1
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Nguyen B, Hsieh J, Fischer CJ, Lohman TM. Subunit Communication within Dimeric SF1 DNA Helicases. J Mol Biol 2024; 436:168578. [PMID: 38648969 PMCID: PMC11128345 DOI: 10.1016/j.jmb.2024.168578] [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: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Monomers of the Superfamily (SF) 1 helicases, E. coli Rep and UvrD, can translocate directionally along single stranded (ss) DNA, but must be activated to function as helicases. In the absence of accessory factors, helicase activity requires Rep and UvrD homo-dimerization. The ssDNA binding sites of SF1 helicases contain a conserved aromatic amino acid (Trp250 in Rep and Trp256 in UvrD) that stacks with the DNA bases. Here we show that mutation of this Trp to Ala eliminates helicase activity in both Rep and UvrD. Rep(W250A) and UvrD(W256A) can still dimerize, bind DNA, and monomers still retain ATP-dependent ssDNA translocase activity, although with ∼10-fold lower rates and lower processivities than wild type monomers. Although neither wtRep monomers nor Rep(W250A) monomers possess helicase activity by themselves, using both ensemble and single molecule methods, we show that helicase activity is achieved upon formation of a Rep(W250A)/wtRep hetero-dimer. An ATPase deficient Rep monomer is unable to activate a wtRep monomer indicating that ATPase activity is needed in both subunits of the Rep hetero-dimer. We find the same results with E. coli UvrD and its equivalent mutant (UvrD(W256A)). Importantly, Rep(W250A) is unable to activate a wtUvrD monomer and UvrD(W256A) is unable to activate a wtRep monomer indicating that specific dimer interactions are required for helicase activity. We also demonstrate subunit communication within the dimer by virtue of Trp fluorescence signals that only are present within the Rep dimer, but not the monomers. These results bear on proposed subunit switching mechanisms for dimeric helicase activity.
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Affiliation(s)
- Binh Nguyen
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO 63110, USA
| | - John Hsieh
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO 63110, USA; Biochemistry & Biophysics, Blueprint Medicines, Cambridge, MA 02139, USA
| | | | - Timothy M Lohman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO 63110, USA.
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2
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Serwanja J, Wieland AC, Haubenhofer A, Brandstetter H, Schönauer E. A conserved strategy to attack collagen: The activator domain in bacterial collagenases unwinds triple-helical collagen. Proc Natl Acad Sci U S A 2024; 121:e2321002121. [PMID: 38593072 PMCID: PMC11032491 DOI: 10.1073/pnas.2321002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Bacterial collagenases are important virulence factors, secreted by several pathogenic Clostridium, Bacillus, Spirochaetes, and Vibrio species. Yet, the mechanism by which these enzymes cleave collagen is not well understood. Based on biochemical and mutational studies we reveal that collagenase G (ColG) from Hathewaya histolytica recognizes and processes collagen substrates differently depending on their nature (fibrillar vs. soluble collagen); distinct dynamic interactions between the activator and peptidase domain are required based on the substrate type. Using biochemical and circular dichroism studies, we identify the presumed noncatalytic activator domain as the single-domain triple helicase that unwinds collagen locally, transiently, and reversibly.
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Affiliation(s)
- Jamil Serwanja
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Alexander C. Wieland
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Astrid Haubenhofer
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
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3
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Hall-Thomsen H, Small S, Gavrilov M, Ha T, Schulman R, Moerman PG. Directing Uphill Strand Displacement with an Engineered Superhelicase. ACS Synth Biol 2023; 12:3424-3432. [PMID: 37844274 PMCID: PMC10661026 DOI: 10.1021/acssynbio.3c00452] [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: 07/24/2023] [Indexed: 10/18/2023]
Abstract
The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and the ability to transiently respond to successive input signals that require the continuous input of chemical energy. Here, we introduce a method for providing such energy to strand displacement networks in a controlled fashion: an engineered DNA helicase, Rep-X, that transiently dehybridizes specific DNA complexes, enabling the strands in the complex to participate in downstream hybridization or strand displacement reactions. We demonstrate how this process can direct the formation of specific metastable structures by design and that this dehybridization process can be controlled by DNA strand displacement reactions that effectively protect and deprotect a double-stranded complex from unwinding by Rep-X. These findings can guide the design of active DNA strand displacement regulatory networks, in which sustained dynamical behavior is fueled by helicase-regulated unwinding.
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Affiliation(s)
- Helena Hall-Thomsen
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Shavier Small
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Momcilo Gavrilov
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Biomedical
Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Rebecca Schulman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Computer
Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Pepijn Gerben Moerman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Chemical
Engineering and Chemistry, Eindhoven University
of Technology, Eindhoven 5612 AP, Netherlands
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4
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Bobrovnikov D, Makurath MA, Wolfe CH, Chemla YR, Ha T. Helicase Activity Modulation with On-Demand Light-Based Conformational Control. J Am Chem Soc 2023; 145:21253-21262. [PMID: 37739407 PMCID: PMC10557133 DOI: 10.1021/jacs.3c05254] [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: 05/19/2023] [Indexed: 09/24/2023]
Abstract
Engineering a protein variant with a desired role relies on deep knowledge of the relationship between a protein's native structure and function. Using our structural understanding of a regulatory subdomain found in a family of DNA helicases, we engineered novel helicases for which the subdomain orientation is designed to switch between unwinding-inactive and -active conformations upon trans-cis isomerization of an azobenzene-based crosslinker. This on-demand light-based conformational control directly alters helicase activity as demonstrated by both bulk phase experiments and single-molecule optical tweezers analysis of one of the engineered helicases. The "opto-helicase" may be useful in future applications that require spatiotemporal control of DNA hybridization states.
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Affiliation(s)
- Dmitriy Bobrovnikov
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Monika A. Makurath
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Clara H. Wolfe
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Yann R. Chemla
- Department
of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Taekjip Ha
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Department
of Biophysics, Department of Biological Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard Hughes
Medical Institute, Baltimore, Maryland 21205, United States
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5
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Liao TW, Huang L, Wilson TJ, Ganser LR, Lilley DMJ, Ha T. Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level. Nucleic Acids Res 2023; 51:8957-8969. [PMID: 37522343 PMCID: PMC10516623 DOI: 10.1093/nar/gkad633] [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: 04/19/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Riboswitches are regulatory elements found in bacterial mRNAs that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the translational SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes affect its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a rugged conformational landscape that allows for sampling of the ligand-bound conformation even in the absence of ligand. The addition of ligand shifts the landscape, favoring the ligand-bound conformation. Mutation studies identified a key structural element, the pseudoknot helix, that is crucial for determining ligand-free conformations and their ligand responsiveness. We also investigated ribosomal binding site accessibility under two scenarios: pre-folding and co-transcriptional folding. The regulatory function of the SAM/SAH riboswitch involves kinetically favoring ligand binding, but co-transcriptional folding reduces this preference with a less compact initial conformation that exposes the Shine-Dalgarno sequence and takes min to redistribute to more compact conformations of the pre-folded riboswitch. Such slow equilibration decreases the effective ligand affinity. Overall, our study provides a deeper understanding of the complex folding process and how the riboswitch adapts its folding pattern in response to ligand, modulates ribosome accessibility and the role of co-transcriptional folding in these processes.
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Affiliation(s)
- Ting-Wei Liao
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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6
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Marx SK, Mickolajczyk KJ, Craig J, Thomas C, Pfeffer A, Abell S, Carrasco J, Franzi M, Huang J, Kim H, Brinkerhoff H, Kapoor T, Gundlach J, Laszlo A. Observing inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. Nucleic Acids Res 2023; 51:9266-9278. [PMID: 37560916 PMCID: PMC10516658 DOI: 10.1093/nar/gkad660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
The genome of SARS-CoV-2 encodes for a helicase (nsp13) that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds double-stranded DNA. Our data reveal nsp13's single-nucleotide steps, translocating at ∼1000 nt/s or unwinding at ∼100 bp/s. Nanopore tweezers' high spatiotemporal resolution enables detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. We construct a detailed picture of inhibition in which ATPγS has multiple mechanisms of inhibition. The dominant mechanism of inhibition depends on the application of assisting force. This lays the groundwork for future single-molecule inhibition studies with viral helicases.
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Affiliation(s)
- Sinduja K Marx
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Akira M Pfeffer
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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7
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Serwanja J, Brandstetter H, Schönauer E. Quantitative cross-linking via engineered cysteines to study inter-domain interactions in bacterial collagenases. STAR Protoc 2023; 4:102519. [PMID: 37605531 PMCID: PMC10458335 DOI: 10.1016/j.xpro.2023.102519] [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: 05/25/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/23/2023] Open
Abstract
Inter-domain movements act as important activity modulators in multi-domain proteins. Here, we present a protocol for inter-domain cross-linking via engineered cysteines. Using collagenase G (ColG) from Hathewaya histolytica as a model, we describe steps for the design, expression, purification, and cross-linking of the target protein. We detail a system to monitor the progress of the cross-linking reaction and to confirm the structural integrity of the purified cross-linked proteins. We anticipate this protocol to be readily adaptable to other multi-domain enzymes. For complete details on the use and execution of this protocol, please refer to Serwanja et al.1.
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Affiliation(s)
- Jamil Serwanja
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria.
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8
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Okafor I, Ha T. Single Molecule FRET Analysis of CRISPR Cas9 Single Guide RNA Folding Dynamics. J Phys Chem B 2022; 127:45-51. [PMID: 36563314 PMCID: PMC9841515 DOI: 10.1021/acs.jpcb.2c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CRISPR Cas9 is an RNA guided endonuclease that is part of a bacterial adaptive immune system. Single guide RNA (sgRNA) can be designed to target genomic DNA, making Cas9 a programmable DNA binding/cutting enzyme and allowing applications such as epigenome editing, controlling transcription, and targeted DNA insertion. Some of the main hurdles against an even wider adoption are off-target effects and variability in Cas9 editing outcomes. Most studies that aim to understand the mechanisms that underlie these two areas have focused on Cas9 DNA binding, DNA unwinding, and target cleavage. The assembly of Cas9 RNA ribonucleoprotein complex (RNP) precedes all these steps and includes sgRNA folding and Cas9 binding to sgRNA. We know from the crystal structure of the Cas9 RNP what the final sgRNA conformation is. However, the assembly dynamics has not been studied in detail and a better understanding of RNP assembly could lead to better-designed sgRNAs and better editing outcomes. To study this process, we developed a single molecule FRET assay to monitor the conformation of the sgRNA and the binding of Cas9 to sgRNA. We labeled the sgRNA with a donor fluorophore and an acceptor fluorophore such that when the sgRNA folds, there are changes in FRET efficiency. We measured sgRNA folding dynamics under different ion conditions, under various methods of folding (refolding vs vectorial), and with or without Cas9. sgRNA that closely mimics the sgRNA construct used for high resolution structural analysis of the Cas9-gRNA complex showed two main FRET states without Cas9, and Cas9 addition shifted the distribution toward the higher FRET state attributed to the properly assembled complex. Even in the absence of Cas9, folding the sgRNA vectorially using a superhelicase-dependent release of the sgRNA in the direction of transcription resulted in almost exclusively high FRET state. An addition of Cas9 during vectorial folding greatly reduced a slow-folding fraction. Our studies shed light on the heterogeneous folding dynamics of sgRNA and the impact of co-transcriptional folding and Cas9 binding in sgRNA folding. Further studies of sequence dependence may inform rational design of sgRNAs for optimal function.
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Affiliation(s)
- Ikenna
C. Okafor
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States,Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States,Department
of Biomedical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States,Howard
Hughes Medical Institute, Baltimore, Maryland 21205, United States,
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9
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Wang Y, Cottle WT, Wang H, Gavrilov M, Zou RS, Pham MT, Yegnasubramanian S, Bailey S, Ha T. Achieving single nucleotide sensitivity in direct hybridization genome imaging. Nat Commun 2022; 13:7776. [PMID: 36522352 PMCID: PMC9755149 DOI: 10.1038/s41467-022-35476-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages the high cleavage specificity of eSpCas9(1.1) variant combined with a rationally designed guide RNA to load a superhelicase and reveal probe binding sites through local denaturation. The guide RNA carries an intentionally introduced mismatch so that while wild-type target DNA sequence can be efficiently cleaved, a mutant sequence with an additional mismatch (e.g., caused by a point mutation) cannot be cleaved. Because sgGOLDFISH relies on genomic DNA being cleaved by Cas9 to reveal probe binding sites, the probes will only label the wild-type sequence but not the mutant sequence. Therefore, sgGOLDFISH has the sensitivity to differentiate the wild-type and mutant sequences differing by only a single base pair. Using sgGOLDFISH, we identify base-editor-modified and unmodified progeroid fibroblasts from a heterogeneous population, validate the identification through progerin immunofluorescence, and demonstrate accurate sub-nuclear localization of point mutations.
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Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - W Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Roger S Zou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Minh-Tam Pham
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA.
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10
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Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics. Nat Commun 2022; 13:6312. [PMID: 36274095 PMCID: PMC9588791 DOI: 10.1038/s41467-022-34076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Polymerase Chain Reaction (PCR) is an essential method in molecular diagnostics and life sciences. PCR requires thermal cycling for heating the DNA for strand separation and cooling it for replication. The process uses a specialized hardware and exposes biomolecules to temperatures above 95 °C. Here, we engineer a PcrA M6 helicase with enhanced speed and processivity to replace the heating step by enzymatic DNA unwinding while retaining desired PCR characteristics. We name this isothermal amplification method SHARP (SSB-Helicase Assisted Rapid PCR) because it uses the engineered helicase and single-stranded DNA binding protein (SSB) in addition to standard PCR reagents. SHARP can generate amplicons with lengths of up to 6000 base pairs. SHARP can produce functional DNA, a plasmid that imparts cells with antibiotic resistance, and can amplify specific fragments from genomic DNA of human cells. We further use SHARP to assess the outcome of CRISPR-Cas9 editing at endogenous genomic sites.
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11
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Marx SK, Mickolajczyk KJ, Craig JM, Thomas CA, Pfeffer AM, Abell SJ, Carrasco JD, Franzi MC, Huang JR, Kim HC, Brinkerhoff HD, Kapoor TM, Gundlach JH, Laszlo AH. Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.07.511351. [PMID: 36238723 PMCID: PMC9558434 DOI: 10.1101/2022.10.07.511351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The genome of SARS-CoV-2 encodes for a helicase called nsp13 that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds short DNA duplexes. Our data confirm that nsp13 uses the inchworm mechanism to move along the DNA in single-nucleotide steps, translocating at ~1000 nt/s or unwinding at ~100 bp/s. Nanopore tweezers' high spatio-temporal resolution enables observation of the fundamental physical steps taken by nsp13 even as it translocates at speeds in excess of 1000 nucleotides per second enabling detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. Our data reveals that ATPγS interferes with nsp13's action by affecting several different kinetic processes. The dominant mechanism of inhibition differs depending on the application of assisting force. These advances demonstrate that nanopore tweezers are a powerful method for studying viral helicase mechanism and inhibition.
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Affiliation(s)
- Sinduja K Marx
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Akira M Pfeffer
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | | | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195
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12
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Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution. Proc Natl Acad Sci U S A 2022; 119:e2202489119. [PMID: 36037333 PMCID: PMC9457475 DOI: 10.1073/pnas.2202489119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule picometer-resolution nanopore tweezers (SPRNT) to resolve the millisecond single-nucleotide steps of superfamily 1 helicase PcrA as it translocates on, or unwinds, several kilobase-long DNA molecules. We recorded more than two million enzyme steps under various assisting and opposing forces in diverse adenosine tri- and diphosphate conditions to comprehensively explore the mechanochemistry of PcrA motion. Forces applied in SPRNT mimic forces and physical barriers PcrA experiences in vivo, such as when the helicase encounters bound proteins or duplex DNA. We show how PcrA's kinetics change with such stimuli. SPRNT allows for direct association of the underlying DNA sequence with observed enzyme kinetics. Our data reveal that the underlying DNA sequence passing through the helicase strongly influences the kinetics during translocation and unwinding. Surprisingly, unwinding kinetics are not solely dominated by the base pairs being unwound. Instead, the sequence of the single-stranded DNA on which the PcrA walks determines much of the kinetics of unwinding.
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13
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Otani SK, Martins TT, Muniz SR, de Sousa Filho PC, Sigoli FA, Nome RA. Spectroscopic characterization of rare events in colloidal particle stochastic thermodynamics. Front Chem 2022; 10:879524. [PMID: 36034664 PMCID: PMC9412910 DOI: 10.3389/fchem.2022.879524] [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: 02/19/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Given the remarkable developments in synthetic control over chemical and physical properties of colloidal particles, it is interesting to see how stochastic thermodynamics studies may be performed with new, surrogate, or hybrid model systems. In the present work, we apply stochastic dynamics and nonlinear optical light-matter interaction simulations to study nonequilibrium trajectories of individual Yb (III):Er (III) colloidal particles driven by two-dimensional dynamic optical traps. In addition, we characterize the role of fluctuations at the single-particle level by analyzing position trajectories and time-dependent upconversion emission intensities. By integrating these two complementary perspectives, we show how the methods developed here can be used to characterize rare events.
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Affiliation(s)
- Sandro K. Otani
- Institute of Chemistry, State University of Campinas, Campinas, Brazil
| | - Thalyta T. Martins
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Sérgio R. Muniz
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | | | | | - René A. Nome
- Institute of Chemistry, State University of Campinas, Campinas, Brazil
- *Correspondence: René A. Nome,
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14
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Moerman PG, Gavrilov M, Ha T, Schulman R. Catalytic DNA Polymerization Can Be Expedited by Active Product Release**. Angew Chem Int Ed Engl 2022; 61:e202114581. [PMID: 35302706 PMCID: PMC9325435 DOI: 10.1002/anie.202114581] [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: 10/30/2021] [Indexed: 12/02/2022]
Abstract
The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.
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Affiliation(s)
- Pepijn G. Moerman
- Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMD 21218USA
| | - Momcilo Gavrilov
- Biophysics & Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD 21205USA
| | - Taekjip Ha
- Biophysics & Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD 21205USA
- Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD 21218USA
- Howard Hughes Medical InstituteBaltimoreMD 21205USA
| | - Rebecca Schulman
- Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMD 21218USA
- ChemistryJohns Hopkins UniversityBaltimoreMD 21218USA
- Computer ScienceJohns Hopkins UniversityBaltimoreMD 21218USA
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15
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Paul T, Opresko PL, Ha T, Myong S. Vectorial folding of telomere overhang promotes higher accessibility. Nucleic Acids Res 2022; 50:6271-6283. [PMID: 35687089 PMCID: PMC9226509 DOI: 10.1093/nar/gkac401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5' to 3') and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5' to 3' direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA15213, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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16
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Improving the specificity of nucleic acid detection with endonuclease-actuated degradation. Commun Biol 2022; 5:290. [PMID: 35361863 PMCID: PMC8971390 DOI: 10.1038/s42003-022-03242-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/07/2022] [Indexed: 11/08/2022] Open
Abstract
Nucleic acid detection is essential for numerous biomedical applications, but often requires complex protocols and/or suffers false-positive readouts. Here, we describe SENTINEL, an approach that combines isothermal amplification with a sequence-specific degradation method to detect nucleic acids with high sensitivity and sequence-specificity. Target single-stranded RNA or double-stranded DNA molecules are amplified by loop-mediated isothermal amplification (LAMP) and subsequently degraded by the combined action of lambda exonuclease and a sequence-specific DNA endonuclease (e.g., Cas9). By combining the sensitivity of LAMP with the precision of DNA endonucleases, the protocol achieves attomolar limits of detection while differentiating between sequences that differ by only one or two base pairs. The protocol requires less than an hour to complete using a 65 °C heat block and fluorometer, and detects SARS-CoV-2 virus particles in human saliva and nasopharyngeal swabs with high sensitivity.
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17
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Moerman PG, Gavrilov M, Ha T, Schulman R. Catalytic DNA Polymerization Can Be Expedited by Active Product Release. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pepijn Gerben Moerman
- Johns Hopkins University Whiting School of Engineering Chemical and Biomolecular Engineering 3400 N Charles Street 21218 Baltimore UNITED STATES
| | - Momcilo Gavrilov
- Johns Hopkins University Biophysics and Biophysical Chemistry UNITED STATES
| | - Taekjip Ha
- Johns Hopkins University - Homewood Campus: Johns Hopkins University Biophysics UNITED STATES
| | - Rebecca Schulman
- Johns Hopkins University chemical and biomolecular engineering 3400 N. Charles St, Maryland Hall 221 21218 Baltimore UNITED STATES
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18
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Lee H, Cho H, Kim J, Lee S, Yoo J, Park D, Lee G. RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids. Nucleic Acids Res 2022; 50:1801-1814. [PMID: 34788459 PMCID: PMC8886854 DOI: 10.1093/nar/gkab1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3' DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5' DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.
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Affiliation(s)
- Hyunjee Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - HyeokJin Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jooyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sua Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungmin Yoo
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Daeho Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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19
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Mycobacterium tuberculosis DNA repair helicase UvrD1 is activated by redox-dependent dimerization via a 2B domain cysteine. Proc Natl Acad Sci U S A 2022; 119:2114501119. [PMID: 35173050 PMCID: PMC8872793 DOI: 10.1073/pnas.2114501119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) causes tuberculosis and, during infection, is exposed to reactive oxygen species and reactive nitrogen intermediates from the host immune response that can cause DNA damage. UvrD-like proteins are involved in DNA repair and replication and belong to the SF1 family of DNA helicases that use ATP hydrolysis to catalyze DNA unwinding. In Mtb, there are two UvrD-like enzymes, where UvrD1 is most closely related to other family members. Previous studies have suggested that UvrD1 is exclusively monomeric; however, it is well known that Escherichia coli UvrD and other UvrD family members exhibit monomer-dimer equilibria and unwind as dimers in the absence of accessory factors. Here, we reconcile these incongruent studies by showing that Mtb UvrD1 exists in monomer, dimer, and higher-order oligomeric forms, where dimerization is regulated by redox potential. We identify a 2B domain cysteine, conserved in many Actinobacteria, that underlies this effect. We also show that UvrD1 DNA-unwinding activity correlates specifically with the dimer population and is thus titrated directly via increasing positive (i.e., oxidative) redox potential. Consistent with the regulatory role of the 2B domain and the dimerization-based activation of DNA unwinding in UvrD family helicases, these results suggest that UvrD1 is activated under oxidizing conditions when it may be needed to respond to DNA damage during infection.
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20
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Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo. Mol Cell 2022; 82:304-314. [PMID: 35063098 DOI: 10.1016/j.molcel.2021.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.
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Affiliation(s)
- Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| | - Christian Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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21
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Paul T, Myong S. Helicase mediated vectorial folding of telomere G-quadruplex. Methods Enzymol 2022; 672:283-297. [DOI: 10.1016/bs.mie.2022.03.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Yokota H. Quantitative and kinetic single-molecule analysis of DNA unwinding by <i>Escherichia coli</i> UvrD helicase. Biophys Physicobiol 2022; 19:1-16. [PMID: 35435650 PMCID: PMC8967476 DOI: 10.2142/biophysico.bppb-v19.0006] [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: 11/29/2021] [Accepted: 03/07/2022] [Indexed: 12/01/2022] Open
Abstract
Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several “helicase motifs” that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their functional units. One class that includes SFs 3–6 functions as a hexamer that can form a ring around DNA. Another class that includes SFs 1 and 2 functions in a non-hexameric form. The high homology in the primary and tertiary structures among SF1 helicases suggests that SF1 helicases have a common underlying mechanism. However, two opposing models for the functional unit, monomer and dimer models, have been proposed to explain DNA unwinding by SF1 helicases. This paper briefly describes the classification of helicase SFs and discusses the structural homology and the two opposing non-hexameric helicase models of SF1 helicases by focusing on Escherichia coli SF1 helicase UvrD, which plays a significant role in both nucleotide-excision repair and methyl-directed mismatch repair. This paper reviews past and recent studies on UvrD, including the author's single-molecule direct visualization of wild-type UvrD and a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C), the latter of which was used in genetic and biochemical assays that supported the monomer model. The visualization revealed that multiple UvrDΔ40C molecules jointly unwind DNA, presumably in an oligomeric form, similar to wild-type UvrD. Therefore, single-molecule direct visualization of nucleic acid-binding proteins can provide quantitative and kinetic information to reveal their fundamental mechanisms.
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Affiliation(s)
- Hiroaki Yokota
- The Graduate School for the Creation of New Photonics Industries
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23
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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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24
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Yi X, Khey J, Kazlauskas RJ, Travisano M. Plasmid hypermutation using a targeted artificial DNA replisome. SCIENCE ADVANCES 2021; 7:7/29/eabg8712. [PMID: 34272238 PMCID: PMC8284885 DOI: 10.1126/sciadv.abg8712] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Extensive exploration of a protein's sequence space for improved or new molecular functions requires in vivo evolution with large populations. But disentangling the evolution of a target protein from the rest of the proteome is challenging. Here, we designed a protein complex of a targeted artificial DNA replisome (TADR) that operates in live cells to processively replicate one strand of a plasmid with errors. It enhanced mutation rates of the target plasmid up to 2.3 × 105-fold with only a 78-fold increase in off-target mutagenesis. It was used to evolve itself to increase error rate and increase the efficiency of an efflux pump while simultaneously expanding the substrate repertoire. TADR enables multiple simultaneous substitutions to discover functions inaccessible by accumulating single substitutions, affording potential for solving hard problems in molecular evolution and developing biologic drugs and industrial catalysts.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Joleen Khey
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | - Romas J Kazlauskas
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA.
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Michael Travisano
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
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Yoo J, Lee D, Im H, Ji S, Oh S, Shin M, Park D, Lee G. The mechanism of gap creation by a multifunctional nuclease during base excision repair. SCIENCE ADVANCES 2021; 7:7/29/eabg0076. [PMID: 34261654 PMCID: PMC8279506 DOI: 10.1126/sciadv.abg0076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/28/2021] [Indexed: 05/30/2023]
Abstract
During base excision repair, a transient single-stranded DNA (ssDNA) gap is produced at the apurinic/apyrimidinic (AP) site. Exonuclease III, capable of performing both AP endonuclease and exonuclease activity, are responsible for gap creation in bacteria. We used single-molecule fluorescence resonance energy transfer to examine the mechanism of gap creation. We found an AP site anchor-based mechanism by which the intrinsically distributive enzyme binds strongly to the AP site and becomes a processive enzyme, rapidly creating a gap and an associated transient ssDNA loop. The gap size is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA and is limited to a few nucleotides to maintain genomic stability. When the 3' end is released from the AP endonuclease, polymerase I quickly initiates DNA synthesis and fills the gap. Our work provides previously unidentified insights into how a signal of DNA damage changes the enzymatic functions.
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Affiliation(s)
- Jungmin Yoo
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Donghun Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Hyeryeon Im
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sangmi Ji
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sanghoon Oh
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-Ro, Jung-gu, Daegu 41944, Korea
| | - Daeho Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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26
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Fairlamb MS, Whitaker AM, Bain FE, Spies M, Freudenthal BD. Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules. BIOLOGY 2021; 10:biology10070571. [PMID: 34201434 PMCID: PMC8301196 DOI: 10.3390/biology10070571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023]
Abstract
Simple Summary Prism-based single-molecule total internal reflection fluorescence (prismTIRF) microscopes are excellent tools for studying macromolecular dynamics and interactions. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope using commercially available components with the hope of assisting those who aim to implement TIRF imaging techniques in their laboratory. Abstract Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology.
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Affiliation(s)
- Max S. Fairlamb
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Amy M. Whitaker
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Fletcher E. Bain
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
- Correspondence:
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27
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Nguyen B, Shinn MK, Weiland E, Lohman TM. Regulation of E. coli Rep helicase activity by PriC. J Mol Biol 2021; 433:167072. [PMID: 34081984 DOI: 10.1016/j.jmb.2021.167072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/28/2022]
Abstract
Stalled DNA replication forks can result in incompletely replicated genomes and cell death. DNA replication restart pathways have evolved to deal with repair of stalled forks and E. coli Rep helicase functions in this capacity. Rep and an accessory protein, PriC, assemble at a stalled replication fork to facilitate loading of other replication proteins. A Rep monomer is a rapid and processive single stranded (ss) DNA translocase but needs to be activated to function as a helicase. Activation of Rep in vitro requires self-assembly to form a dimer, removal of its auto-inhibitory 2B sub-domain, or interactions with an accessory protein. Rep helicase activity has been shown to be stimulated by PriC, although the mechanism of activation is not clear. Using stopped flow kinetics, analytical sedimentation and single molecule fluorescence methods, we show that a PriC dimer activates the Rep monomer helicase and can also stimulate the Rep dimer helicase. We show that PriC can self-assemble to form dimers and tetramers and that Rep and PriC interact in the absence of DNA. We further show that PriC serves as a Rep processivity factor, presumably co-translocating with Rep during DNA unwinding. Activation is specific for Rep since PriC does not activate the UvrD helicase. Interaction of PriC with the C-terminal acidic tip of the ssDNA binding protein, SSB, eliminates Rep activation by stabilizing the PriC monomer. This suggests a likely mechanism for Rep activation by PriC at a stalled replication fork.
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Affiliation(s)
- Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Min Kyung Shinn
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Box 8231, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
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28
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Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG. Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition. Nucleic Acids Res 2021; 49:4129-4143. [PMID: 33784404 PMCID: PMC8053095 DOI: 10.1093/nar/gkab188] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies.
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Affiliation(s)
- Yang-Xue Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang-Yuan Teng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hai-Lei Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Stephane Rety
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.,Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D'Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France
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29
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Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T. Genome oligopaint via local denaturation fluorescence in situ hybridization. Mol Cell 2021; 81:1566-1577.e8. [PMID: 33657402 PMCID: PMC8026568 DOI: 10.1016/j.molcel.2021.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/22/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Cas9 in complex with a programmable guide RNA targets specific double-stranded DNA for cleavage. By harnessing Cas9 as a programmable loader of superhelicase to genomic DNA, we report a physiological-temperature DNA fluorescence in situ hybridization (FISH) method termed genome oligopaint via local denaturation (GOLD) FISH. Instead of global denaturation as in conventional DNA FISH, loading a superhelicase at a Cas9-generated nick allows for local DNA denaturation, reducing nonspecific binding of probes and avoiding harsh treatments such as heat denaturation. GOLD FISH relies on Cas9 cleaving target DNA sequences and avoids the high nuclear background associated with other genome labeling methods that rely on Cas9 binding. The excellent signal brightness and specificity enable us to image nonrepetitive genomic DNA loci and analyze the conformational differences between active and inactive X chromosomes. Finally, GOLD FISH could be used for rapid identification of HER2 gene amplification in patient tissue.
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Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinyu Ashlee Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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30
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Schärfen L, Neugebauer KM. Transcription Regulation Through Nascent RNA Folding. J Mol Biol 2021; 433:166975. [PMID: 33811916 DOI: 10.1016/j.jmb.2021.166975] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
Folding of RNA into secondary structures through intramolecular base pairing determines an RNA's three-dimensional architecture and associated function. Simple RNA structures like stem loops can provide specialized functions independent of coding capacity, such as protein binding, regulation of RNA processing and stability, stimulation or inhibition of translation. RNA catalysis is dependent on tertiary structures found in the ribosome, tRNAs and group I and II introns. While the extent to which non-coding RNAs contribute to cellular maintenance is generally appreciated, the fact that both non-coding and coding RNA can assume relevant structural states has only recently gained attention. In particular, the co-transcriptional folding of nascent RNA of all classes has the potential to regulate co-transcriptional processing, RNP (ribonucleoprotein particle) formation, and transcription itself. Riboswitches are established examples of co-transcriptionally folded coding RNAs that directly regulate transcription, mainly in prokaryotes. Here we discuss recent studies in both prokaryotes and eukaryotes showing that structure formation may carry a more widespread regulatory logic during RNA synthesis. Local structures forming close to the catalytic center of RNA polymerases have the potential to regulate transcription by reducing backtracking. In addition, stem loops or more complex structures may alter co-transcriptional RNA processing or its efficiency. Several examples of functional structures have been identified to date, and this review provides an overview of physiologically distinct processes where co-transcriptionally folded RNA plays a role. Experimental approaches such as single-molecule FRET and in vivo structural probing to further advance our insight into the significance of co-transcriptional structure formation are discussed.
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Affiliation(s)
- Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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31
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Bustamante CJ, Chemla YR, Liu S, Wang MD. Optical tweezers in single-molecule biophysics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:25. [PMID: 34849486 PMCID: PMC8629167 DOI: 10.1038/s43586-021-00021-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.
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Affiliation(s)
- Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
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32
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Stekas B, Yeo S, Troitskaia A, Honda M, Sho S, Spies M, Chemla YR. Switch-like control of helicase processivity by single-stranded DNA binding protein. eLife 2021; 10:60515. [PMID: 33739282 PMCID: PMC7997660 DOI: 10.7554/elife.60515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Helicases utilize nucleotide triphosphate (NTP) hydrolysis to translocate along single-stranded nucleic acids (NA) and unwind the duplex. In the cell, helicases function in the context of other NA-associated proteins such as single-stranded DNA binding proteins. Such encounters regulate helicase function, although the underlying mechanisms remain largely unknown. Ferroplasma acidarmanus xeroderma pigmentosum group D (XPD) helicase serves as a model for understanding the molecular mechanisms of superfamily 2B helicases, and its activity is enhanced by the cognate single-stranded DNA binding protein replication protein A 2 (RPA2). Here, optical trap measurements of the unwinding activity of a single XPD helicase in the presence of RPA2 reveal a mechanism in which XPD interconverts between two states with different processivities and transient RPA2 interactions stabilize the more processive state, activating a latent 'processivity switch' in XPD. A point mutation at a regulatory DNA binding site on XPD similarly activates this switch. These findings provide new insights on mechanisms of helicase regulation by accessory proteins.
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Affiliation(s)
- Barbara Stekas
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, United States
| | - Steve Yeo
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, United States
| | - Alice Troitskaia
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, United States
| | - Masayoshi Honda
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Sei Sho
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Yann R Chemla
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, United States.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, United States.,Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Urbana, United States
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33
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Paul T, Ha T, Myong S. Regeneration of PEG slide for multiple rounds of single-molecule measurements. Biophys J 2021; 120:1788-1799. [PMID: 33675764 DOI: 10.1016/j.bpj.2021.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022] Open
Abstract
Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois.
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34
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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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35
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Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape. Nat Commun 2020; 11:4531. [PMID: 32913225 PMCID: PMC7484762 DOI: 10.1038/s41467-020-18283-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/10/2020] [Indexed: 11/08/2022] Open
Abstract
RNAs begin to fold and function during transcription. Riboswitches undergo cotranscriptional switching in the context of transcription elongation, RNA folding, and ligand binding. To investigate how these processes jointly modulate the function of the folate stress-sensing Fusobacterium ulcerans ZTP riboswitch, we apply a single-molecule vectorial folding (VF) assay in which an engineered superhelicase Rep-X sequentially releases fluorescently labeled riboswitch RNA from a heteroduplex in a 5′-to-3′ direction, at ~60 nt s−1 [comparable to the speed of bacterial RNA polymerase (RNAP)]. We demonstrate that the ZTP riboswitch is kinetically controlled and that its activation is favored by slower unwinding, strategic pausing between but not before key folding elements, or a weakened transcription terminator. Real-time single-molecule monitoring captures folding riboswitches in multiple states, including an intermediate responsible for delayed terminator formation. These results show how individual nascent RNAs occupy distinct channels within the folding landscape that controls the fate of the riboswitch. Many RNAs become functional before their synthesis completes. Here the authors employ a single-molecule vectorial folding assay mimicking RNA transcription and show that the ZTP riboswitch is kinetically controlled and activated by slower unwinding and strategic pausing.
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36
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Paul T, Voter AF, Cueny RR, Gavrilov M, Ha T, Keck J, Myong S. E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands. Nucleic Acids Res 2020; 48:6640-6653. [PMID: 32449930 PMCID: PMC7337899 DOI: 10.1093/nar/gkaa442] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 05/21/2020] [Indexed: 11/30/2022] Open
Abstract
G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that Rep and Rep-X (an enhanced version of Rep) display G4 unwinding activities in vitro that are significantly higher than the closely related UvrD helicase. G4 unwinding mediated by Rep involves repetitive cycles of G4 unfolding and refolding fueled by ATP hydrolysis. Rep-X and Rep also dislodge G4-stabilizing ligands, in agreement with our in vivo G4-ligand sensitivity result. We further demonstrate that RecA filaments disrupt G4 structures and remove G4 ligands in vitro, consistent with its role in countering cellular toxicity of G4-stabilizing ligands. Together, our study reveals novel genome caretaking functions for Rep and RecA in resolving deleterious G4 structures.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew F Voter
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Rachel R Cueny
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Momčilo Gavrilov
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
- Howard Hughes Medical Institute, Johns Hopkins University, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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37
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Mitra J, Ha T. Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy. Nucleic Acids Res 2020; 47:11044-11056. [PMID: 31617570 PMCID: PMC6868435 DOI: 10.1093/nar/gkz906] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 01/26/2023] Open
Abstract
A human telomere ends in a single-stranded 3′ tail, composed of repeats of T2AG3. G-quadruplexes (GQs) formed from four consecutive repeats have been shown to possess high-structural and mechanical diversity. In principle, a GQ can form from any four repeats that are not necessarily consecutive. To understand the dynamics of GQs with positional multiplicity, we studied five and six repeats human telomeric sequence using a combination of single molecule FRET and optical tweezers. Our results suggest preferential formation of GQs at the 3′ end both in K+ and Na+ solutions, with minor populations of 5′-GQ or long-loop GQs. A vectorial folding assay which mimics the directional nature of telomere extension showed that the 3′ preference holds even when folding is allowed to begin from the 5′ side. In 100 mM K+, the unassociated T2AG3 segment has a streamlining effect in that one or two mechanically distinct species was observed at a single position instead of six or more observed without an unassociated repeat. We did not observe such streamlining effect in 100 mM Na+. Location of GQ and reduction in conformational diversity in the presence of extra repeats have implications in telomerase inhibition, T-loop formation and telomere end protection.
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Affiliation(s)
- Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana IL 61801, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21218, USA
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38
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Yokota H. DNA-Unwinding Dynamics of Escherichia coli UvrD Lacking the C-Terminal 40 Amino Acids. Biophys J 2020; 118:1634-1648. [PMID: 32142643 DOI: 10.1016/j.bpj.2020.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
The E. coli UvrD protein is a nonhexameric DNA helicase that belongs to superfamily I and plays a crucial role in both nucleotide excision repair and methyl-directed mismatch repair. Previous data suggested that wild-type UvrD has optimal activity in its oligomeric form. However, crystal structures of the UvrD-DNA complex were only resolved for monomeric UvrD, using a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C). However, biochemical findings performed using UvrDΔ40C indicated that this mutant failed to dimerize, although its DNA-unwinding activity was comparable to that of wild-type UvrD. Although the C-terminus plays essential roles in nucleic acid binding for many proteins with helicase and dimerization activities, the exact function of the C-terminus is poorly understood. Thus, to understand the function of the C-terminal amino acids of UvrD, we performed single-molecule direct visualization. Photobleaching of dye-labeled UvrDΔ40C molecules revealed that two or three UvrDΔ40C molecules could bind simultaneously to an 18-bp double-stranded DNA with a 20-nucleotide, 3' single-stranded DNA tail in the absence of ATP. Simultaneous visualization of association/dissociation of the mutant with/from DNA and the DNA-unwinding dynamics of the mutant in the presence of ATP demonstrated that, as with wild-type UvrD, two or three UvrDΔ40C molecules were primarily responsible for DNA unwinding. The determined association/dissociation rate constants for the second bound monomer were ∼2.5-fold larger than that of wild-type UvrD. The involvement of multiple UvrDΔ40C molecules in DNA unwinding was also observed under a physiological salt concentration (200 mM NaCl). These results suggest that multiple UvrDΔ40C molecules, which may form an oligomer, play an active role in DNA unwinding in vivo and that deleting the C-terminal 40 residues altered the interaction of the second UvrD monomer with DNA without affecting the interaction with the first bound UvrD monomer.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Hamamatsu, Shizuoka, Japan.
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39
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Choi S, Lee SW, Kim H, Ahn B. Molecular characteristics of reiterative DNA unwinding by the Caenorhabditis elegans RecQ helicase. Nucleic Acids Res 2019; 47:9708-9720. [PMID: 31435650 PMCID: PMC6765134 DOI: 10.1093/nar/gkz708] [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: 01/16/2019] [Revised: 07/31/2019] [Accepted: 08/13/2019] [Indexed: 12/31/2022] Open
Abstract
The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles in genome maintenance. Recent advances in single-molecule techniques have revealed the reiterative unwinding behavior of RecQ helicases. However, the molecular mechanisms involved in this process remain unclear, with contradicting reports. Here, we characterized the unwinding dynamics of the Caenorhabditis elegans RecQ helicase HIM-6 using single-molecule fluorescence resonance energy transfer measurements. We found that HIM-6 exhibits reiterative DNA unwinding and the length of DNA unwound by the helicase is sharply defined at 25-31 bp. Experiments using various DNA substrates revealed that HIM-6 utilizes the mode of 'sliding back' on the translocated strand, without strand-switching for rewinding. Furthermore, we found that Caenorhabditis elegans replication protein A, a single-stranded DNA binding protein, suppresses the reiterative behavior of HIM-6 and induces unidirectional, processive unwinding, possibly through a direct interaction between the proteins. Our findings shed new light on the mechanism of DNA unwinding by RecQ family helicases and their co-operation with RPA in processing DNA.
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Affiliation(s)
- Seoyun Choi
- Department of Life Sciences, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44610, Republic of Korea
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44610, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44610, Republic of Korea
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan 44610, Republic of Korea
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40
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Branched unwinding mechanism of the Pif1 family of DNA helicases. Proc Natl Acad Sci U S A 2019; 116:24533-24541. [PMID: 31744872 DOI: 10.1073/pnas.1915654116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Members of the Pif1 family of helicases function in multiple pathways that involve DNA synthesis: DNA replication across G-quadruplexes; break-induced replication; and processing of long flaps during Okazaki fragment maturation. Furthermore, Pif1 increases strand-displacement DNA synthesis by DNA polymerase δ and allows DNA replication across arrays of proteins tightly bound to DNA. This is a surprising feat since DNA rewinding or annealing activities limit the amount of single-stranded DNA product that Pif1 can generate, leading to an apparently poorly processive helicase. In this work, using single-molecule Förster resonance energy transfer approaches, we show that 2 members of the Pif1 family of helicases, Pif1 from Saccharomyces cerevisiae and Pfh1 from Schizosaccharomyces pombe, unwind double-stranded DNA by a branched mechanism with 2 modes of activity. In the dominant mode, only short stretches of DNA can be processively and repetitively opened, with reclosure of the DNA occurring by mechanisms other than strand-switching. In the other less frequent mode, longer stretches of DNA are unwound via a path that is separate from the one leading to repetitive unwinding. Analysis of the kinetic partitioning between the 2 different modes suggests that the branching point in the mechanism is established by conformational selection, controlled by the interaction of the helicase with the 3' nontranslocating strand. The data suggest that the dominant and repetitive mode of DNA opening of the helicase can be used to allow efficient DNA replication, with DNA synthesis on the nontranslocating strand rectifying the DNA unwinding activity.
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41
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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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42
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Makurath MA, Whitley KD, Nguyen B, Lohman TM, Chemla YR. Regulation of Rep helicase unwinding by an auto-inhibitory subdomain. Nucleic Acids Res 2019; 47:2523-2532. [PMID: 30690484 PMCID: PMC6412110 DOI: 10.1093/nar/gkz023] [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: 06/04/2018] [Revised: 12/26/2018] [Accepted: 01/16/2019] [Indexed: 11/29/2022] Open
Abstract
Helicases are biomolecular motors that unwind nucleic acids, and their regulation is essential for proper maintenance of genomic integrity. Escherichia coli Rep helicase, whose primary role is to help restart stalled replication, serves as a model for Superfamily I helicases. The activity of Rep-like helicases is regulated by two factors: their oligomeric state, and the conformation of the flexible subdomain 2B. However, the mechanism of control is not well understood. To understand the factors that regulate the active state of Rep, here we investigate the behavior of a 2B-deficient variant (RepΔ2B) in relation to wild-type Rep (wtRep). Using a single-molecule optical tweezers assay, we explore the effects of oligomeric state, DNA geometry, and duplex stability on wtRep and RepΔ2B unwinding activity. We find that monomeric RepΔ2B unwinds more processively and at a higher speed than the activated, dimeric form of wtRep. The unwinding processivity of RepΔ2B and wtRep is primarily limited by ‘strand-switching’—during which the helicases alternate between strands of the duplex—which does not require the 2B subdomain, contrary to a previous proposal. We provide a quantitative model of the factors that enhance unwinding processivity. Our work sheds light on the mechanisms of regulation of unwinding by Rep-like helicases.
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Affiliation(s)
- Monika A Makurath
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin D Whitley
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yann R Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Mitra J, Ha T. Nanomechanics and co-transcriptional folding of Spinach and Mango. Nat Commun 2019; 10:4318. [PMID: 31541108 PMCID: PMC6754394 DOI: 10.1038/s41467-019-12299-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/03/2019] [Indexed: 11/24/2022] Open
Abstract
Recent advances in fluorogen-binding “light-up” RNA aptamers have enabled protein-free detection of RNA in cells. Detailed biophysical characterization of folding of G-Quadruplex (GQ)-based light-up aptamers such as Spinach, Mango and Corn is still lacking despite the potential implications on their folding and function. In this work we employ single-molecule fluorescence-force spectroscopy to examine mechanical responses of Spinach2, iMangoIII and MangoIV. Spinach2 unfolds in four discrete steps as force is increased to 7 pN and refolds in reciprocal steps upon force relaxation. In contrast, GQ-core unfolding in iMangoIII and MangoIV occurs in one discrete step at forces >10 pN and refolding occurred at lower forces showing hysteresis. Co-transcriptional folding using superhelicases shows reduced misfolding propensity and allowed a folding pathway different from refolding. Under physiologically relevant pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold. Understanding of the dynamics of RNA aptamers will aid engineering of improved fluorogenic modules for cellular applications. Light-up aptamers are widely used for fluorescence visualization of non-coding RNA in vivo. Here the authors employ single-molecule fluorescence-force spectroscopy to characterize the mechanical responses of the G-Quadruplex based light-up aptamers Spinach2, iMangoIII and MangoIV, which is of interest for the development of improved fluorogenic modules for imaging applications.
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Affiliation(s)
- Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA. .,Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Howard Hughes Medical Institute, Baltimore, MD, 21218, USA.
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44
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UvrD helicase activation by MutL involves rotation of its 2B subdomain. Proc Natl Acad Sci U S A 2019; 116:16320-16325. [PMID: 31363055 DOI: 10.1073/pnas.1905513116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli UvrD is a superfamily 1 helicase/translocase that functions in DNA repair, replication, and recombination. Although a UvrD monomer can translocate along single-stranded DNA, self-assembly or interaction with an accessory protein is needed to activate its helicase activity in vitro. Our previous studies have shown that an Escherichia coli MutL dimer can activate the UvrD monomer helicase in vitro, but the mechanism is not known. The UvrD 2B subdomain is regulatory and can exist in extreme rotational conformational states. By using single-molecule FRET approaches, we show that the 2B subdomain of a UvrD monomer bound to DNA exists in equilibrium between open and closed states, but predominantly in an open conformation. However, upon MutL binding to a UvrD monomer-DNA complex, a rotational conformational state is favored that is intermediate between the open and closed states. Parallel kinetic studies of MutL activation of the UvrD helicase and of MutL-dependent changes in the UvrD 2B subdomain show that the transition from an open to an intermediate 2B subdomain state is on the pathway to helicase activation. We further show that MutL is unable to activate the helicase activity of a chimeric UvrD containing the 2B subdomain of the structurally similar Rep helicase. Hence, MutL activation of the monomeric UvrD helicase is regulated specifically by its 2B subdomain.
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45
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Lee M, Shin S, Uhm H, Hong H, Kirk J, Hyun K, Kulikowicz T, Kim J, Ahn B, Bohr VA, Hohng S. Multiple RPAs make WRN syndrome protein a superhelicase. Nucleic Acids Res 2019; 46:4689-4698. [PMID: 29668972 PMCID: PMC5961295 DOI: 10.1093/nar/gky272] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/11/2018] [Indexed: 02/01/2023] Open
Abstract
RPA is known to stimulate the helicase activity of Werner syndrome protein (WRN), but the exact stimulation mechanism is not understood. We use single-molecule FRET and magnetic tweezers to investigate the helicase activity of WRN and its stimulation by RPA. We show that WRN alone is a weak helicase which repetitively unwind just a few tens of base pairs, but that binding of multiple RPAs to the enzyme converts WRN into a superhelicase that unidirectionally unwinds double-stranded DNA more than 1 kb. Our study provides a good case in which the activity and biological functions of the enzyme may be fundamentally altered by the binding of cofactors.
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Affiliation(s)
- Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesoo Uhm
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesun Hong
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Jaewon Kirk
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
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46
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Bagchi D, Manosas M, Zhang W, Manthei KA, Hodeib S, Ducos B, Keck JL, Croquette V. Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interaction with SSB. Nucleic Acids Res 2019; 46:8500-8515. [PMID: 30053104 PMCID: PMC6144805 DOI: 10.1093/nar/gky647] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/15/2018] [Indexed: 12/16/2022] Open
Abstract
Most RecQ DNA helicases share a conserved domain arrangement that mediates their activities in genomic stability. This arrangement comprises a helicase motor domain, a RecQ C-terminal (RecQ-C) region including a winged-helix (WH) domain, and a ‘Helicase and RNase D C-terminal’ (HRDC) domain. Single-molecule real-time translocation and DNA unwinding by full-length Escherichia coli RecQ and variants lacking either the HRDC or both the WH and HRDC domains was analyzed. RecQ operated under two interconvertible kinetic modes, ‘slow’ and ‘normal’, as it unwound duplex DNA and translocated on single-stranded (ss) DNA. Consistent with a crystal structure of bacterial RecQ bound to ssDNA by base stacking, abasic sites blocked RecQ unwinding. Removal of the HRDC domain eliminates the slow mode while preserving the normal mode of activity. Unexpectedly, a RecQ variant lacking both the WH and HRDC domains retains weak helicase activity. The inclusion of E. coli ssDNA-binding protein (SSB) induces a third ‘fast’ unwinding mode four times faster than the normal RecQ mode and enhances the overall helicase activity (affinity, rate, and processivity). SSB stimulation was, furthermore, observed in the RecQ deletion variants, including the variant missing the WH domain. Our results support a model in which RecQ and SSB have multiple interacting modes.
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Affiliation(s)
- Debjani Bagchi
- Physics Department, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat - 390002, India
| | - Maria Manosas
- Departament de Física de la Materia Condensada, Universitat de Barcelona, Barcelona 08028, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Weiting Zhang
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Kelly A Manthei
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Samar Hodeib
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Bertrand Ducos
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | - Vincent Croquette
- Laboratoire de physique statistique, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France. IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
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47
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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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48
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Jones CP, Panja S, Woodson SA, Ferré-D'Amaré AR. Monitoring co-transcriptional folding of riboswitches through helicase unwinding. Methods Enzymol 2019; 623:209-227. [PMID: 31239047 DOI: 10.1016/bs.mie.2019.05.031] [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] [Indexed: 12/12/2022]
Abstract
In the cell, RNAs fold and begin to function as they are being transcribed. In contrast, in the laboratory, RNAs are typically studied after transcription is completed. Co-transcriptional folding can regulate the function of riboswitches and ribozymes and dictate the order of ribonucleoprotein assembly. Methods to observe and investigate RNA folding and activity during transcription are therefore desirable, yet synchronizing RNA polymerases and incorporating labels at specific sites for biophysical studies can be challenging. A recent methodological advance has been to harness highly processive, engineered "super-helicases" to unwind hybrid RNA-DNA duplexes, thereby releasing the RNA 5'-3'. When combined with single-molecule fluorescence detection, RNA folding and concomitant activity can be studied in vitro in a manner that mimics vectorial folding during transcription. Herein, we describe methods for designing and preparing fluorescently labeled RNA-DNA duplex substrates for sequential helicase-dependent RNA folding experiments.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, United States.
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49
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UPF1-like helicase grip on nucleic acids dictates processivity. Nat Commun 2018; 9:3752. [PMID: 30218034 PMCID: PMC6138625 DOI: 10.1038/s41467-018-06313-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022] Open
Abstract
Helicases are molecular engines which translocate along nucleic acids (NA) to unwind double-strands or remodel NA–protein complexes. While they have an essential role in genome structure and expression, the rules dictating their processivity remain elusive. Here, we developed single-molecule methods to investigate helicase binding lifetime on DNA. We found that UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. Conversely, the structurally similar IGHMBP2 helicase has a short residence time. UPF1 mutants with variable grip on DNA show that grip tightness dictates helicase residence time and processivity. In addition, we discovered via functional studies that a decrease in UPF1 grip impairs NMD efficiency in vivo. Finally, we propose a three-state model with bound, sliding and unbound molecular clips, that can accurately predict the modulation of helicase processivity. UPF1 is a highly processive helicase that plays an essential role in nonsense-mediated mRNA decay. Here the authors use single molecule binding assays to establish a functionally important relationship between helicase grip to nucleic acids, binding lifetime and the duration of translocation.
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50
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Ordabayev YA, Nguyen B, Niedziela-Majka A, Lohman TM. Regulation of UvrD Helicase Activity by MutL. J Mol Biol 2018; 430:4260-4274. [PMID: 30171840 DOI: 10.1016/j.jmb.2018.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/03/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022]
Abstract
Escherichia coli UvrD is a superfamily 1 helicase/translocase involved in multiple DNA metabolic processes including methyl-directed mismatch DNA repair. Although a UvrD monomer can translocate along single-stranded DNA, a UvrD dimer is needed for processive helicase activity in vitro. E. coli MutL, a regulatory protein involved in methyl-directed mismatch repair, stimulates UvrD helicase activity; however, the mechanism is not well understood. Using single-molecule fluorescence and ensemble approaches, we find that a single MutL dimer can activate latent UvrD monomer helicase activity. However, we also find that MutL stimulates UvrD dimer helicase activity. We further find that MutL enhances the DNA-unwinding processivity of UvrD. Hence, MutL acts as a processivity factor by binding to and presumably moving along with UvrD to facilitate DNA unwinding.
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Affiliation(s)
- Yerdos A Ordabayev
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110, United States
| | - Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110, United States
| | - Anita Niedziela-Majka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110, United States.
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