nearby. Here, we discuss the multitude of mutations in each subunit that affect one or another activity of RecBCD and its control by Chi. These mutants have given deep insights into how the multiple activities of this complex enzyme are coordinated and how it acts in living cells. Similar studies could help reveal how other complex enzymes are controlled by inter-subunit interactions and conformational changes.
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Affiliation(s)
| | - Gerald R. Smith
- Fred Hutchinson Cancer Center Seattle, Seattle, Washington, USA
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4
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Zou Z, Liang J, Jia Q, Bai D, Xie W, Wu W, Tan C, Ma J. A versatile and high-throughput flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. NANOSCALE 2023; 15:17443-17454. [PMID: 37859523 DOI: 10.1039/d3nr03214k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A flow-cell offers many advantages for single-molecule studies. But, its merit as a quantitative single-molecule tool has long been underestimated. In this work, we developed a gas-pumped fully calibrated flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. Such a flow-cell system has considered the hydrodynamic drags on biomolecules and hence can apply and measure force up to more than 100 pN in sub-pN precision with an ultra-high force stability (force drift <0.01 pN in 10 minutes) and tuning accuracy (∼0.04 pN). Meanwhile, it also allows acquiring force signals and fluorescence images at the same time, parallelly tracking hundreds of protein motors in real time as well as monitoring the conformational changes of biomolecules under a well-controlled force, as demonstrated by a series of single-molecule experiments in this work, including the studies of DNA overstretching dynamics, transcription under force and DNA folding/unfolding dynamics. Interesting findings, such as the very tight association of single-stranded binding (SSB) proteins with ssDNA and the reversed transcription, have also been made. These results together lay down an essential foundation for a flow-cell to be used as a versatile, quantitative and high-throughput tool for single-molecule manipulation and visualization.
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Affiliation(s)
- Zhenyu Zou
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Di Bai
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Wenqiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Chuang Tan
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
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5
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Schaich MA, Schnable BL, Kumar N, Roginskaya V, Jakielski R, Urban R, Zhong Z, Kad NM, Van Houten B. Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE). Nucleic Acids Res 2023; 51:e39. [PMID: 36861323 PMCID: PMC10123111 DOI: 10.1093/nar/gkad095] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Single-molecule characterization of protein-DNA dynamics provides unprecedented mechanistic details about numerous nuclear processes. Here, we describe a new method that rapidly generates single-molecule information with fluorescently tagged proteins isolated from nuclear extracts of human cells. We demonstrated the wide applicability of this novel technique on undamaged DNA and three forms of DNA damage using seven native DNA repair proteins and two structural variants, including: poly(ADP-ribose) polymerase (PARP1), heterodimeric ultraviolet-damaged DNA-binding protein (UV-DDB), and 8-oxoguanine glycosylase 1 (OGG1). We found that PARP1 binding to DNA nicks is altered by tension, and that UV-DDB did not act as an obligate heterodimer of DDB1 and DDB2 on UV-irradiated DNA. UV-DDB bound to UV photoproducts with an average lifetime of 39 seconds (corrected for photobleaching, τc), whereas binding lifetimes to 8-oxoG adducts were < 1 second. Catalytically inactive OGG1 variant K249Q bound oxidative damage 23-fold longer than WT OGG1, at 47 and 2.0 s, respectively. By measuring three fluorescent colors simultaneously, we also characterized the assembly and disassembly kinetics of UV-DDB and OGG1 complexes on DNA. Hence, the SMADNE technique represents a novel, scalable, and universal method to obtain single-molecule mechanistic insights into key protein-DNA interactions in an environment containing physiologically-relevant nuclear proteins.
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Affiliation(s)
- Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Brittani L Schnable
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Namrata Kumar
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Rachel C Jakielski
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Roman Urban
- School of Biosciences, University of Kent, Kent, UK
| | - Zhou Zhong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- LUMICKS, Waltham, MA, USA
| | - Neil M Kad
- School of Biosciences, University of Kent, Kent, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
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6
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Zernia S, Stigler J. DNA curtains for studying phase separation mechanisms of DNA-organizing proteins. Methods Cell Biol 2023; 182:95-108. [PMID: 38359990 DOI: 10.1016/bs.mcb.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Phase separation is one key mechanism to organize chromatin into compartments and to regulate the activity of the genome. The formation of liquid-like droplets within the nucleus is driven by protein association to the DNA via multivalent binding and the recruitment of other proteins building a concentrated reaction environment. Common methods to study phase separation and its liquid-like nature are based on microscopy of the formed droplets but lack the resolution to obtain information on the molecular level. Here, we describe the application of the DNA curtain technique for studying protein-mediated phase separation on DNA. For this, multiple lipid-anchored DNA strands are flow-stretched across a nanobarrier to allow single-molecule studies of protein-DNA interactions in a high-throughput approach. Our protocol describes how protein-induced DNA compaction can be observed in real-time and which wash protocols are suitable to characterize the interactions that promote condensate formation. Furthermore, we demonstrate how fluorescently labeled tracer proteins can serve as orientation points to examine the DNA compaction mechanism in detail.
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Affiliation(s)
- Sarah Zernia
- Gene Center Munich, Ludwig Maximilian University, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig Maximilian University, Munich, Germany.
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7
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Shiriaeva AA, Kuznedelov K, Fedorov I, Musharova O, Khvostikov T, Tsoy Y, Kurilovich E, Smith GR, Semenova E, Severinov K. Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system. SCIENCE ADVANCES 2022; 8:eabn8650. [PMID: 36427302 PMCID: PMC9699676 DOI: 10.1126/sciadv.abn8650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In Escherichia coli, immunity is acquired upon integration of 33-bp spacers into CRISPR arrays. DNA targets complementary to spacers get degraded and serve as a source of new spacers during a process called primed adaptation. Precursors of such spacers, prespacers, are ~33-bp double-stranded DNA fragments with a ~4-nt 3' overhang. The mechanism of prespacer generation is not clear. Here, we use FragSeq and biochemical approaches to determine enzymes involved in generation of defined prespacer ends. We demonstrate that RecJ is the main exonuclease trimming 5' ends of prespacer precursors, although its activity can be partially substituted by ExoVII. The RecBCD complex allows single strand-specific RecJ to process double-stranded regions flanking prespacers. Our results reveal intricate functional interactions of genome maintenance proteins with CRISPR interference and adaptation machineries during generation of prespacers capable of integration into CRISPR arrays.
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Affiliation(s)
- Anna A. Shiriaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Saint Petersburg State University, Saint Petersburg 199034, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Kuznedelov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ivan Fedorov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Olga Musharova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow 123182, Russia
| | - Timofey Khvostikov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Yuliya Tsoy
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Elena Kurilovich
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Gerald R. Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow 123182, Russia
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8
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Kang Y, An S, Min D, Lee JY. Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair. Front Bioeng Biotechnol 2022; 10:973314. [PMID: 36185427 PMCID: PMC9520083 DOI: 10.3389/fbioe.2022.973314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Soyeong An
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Center for Genomic Integrity, Institute of Basic Sciences, Ulsan, South Korea
- *Correspondence: Ja Yil Lee,
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9
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Matozel EK, Parziale S, Price AC. A programmable DNA roadblock system using dCas9 and multivalent target sites. PLoS One 2022; 17:e0268099. [PMID: 35522691 PMCID: PMC9075669 DOI: 10.1371/journal.pone.0268099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regulation as well as DNA binding. Experimental methods for studying the effects of such roadblocks often target endogenous sites or introduce non-variable specific sites into DNAs to create binding sites for artificially introduced protein roadblocks. In this work, we describe a method to create programmable roadblocks using dCas9, a cleavage deficient mutant of the CRISPR effector nuclease Cas9. The programmability allows us to custom design target sites in a synthetic gene intended for in vitro studies. These target sites can be coded with multivalency-in our case, internal restriction sites which can be used in validation studies to verify complete binding of the roadblock. We provide full protocols and sequences and demonstrate how to use the internal restriction sites to verify complete binding of the roadblock. We also provide example results of the effect of DNA roadblocks on the translocation of the restriction endonuclease NdeI, which searches for its cognate site using one dimensional diffusion along DNA.
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Affiliation(s)
- Emily K. Matozel
- Department of Biology, Emmanuel College, Boston, United States of America
| | - Stephen Parziale
- Department of Mathematics, Emmanuel College, Boston, United States of America
| | - Allen C. Price
- Department of Chemistry and Physics, Emmanuel College, Boston, United States of America
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10
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Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
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Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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11
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Warren GM, Meir A, Wang J, Patel DJ, Greene EC, Shuman S. Structure-activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB. Nucleic Acids Res 2021; 50:952-961. [PMID: 34967418 PMCID: PMC8789073 DOI: 10.1093/nar/gkab1270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks. The AdnB subunit hydrolyzes ATP to drive single-nucleotide steps of 3′-to-5′ translocation of AdnAB on the tracking DNA strand via a ratchet-like mechanism. Trp325 in AdnB motif III, which intercalates into the tracking strand and makes a π stack on a nucleobase 5′ of a flipped-out nucleoside, is the putative ratchet pawl without which ATP hydrolysis is mechanically futile. Here, we report that AdnAB mutants wherein Trp325 was replaced with phenylalanine, tyrosine, histidine, leucine, or alanine retained activity in ssDNA-dependent ATP hydrolysis but displayed a gradient of effects on DSB resection. The resection velocities of Phe325 and Tyr325 mutants were 90% and 85% of the wild-type AdnAB velocity. His325 slowed resection rate to 3% of wild-type and Leu325 and Ala325 abolished DNA resection. A cryo-EM structure of the DNA-bound Ala325 mutant revealed that the AdnB motif III peptide was disordered and the erstwhile flipped out tracking strand nucleobase reverted to a continuous base-stacked arrangement with its neighbors. We conclude that π stacking of Trp325 on a DNA nucleobase triggers and stabilizes the flipped-out conformation of the neighboring nucleoside that underlies formation of a ratchet pawl.
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Affiliation(s)
- Garrett M Warren
- Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Aviv Meir
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Juncheng Wang
- Structural Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
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12
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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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13
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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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14
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Liang J, Li J, Zhong Z, Rujiralai T, Ma J. Quantifying the force in flow-cell based single-molecule stretching experiments. NANOSCALE 2021; 13:15916-15927. [PMID: 34522927 DOI: 10.1039/d1nr04748e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flow-cell based single-molecule manipulation technique has found many applications in the study of DNA mechanics and protein-DNA interactions. However, the force in these experiments has not been fully characterized and is usually limited to a moderate force regime (<25 pN). In this work, using the "tethered-bead" assay, the hydrodynamic drag of DNA has been quantitatively evaluated based on a "bead-spring chain" model. The force derived from the Brownian motion of the bead thus contains both contributions from this equivalent hydrodynamic drag of DNA and the pulling force from the tethered bead. Next, using flow-cell based DNA pulling experiments, the linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system has been demonstrated to be valid over a wide force range (0-110 pN). Consequently, the force can be directly converted from the flow rate by a linear factor that can be calibrated either by the bead's Brownian motion at low flow rates or using DNA overstretching transition. Furthermore, the hydrodynamic force and torque due to the shear flow on the bead as well as the equivalent stretching force on DNA are calculated based on theoretical models with the hydrodynamic drag on DNA also considered. The calculated force-extension curves show a good agreement with the measured ones. These results offer important insights into the force in flow-cell based single-molecule stretching experiments and provide a foundation for establishing flow-cells as a simple, low-cost, yet flexible and precise tool for single-molecule force measurements over a wide force range.
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Affiliation(s)
- Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Jiaxi Li
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Thitima Rujiralai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
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15
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Nagae F, Brandani GB, Takada S, Terakawa T. The lane-switch mechanism for nucleosome repositioning by DNA translocase. Nucleic Acids Res 2021; 49:9066-9076. [PMID: 34365508 PMCID: PMC8450081 DOI: 10.1093/nar/gkab664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Translocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone octamers and forms nucleosomes, translocases inevitably encounter nucleosomes. A previous study has shown that a nucleosome repositions downstream when a translocase collides with the nucleosome. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identified the lane-switch mechanism for downstream repositioning with molecular dynamics simulations and validated it with restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding lane to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have broad implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.
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Affiliation(s)
- Fritz Nagae
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan
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16
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [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: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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17
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Clutch mechanism of chemomechanical coupling in a DNA resecting motor nuclease. Proc Natl Acad Sci U S A 2021; 118:2023955118. [PMID: 33836607 DOI: 10.1073/pnas.2023955118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The N-terminal motor domain of the AdnB subunit hydrolyzes ATP to drive rapid and processive 3' to 5' translocation of AdnAB on the tracking DNA strand. ATP hydrolysis is mechanically productive when oscillating protein domain motions synchronized with the ATPase cycle propel the DNA tracking strand forward by a single-nucleotide step, in what is thought to entail a pawl-and-ratchet-like fashion. By gauging the effects of alanine mutations of the 16 amino acids at the AdnB-DNA interface on DNA-dependent ATP hydrolysis, DNA translocation, and DSB resection in ensemble and single-molecule assays, we gained key insights into which DNA contacts couple ATP hydrolysis to motor activity. The results implicate AdnB Trp325, which intercalates into the tracking strand and stacks on a nucleobase, as the singular essential constituent of the ratchet pawl, without which ATP hydrolysis on ssDNA is mechanically futile. Loss of Thr663 and Thr118 contacts with tracking strand phosphates and of His665 with a nucleobase drastically slows the AdnAB motor during DSB resection. Our findings for AdnAB prompt us to analogize its mechanism to that of an automobile clutch.
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18
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Dienerowitz M, Howard JAL, Quinn SD, Dienerowitz F, Leake MC. Single-molecule FRET dynamics of molecular motors in an ABEL trap. Methods 2021; 193:96-106. [PMID: 33571667 DOI: 10.1016/j.ymeth.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap's inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 seconds with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.
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Affiliation(s)
- Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2 - 4, 07743 Jena, Germany.
| | - Jamieson A L Howard
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven D Quinn
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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19
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Amundsen SK, Taylor AF, Smith GR. Chi hotspot control of RecBCD helicase-nuclease by long-range intramolecular signaling. Sci Rep 2020; 10:19415. [PMID: 33154402 PMCID: PMC7644769 DOI: 10.1038/s41598-020-73078-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022] Open
Abstract
Repair of broken DNA by homologous recombination requires coordinated enzymatic reactions to prepare it for interaction with intact DNA. The multiple activities of enterobacterial RecBCD helicase-nuclease are coordinated by Chi recombination hotspots (5′ GCTGGTGG 3′) recognized during DNA unwinding. Chi is recognized in a tunnel in RecC but activates the RecB nuclease, > 25 Ǻ away. How the Chi-dependent signal travels this long distance has been unknown. We found a Chi hotspot-deficient mutant in the RecB helicase domain located > 45 Ǻ from both the Chi-recognition site and the nuclease active site. This unexpected observation led us to find additional mutations that reduced or eliminated Chi hotspot activity in each subunit and widely scattered throughout RecBCD. Each mutation alters the intimate contact between one or another pair of subunits in crystal or cryoEM structures of RecBCD bound to DNA. Collectively, these mutations span a path about 185 Ǻ long from the Chi recognition site to the nuclease active site. We discuss these surprising results in the context of an intramolecular signal transduction accounting for many previous observations.
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Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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20
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Price RM, Budzyński MA, Kundra S, Teves SS. Advances in visualizing transcription factor - DNA interactions. Genome 2020; 64:449-466. [PMID: 33113335 DOI: 10.1139/gen-2020-0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.
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Affiliation(s)
- Rachel M Price
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Marek A Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Shivani Kundra
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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21
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Meijering AEC, Biebricher AS, Sitters G, Brouwer I, Peterman EJG, Wuite GJL, Heller I. Imaging unlabeled proteins on DNA with super-resolution. Nucleic Acids Res 2020; 48:e34. [PMID: 32016413 PMCID: PMC7102996 DOI: 10.1093/nar/gkaa061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Fluorescence microscopy is invaluable to a range of biomolecular analysis approaches. The required labeling of proteins of interest, however, can be challenging and potentially perturb biomolecular functionality as well as cause imaging artefacts and photo bleaching issues. Here, we introduce inverse (super-resolution) imaging of unlabeled proteins bound to DNA. In this new method, we use DNA-binding fluorophores that transiently label bare DNA but not protein-bound DNA. In addition to demonstrating diffraction-limited inverse imaging, we show that inverse Binding-Activated Localization Microscopy or 'iBALM' can resolve biomolecular features smaller than the diffraction limit. The current detection limit is estimated to lie at features between 5 and 15 nm in size. Although the current image-acquisition times preclude super-resolving fast dynamics, we show that diffraction-limited inverse imaging can reveal molecular mobility at ∼0.2 s temporal resolution and that the method works both with DNA-intercalating and non-intercalating dyes. Our experiments show that such inverse imaging approaches are valuable additions to the single-molecule toolkit that relieve potential limitations posed by labeling.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerrit Sitters
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ineke Brouwer
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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22
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Kang Y, Cheon NY, Cha J, Kim A, Kim HI, Lee L, Kim KO, Jo K, Lee JY. High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins. Biotechnol Bioeng 2020; 117:1640-1648. [PMID: 32162675 DOI: 10.1002/bit.27331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.
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Affiliation(s)
- Yujin Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Na Young Cheon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jongjin Cha
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Ayoung Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hyung-Il Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Luda Lee
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kang O Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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23
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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24
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Shin E, Kim W, Lee S, Bae J, Kim S, Ko W, Seo HS, Lim S, Lee HS, Jo K. Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer. Sci Rep 2019; 9:17197. [PMID: 31748571 PMCID: PMC6868158 DOI: 10.1038/s41598-019-53722-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.
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Affiliation(s)
- Eunji Shin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Woojung Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Sanggil Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Wooseok Ko
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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25
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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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26
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Ahmadi A, Till K, Hafting Y, Schüttpelz M, Bjørås M, Glette K, Tørresen J, Rowe AD, Dalhus B. Additive manufacturing of laminar flow cells for single-molecule experiments. Sci Rep 2019; 9:16784. [PMID: 31727950 PMCID: PMC6856346 DOI: 10.1038/s41598-019-53151-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/22/2019] [Indexed: 11/08/2022] Open
Abstract
A microfluidic laminar flow cell (LFC) forms an indispensable component in single-molecule experiments, enabling different substances to be delivered directly to the point under observation and thereby tightly controlling the biochemical environment immediately surrounding single molecules. Despite substantial progress in the production of such components, the process remains relatively inefficient, inaccurate and time-consuming. Here we address challenges and limitations in the routines, materials and the designs that have been commonly employed in the field, and introduce a new generation of LFCs designed for single-molecule experiments and assembled using additive manufacturing. We present single- and multi-channel, as well as reservoir-based LFCs produced by 3D printing to perform single-molecule experiments. Using these flow cells along with optical tweezers, we show compatibility with single-molecule experiments including the isolation and manipulation of single DNA molecules either attached to the surface of a coverslip or as freely movable DNA dumbbells, as well as direct observation of protein-DNA interactions. Using additive manufacturing to produce LFCs with versatility of design and ease of production allow experimentalists to optimize the flow cells to their biological experiments and provide considerable potential for performing multi-component single-molecule experiments.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katharina Till
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Yngve Hafting
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Kyrre Glette
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
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27
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Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System. Genes (Basel) 2019; 10:genes10110872. [PMID: 31683605 PMCID: PMC6896009 DOI: 10.3390/genes10110872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders’ genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.
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28
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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29
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Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure. Methods 2019; 169:46-56. [PMID: 31351926 DOI: 10.1016/j.ymeth.2019.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/01/2019] [Accepted: 07/22/2019] [Indexed: 01/05/2023] Open
Abstract
Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.
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30
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Wiktor J, van der Does M, Büller L, Sherratt DJ, Dekker C. Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo. Nucleic Acids Res 2019; 46:1821-1833. [PMID: 29294118 PMCID: PMC5829741 DOI: 10.1093/nar/gkx1290] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/18/2017] [Indexed: 11/13/2022] Open
Abstract
The formation of 3′ single-stranded DNA overhangs is a first and essential step during homology-directed repair of double-stranded breaks (DSB) of DNA, a task that in Escherichia coli is performed by RecBCD. While this protein complex has been well characterized through in vitro single-molecule studies, it has remained elusive how end resection proceeds in the crowded and complex environment in live cells. Here, we develop a two-color fluorescent reporter to directly observe the resection of individual inducible DSB sites within live E. coli cells. Real-time imaging shows that RecBCD during end resection degrades DNA with remarkably high speed (∼1.6 kb/s) and high processivity (>∼100 kb). The results show a pronounced asymmetry in the processing of the two DNA ends of a DSB, where much longer stretches of DNA are degraded in the direction of terminus. The microscopy observations are confirmed using quantitative polymerase chain reaction measurements of the DNA degradation. Deletion of the recD gene drastically decreased the length of resection, allowing for recombination with short ectopic plasmid homologies and significantly increasing the efficiency of horizontal gene transfer between strains. We thus visualized and quantified DNA end resection by the RecBCD complex in live cells, recorded DNA-degradation linked to end resection and uncovered a general relationship between the length of end resection and the choice of the homologous recombination template.
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Affiliation(s)
- Jakub Wiktor
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Marit van der Does
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lisa Büller
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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31
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Radovcic M, Killelea T, Savitskaya E, Wettstein L, Bolt EL, Ivancic-Bace I. CRISPR-Cas adaptation in Escherichia coli requires RecBCD helicase but not nuclease activity, is independent of homologous recombination, and is antagonized by 5' ssDNA exonucleases. Nucleic Acids Res 2019; 46:10173-10183. [PMID: 30189098 PMCID: PMC6212769 DOI: 10.1093/nar/gky799] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/25/2018] [Indexed: 12/29/2022] Open
Abstract
Prokaryotic adaptive immunity is established against mobile genetic elements (MGEs) by ‘naïve adaptation’ when DNA fragments from a newly encountered MGE are integrated into CRISPR–Cas systems. In Escherichia coli, DNA integration catalyzed by Cas1–Cas2 integrase is well understood in mechanistic and structural detail but much less is known about events prior to integration that generate DNA for capture by Cas1–Cas2. Naïve adaptation in E. coli is thought to depend on the DNA helicase-nuclease RecBCD for generating DNA fragments for capture by Cas1–Cas2. The genetics presented here show that naïve adaptation does not require RecBCD nuclease activity but that helicase activity may be important. RecA loading by RecBCD inhibits adaptation explaining previously observed adaptation phenotypes that implicated RecBCD nuclease activity. Genetic analysis of other E. coli nucleases and naïve adaptation revealed that 5′ ssDNA tailed DNA molecules promote new spacer acquisition. We show that purified E. coli Cas1–Cas2 complex binds to and nicks 5′ ssDNA tailed duplexes and propose that E. coli Cas1–Cas2 nuclease activity on such DNA structures supports naïve adaptation.
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Affiliation(s)
- Marin Radovcic
- Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Tom Killelea
- School of Life Sciences, University of Nottingham, UK
| | - Ekaterina Savitskaya
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | | | - Edward L Bolt
- School of Life Sciences, University of Nottingham, UK
| | - Ivana Ivancic-Bace
- Department of Biology, Faculty of Science, University of Zagreb, Croatia
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32
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Rudnizky S, Khamis H, Malik O, Squires AH, Meller A, Melamed P, Kaplan A. Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context. Nucleic Acids Res 2019; 46:1513-1524. [PMID: 29253225 PMCID: PMC5815098 DOI: 10.1093/nar/gkx1252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/11/2017] [Indexed: 12/31/2022] Open
Abstract
Most functional transcription factor (TF) binding sites deviate from their ‘consensus’ recognition motif, although their sites and flanking sequences are often conserved across species. Here, we used single-molecule DNA unzipping with optical tweezers to study how Egr-1, a TF harboring three zinc fingers (ZF1, ZF2 and ZF3), is modulated by the sequence and context of its functional sites in the Lhb gene promoter. We find that both the core 9 bp bound to Egr-1 in each of the sites, and the base pairs flanking them, modulate the affinity and structure of the protein–DNA complex. The effect of the flanking sequences is asymmetric, with a stronger effect for the sequence flanking ZF3. Characterization of the dissociation time of Egr-1 revealed that a local, mechanical perturbation of the interactions of ZF3 destabilizes the complex more effectively than a perturbation of the ZF1 interactions. Our results reveal a novel role for ZF3 in the interaction of Egr-1 with other proteins and the DNA, providing insight on the regulation of Lhb and other genes by Egr-1. Moreover, our findings reveal the potential of small changes in DNA sequence to alter transcriptional regulation, and may shed light on the organization of regulatory elements at promoters.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Malik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Amit Meller
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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33
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Brüning JG, Howard JAL, Myka KK, Dillingham MS, McGlynn P. The 2B subdomain of Rep helicase links translocation along DNA with protein displacement. Nucleic Acids Res 2019; 46:8917-8925. [PMID: 30060236 PMCID: PMC6158625 DOI: 10.1093/nar/gky673] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Helicases catalyse DNA and RNA strand separation. Proteins bound to the nucleic acid must also be displaced in order to unwind DNA. This is exemplified by accessory helicases that clear protein barriers from DNA ahead of advancing replication forks. How helicases catalyse DNA unwinding is increasingly well understood but how protein displacement is achieved is unclear. Escherichia coli Rep accessory replicative helicase lacking one of its four subdomains, 2B, has been shown to be hyperactivated for DNA unwinding in vitro but we show here that RepΔ2B is, in contrast, deficient in displacing proteins from DNA. This defect correlates with an inability to promote replication of protein-bound DNA in vitro and lack of accessory helicase function in vivo. Defective protein displacement is manifested on double-stranded and single-stranded DNA. Thus binding and distortion of duplex DNA by the 2B subdomain ahead of the helicase is not the missing function responsible for this deficiency. These data demonstrate that protein displacement from DNA is not simply achieved by helicase translocation alone. They also imply that helicases may have evolved different specific features to optimise DNA unwinding and protein displacement, both of which are now recognised as key functions in all aspects of nucleic acid metabolism.
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Affiliation(s)
| | | | - Kamila K Myka
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Peter McGlynn
- Department of Biology, University of York, York YO10 5DD, UK
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34
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Soniat MM, Myler LR, Kuo HC, Paull TT, Finkelstein IJ. RPA Phosphorylation Inhibits DNA Resection. Mol Cell 2019; 75:145-153.e5. [PMID: 31153714 DOI: 10.1016/j.molcel.2019.05.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/26/2019] [Accepted: 05/01/2019] [Indexed: 01/20/2023]
Abstract
Genetic recombination in all kingdoms of life initiates when helicases and nucleases process (resect) the free DNA ends to expose single-stranded DNA (ssDNA) overhangs. Resection regulation in bacteria is programmed by a DNA sequence, but a general mechanism limiting resection in eukaryotes has remained elusive. Using single-molecule imaging of reconstituted human DNA repair factors, we identify phosphorylated RPA (pRPA) as a negative resection regulator. Bloom's syndrome (BLM) helicase together with exonuclease 1 (EXO1) and DNA2 nucleases catalyze kilobase-length DNA resection on nucleosome-coated DNA. The resulting ssDNA is rapidly bound by RPA, which further stimulates DNA resection. RPA is phosphorylated during resection as part of the DNA damage response (DDR). Remarkably, pRPA inhibits DNA resection in cellular assays and in vitro via inhibition of BLM helicase. pRPA suppresses BLM initiation at DNA ends and promotes the intrinsic helicase strand-switching activity. These findings establish that pRPA provides a feedback loop between DNA resection and the DDR.
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Affiliation(s)
- Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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35
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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36
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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37
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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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38
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Abstract
DNA double-strand breaks (DSBs) are a potentially lethal DNA lesions that disrupt both the physical and genetic continuity of the DNA duplex. Homologous recombination (HR) is a universally conserved genome maintenance pathway that initiates via nucleolytic processing of the broken DNA ends (resection). Eukaryotic DNA resection is catalyzed by the resectosome-a multicomponent molecular machine consisting of the nucleases DNA2 or Exonuclease 1 (EXO1), Bloom's helicase (BLM), the MRE11-RAD50-NBS1 (MRN) complex, and additional regulatory factors. Here, we describe methods for purification and single-molecule imaging and analysis of EXO1, DNA2, and BLM. We also describe how to adapt resection assays to the high-throughput single-molecule DNA curtain assay. By organizing hundreds of individual molecules on the surface of a microfluidic flowcell, DNA curtains visualize protein complexes with the required spatial and temporal resolution to resolve the molecular choreography during critical DNA-processing reactions.
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39
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Schaub JM, Zhang H, Soniat MM, Finkelstein IJ. Assessing Protein Dynamics on Low-Complexity Single-Stranded DNA Curtains. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14882-14890. [PMID: 30044093 PMCID: PMC6679933 DOI: 10.1021/acs.langmuir.8b01812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-stranded DNA (ssDNA) is a critical intermediate in all DNA transactions. Because ssDNA is more flexible than double-stranded (ds) DNA, interactions with ssDNA-binding proteins (SSBs) may significantly compact or elongate the ssDNA molecule. Here, we develop and characterize low-complexity ssDNA curtains, a high-throughput single-molecule assay to simultaneously monitor protein binding and correlated ssDNA length changes on supported lipid bilayers. Low-complexity ssDNA is generated via rolling circle replication of short synthetic oligonucleotides, permitting control over the sequence composition and secondary structure-forming propensity. One end of the ssDNA is functionalized with a biotin, while the second is fluorescently labeled to track the overall DNA length. Arrays of ssDNA molecules are organized at microfabricated barriers for high-throughput single-molecule imaging. Using this assay, we demonstrate that E. coli SSB drastically and reversibly compacts ssDNA templates upon changes in NaCl concentration. We also examine the interactions between a phosphomimetic RPA and ssDNA. Our results indicate that RPA-ssDNA interactions are not significantly altered by these modifications. We anticipate that low-complexity ssDNA curtains will be broadly useful for single-molecule studies of ssDNA-binding proteins involved in DNA replication, transcription, and repair.
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Affiliation(s)
- Jeffrey M. Schaub
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Hongshan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Michael M. Soniat
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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40
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Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase. Proc Natl Acad Sci U S A 2018; 115:E11614-E11622. [PMID: 30487222 DOI: 10.1073/pnas.1816606115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Gam protein of transposable phage Mu is an ortholog of eukaryotic and bacterial Ku proteins, which carry out nonhomologous DNA end joining (NHEJ) with the help of dedicated ATP-dependent ligases. Many bacteria carry Gam homologs associated with either complete or defective Mu-like prophages, but the role of Gam in the life cycle of Mu or in bacteria is unknown. Here, we show that MuGam is part of a two-component bacterial NHEJ DNA repair system. Ensemble and single-molecule experiments reveal that MuGam binds to DNA ends, slows the progress of RecBCD exonuclease, promotes binding of NAD+-dependent Escherichia coli ligase A, and stimulates ligation. In vivo, Gam equally promotes both precise and imprecise joining of restriction enzyme-digested linear plasmid DNA, as well as of a double-strand break (DSB) at an engineered I-SceI site in the chromosome. Cell survival after the induced DSB is specific to the stationary phase. In long-term growth competition experiments, particularly upon treatment with a clastogen, the presence of gam in a Mu lysogen confers a distinct fitness advantage. We also show that the role of Gam in the life of phage Mu is related not to transposition but to protection of genomic Mu copies from RecBCD when viral DNA packaging begins. Taken together, our data show that MuGam provides bacteria with an NHEJ system and suggest that the resulting fitness advantage is a reason that bacteria continue to retain the gam gene in the absence of an intact prophage.
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Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell 2018; 175:934-946.e15. [PMID: 30343903 DOI: 10.1016/j.cell.2018.09.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/20/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the CRISPR locus. In type I CRISPR-Cas systems, efficient "primed" spacer acquisition and viral degradation (interference) require both the Cascade complex and the Cas3 helicase/nuclease. Here, we present single-molecule characterization of the Thermobifida fusca (Tfu) primed acquisition complex (PAC). We show that TfuCascade rapidly samples non-specific DNA via facilitated one-dimensional diffusion. Cas3 loads at target-bound Cascade and the Cascade/Cas3 complex translocates via a looped DNA intermediate. Cascade/Cas3 complexes stall at diverse protein roadblocks, resulting in a double strand break at the stall site. In contrast, Cas1-Cas2 samples DNA transiently via 3D collisions. Moreover, Cas1-Cas2 associates with Cascade and translocates with Cascade/Cas3, forming the PAC. PACs can displace different protein roadblocks, suggesting a mechanism for long-range spacer acquisition. This work provides a molecular basis for the coordinated steps in CRISPR-based adaptive immunity.
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Affiliation(s)
- Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Maxwell W Brown
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Adam Dolan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Erik Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel D Dahlhauser
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
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Sivaramakrishnan P, Gordon AJE, Halliday JA, Herman C. How Acts of Infidelity Promote DNA Break Repair: Collision and Collusion Between DNA Repair and Transcription. Bioessays 2018; 40:e1800045. [PMID: 30091472 PMCID: PMC6334755 DOI: 10.1002/bies.201800045] [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: 03/12/2018] [Revised: 07/07/2018] [Indexed: 12/20/2022]
Abstract
Transcription is a fundamental cellular process and the first step in gene regulation. Although RNA polymerase (RNAP) is highly processive, in growing cells the progression of transcription can be hindered by obstacles on the DNA template, such as damaged DNA. The authors recent findings highlight a trade-off between transcription fidelity and DNA break repair. While a lot of work has focused on the interaction between transcription and nucleotide excision repair, less is known about how transcription influences the repair of DNA breaks. The authors suggest that when the cell experiences stress from DNA breaks, the control of RNAP processivity affects the balance between preserving transcription integrity and DNA repair. Here, how the conflict between transcription and DNA double-strand break (DSB) repair threatens the integrity of both RNA and DNA are discussed. In reviewing this field, the authors speculate on cellular paradigms where this equilibrium is well sustained, and instances where the maintenance of transcription fidelity is favored over genome stability.
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Affiliation(s)
- Priya Sivaramakrishnan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Dan L. Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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King G, Biebricher AS, Heller I, Peterman EJG, Wuite GJL. Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence. NANO LETTERS 2018; 18:2274-2281. [PMID: 29473755 PMCID: PMC6023266 DOI: 10.1021/acs.nanolett.7b04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/25/2023]
Abstract
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.
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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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45
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The transcription fidelity factor GreA impedes DNA break repair. Nature 2017; 550:214-218. [PMID: 28976965 PMCID: PMC5654330 DOI: 10.1038/nature23907] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/07/2017] [Indexed: 01/07/2023]
Abstract
Homologous recombination repairs DNA double-strand breaks and must function even on actively transcribed DNA. Because break repair prevents chromosome loss, the completion of repair is expected to outweigh the transcription of broken templates. Yet, the interplay between DNA break repair and transcription processivity is unclear. Here we show that the transcription factor GreA inhibits break repair in Escherichia coli. GreA restarts backtracked RNA polymerase (RNAP) and hence promotes transcription fidelity. We report that removal of GreA results in dramatically enhanced break repair via the classical RecBCD-RecA pathway. Using a deep-sequencing method to measure chromosomal exonucleolytic degradation (XO-Seq), we demonstrate that the absence of GreA limits RecBCD-mediated resection. Our findings suggest that increased RNAP backtracking promotes break repair by instigating RecA loading by RecBCD, without the influence of canonical Chi signals. The idea that backtracked RNAP can stimulate recombination presents a DNA transaction conundrum: a transcription fidelity factor compromises genomic integrity.
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47
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The more the merrier: high-throughput single-molecule techniques. Biochem Soc Trans 2017; 45:759-769. [PMID: 28620037 DOI: 10.1042/bst20160137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 12/24/2022]
Abstract
The single-molecule approach seeks to understand molecular mechanisms by observing biomolecular processes at the level of individual molecules. These methods have led to a developing understanding that for many processes, a diversity of behaviours will be observed, representing a multitude of pathways. This realisation necessitates that an adequate number of observations are recorded to fully characterise this diversity. The requirement for large numbers of observations to adequately sample distributions, subpopulations, and rare events presents a significant challenge for single-molecule techniques, which by their nature do not typically provide very high throughput. This review will discuss many developing techniques which address this issue by combining nanolithographic approaches, such as zero-mode waveguides and DNA curtains, with single-molecule fluorescence microscopy, and by drastically increasing throughput of force-based approaches such as magnetic tweezers and laminar-flow techniques. These methods not only allow the collection of large volumes of single-molecule data in single experiments, but have also made improvements to ease-of-use, accessibility, and automation of data analysis.
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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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Yeh JW, Szeto K. Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits. BIOMICROFLUIDICS 2017; 11:044108. [PMID: 28794818 PMCID: PMC5526712 DOI: 10.1063/1.4996340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/16/2017] [Indexed: 05/16/2023]
Abstract
Stretching single chromosomal DNA fibers in nanofluidic devices has become a valuable tool for studying the genome and more recently the epigenome. Although nanofluidic technology has been extensively used in single molecular DNA analysis, compared to bare DNA, much less work has been done to elongate chromatin, and only a few studies utilize more biologically relevant samples such as native eukaryotic chromatin. Here, we provide a method for stretching and imaging individual chromatin fibers within a micro- and nanofluidic device. This device was used to electrophoretically stretch and image single native chromatin fibers extracted from human cancer cells (HeLa cells) by attaching the chromatin to microspheres held at the entrance of a nanoslit. To further demonstrate the potential of this device in epigenetics, histone modification H3k79me2 was optically detected by fluorescence microscopy.
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Affiliation(s)
- Jia-Wei Yeh
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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50
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Han D, Crouch GM, Fu K, Zaino Iii LP, Bohn PW. Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides. Chem Sci 2017; 8:5345-5355. [PMID: 28970913 PMCID: PMC5609146 DOI: 10.1039/c7sc02250f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/18/2017] [Indexed: 11/21/2022] Open
Abstract
The ability of zero-mode waveguides (ZMW) to guide light into subwavelength-diameter nanoapertures has been exploited for studying electron transfer dynamics in zeptoliter-volume nanopores under single-molecule occupancy conditions. In this work, we report the spectroelectrochemical detection of individual molecules of the redox-active, fluorogenic molecule flavin mononucleotide (FMN) freely diffusing in solution. Our approach is based on an array of nanopore-confined recessed dual ring electrodes, wherein repeated reduction and oxidation of a single molecule at two closely spaced annular working electrodes yields amplified electrochemical signals. We have articulated these structures with an optically transparent bottom, so that the nanopores are bifunctional, exhibiting both nanophotonic and nanoelectrochemical behaviors allowing the coupling between electron transfer and fluorescence dynamics to be studied under redox cycling conditions. We also investigated the electric field intensity in electrochemical ZMWs (E-ZMW) through finite-element simulations, and the amplification of fluorescence by redox cycling agrees well with predictions based on optical confinement effects inside the E-ZMW. Proof-of-principle experiments are conducted showing that electrochemical and fluorescence signals may be correlated to reveal single molecule fluctuations in the array population. Cross-correlation of single molecule fluctuations in amperometric response and single photon emission provides unequivocal evidence of single molecule sensitivity.
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Affiliation(s)
- Donghoon Han
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849
| | - Garrison M Crouch
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849
| | - Kaiyu Fu
- Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
| | - Lawrence P Zaino Iii
- Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
| | - Paul W Bohn
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849.,Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
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