1
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Kashyap P, Bertelli S, Cao F, Kostritskaia Y, Blank F, Srikanth NA, Schlack-Leigers C, Saleppico R, Bierhuizen D, Lu X, Nickel W, Campbell RE, Plested AJR, Stauber T, Taylor MJ, Ewers H. An optogenetic method for the controlled release of single molecules. Nat Methods 2024; 21:666-672. [PMID: 38459384 PMCID: PMC11009104 DOI: 10.1038/s41592-024-02204-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
We developed a system for optogenetic release of single molecules in cells. We confined soluble and transmembrane proteins to the Golgi apparatus via a photocleavable protein and released them by short pulses of light. Our method allows for a light dose-dependent delivery of functional proteins to the cytosol and plasma membrane in amounts compatible with single-molecule imaging, greatly simplifying access to single-molecule microscopy of any protein in live cells. We were able to reconstitute ion conductance by delivering BK and LRRC8/volume-regulated anion channels to the plasma membrane. Finally we were able to induce NF-kB signaling in T lymphoblasts stimulated by interleukin-1 by controlled release of a signaling protein that had been knocked out. We observed light-induced formation of functional inflammatory signaling complexes that triggered phosphorylation of the inhibitor of nuclear factor kappa-B kinase only in activated cells. We thus developed an optogenetic method for the reconstitution and investigation of cellular function at the single-molecule level.
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Affiliation(s)
- Purba Kashyap
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Sara Bertelli
- Humboldt-Universität zu Berlin and Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Fakun Cao
- Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Yulia Kostritskaia
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | - Fenja Blank
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Niranjan A Srikanth
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
- Max-Planck-Institute for Infection Biology, Berlin, Germany
| | | | | | - Dolf Bierhuizen
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Andrew J R Plested
- Humboldt-Universität zu Berlin and Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Tobias Stauber
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | | | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany.
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2
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Chen C, Ge X, Zhao Y, Wang D, Ling L, Zheng S, Ding K, Wang J, Sun L. Molecular Alterations in Metastatic Ovarian Cancer From Gastrointestinal Cancer. Front Oncol 2020; 10:605349. [PMID: 33363035 PMCID: PMC7758447 DOI: 10.3389/fonc.2020.605349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Reports indicate that most metastatic ovarian cancer (MOC) originates from gastrointestinal cancer (GIC). Notably, GICs metastasize to the ovary frequently via 3 main routes including hematogenous spread, lymphogenous spread, and transcoelomic spread. Nonetheless, the mechanism of the progression remains unknown, and only a handful of literature exists on the molecular alteration implicated in MOC from GIC. This work collected existing evidence and literature on the vital molecules of the metastatic pathway and systematically analyzed them geared toward exploring the mechanism of the metastatic pathway of MOC. Further, this review described dominating molecular alteration in the metastatic process from cancer cells detaching away from lesions to arrive at the ovary, including factors for regulating signaling pathways in epithelial-interstitial transformation, invading, and surviving in the circulatory system or abdominal cavity. We interrogated the basis of the ovary as a distant metastatic site. This article provides new insights into the metastatic pathway and generates novel therapeutic targets for effective treatment and satisfactory outcomes in GIC patients.
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Affiliation(s)
- Chao Chen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxu Ge
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yamei Zhao
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Da Wang
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Limian Ling
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shu Zheng
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kefeng Ding
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Wang
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lifeng Sun
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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3
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Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O'Shea VL, Berger JM, Dixon NE, van Oijen AM. A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome. Mol Cell 2020; 79:140-154.e7. [PMID: 32464091 DOI: 10.1016/j.molcel.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly found plasticity lies in the 500-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747, the Netherlands
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Valerie L O'Shea
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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4
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Spenkelink LM, Lewis JS, Jergic S, Xu ZQ, Robinson A, Dixon NE, van Oijen AM. Recycling of single-stranded DNA-binding protein by the bacterial replisome. Nucleic Acids Res 2019; 47:4111-4123. [PMID: 30767010 PMCID: PMC6486552 DOI: 10.1093/nar/gkz090] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/30/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the replisome that is much more complex in how it retains or recycles protein components. Here, we visualize how an in vitro reconstituted Escherichia coli replisome recruits SSB by relying on two different molecular mechanisms. Not only does it recruit new SSB molecules from solution to coat newly formed single-stranded DNA on the lagging strand, but it also internally recycles SSB from one Okazaki fragment to the next. We show that this internal transfer mechanism is balanced against recruitment from solution in a manner that is concentration dependent. By visualizing SSB dynamics in live cells, we show that both internal transfer and external exchange mechanisms are physiologically relevant.
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Affiliation(s)
- Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG, the Netherlands
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Andrew Robinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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5
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Mueller SH, Spenkelink LM, van Oijen AM. When proteins play tag: the dynamic nature of the replisome. Biophys Rev 2019; 11:641-651. [PMID: 31273608 PMCID: PMC6682189 DOI: 10.1007/s12551-019-00569-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication, or the copying of DNA, is a fundamental process to all life. The system of proteins that carries out replication, the replisome, encounters many roadblocks on its way. An inability of the replisome to properly overcome these roadblocks will negatively affect genomic integrity which in turn can lead to disease. Over the past decades, efforts by many researchers using a broad array of approaches have revealed roles for many different proteins during the initial response of the replisome upon encountering roadblocks. Here, we revisit what is known about DNA replication and the effect of roadblocks during DNA replication across different organisms. We also address how advances in single-molecule techniques have changed our view of the replisome from a highly stable machine with behavior dictated by deterministic principles to a dynamic system that is controlled by stochastic processes. We propose that these dynamics will play crucial roles in roadblock bypass. Further single-molecule studies of this bypass will, therefore, be essential to facilitate the in-depth investigation of multi-protein complexes that is necessary to understand complicated collisions on the DNA.
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Affiliation(s)
- Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
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6
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Xu ZQ, Dixon NE. Bacterial replisomes. Curr Opin Struct Biol 2018; 53:159-168. [PMID: 30292863 DOI: 10.1016/j.sbi.2018.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 01/18/2023]
Abstract
Bacterial replisomes are dynamic multiprotein DNA replication machines that are inherently difficult for structural studies. However, breakthroughs continue to come. The structures of Escherichia coli DNA polymerase III (core)-clamp-DNA subcomplexes solved by single-particle cryo-electron microscopy in both polymerization and proofreading modes and the discovery of the stochastic nature of the bacterial replisomes represent notable progress. The structures reveal an intricate interaction network in the polymerase-clamp subassembly, providing insights on how replisomes may work. Meantime, ensemble and single-molecule functional assays and fluorescence microscopy show that the bacterial replisomes can work in a decoupled and uncoordinated way, with polymerases quickly exchanging and both leading-strand and lagging-strand polymerases and the helicase working independently, contradictory to the elegant textbook view of a highly coordinated machine.
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Affiliation(s)
- Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.
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7
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Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome. Proc Natl Acad Sci U S A 2017; 114:10630-10635. [PMID: 28923950 DOI: 10.1073/pnas.1711291114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.
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8
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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand J, Bensimon D, Croquette V. A mechanistic study of helicases with magnetic traps. Protein Sci 2017; 26:1314-1336. [PMID: 28474797 PMCID: PMC5477542 DOI: 10.1002/pro.3187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023]
Abstract
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
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Affiliation(s)
- Samar Hodeib
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Saurabh Raj
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Maria Manosas
- Departament de Física FonamentalFacultat de Física, Universitat de BarcelonaBarcelona08028Spain
- CIBER‐BBN de BioingenieriaBiomateriales y Nanomedicina, Instituto de Sanidad Carlos IIIMadridSpain
| | - Weiting Zhang
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Debjani Bagchi
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Present address: Physics DepartmentFaculty of Science, The M.S. University of BarodaVadodaraGujarat390002India
| | - Bertrand Ducos
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Francesca Fiorini
- Univ Lyon, Molecular Microbiology and Structural Biochemistry, MMSB‐IBCP UMR5086 CNRS/Lyon1Lyon Cedex 769367France
| | - Joanne Kanaan
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Jean‐François Allemand
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - David Bensimon
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia90095
| | - Vincent Croquette
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
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9
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Lewis JS, Spenkelink LM, Jergic S, Wood EA, Monachino E, Horan NP, Duderstadt KE, Cox MM, Robinson A, Dixon NE, van Oijen AM. Single-molecule visualization of fast polymerase turnover in the bacterial replisome. eLife 2017; 6. [PMID: 28432790 PMCID: PMC5419744 DOI: 10.7554/elife.23932] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli DNA replication machinery has been used as a road map to uncover design rules that enable DNA duplication with high efficiency and fidelity. Although the enzymatic activities of the replicative DNA Pol III are well understood, its dynamics within the replisome are not. Here, we test the accepted view that the Pol III holoenzyme remains stably associated within the replisome. We use in vitro single-molecule assays with fluorescently labeled polymerases to demonstrate that the Pol III* complex (holoenzyme lacking the β2 sliding clamp), is rapidly exchanged during processive DNA replication. Nevertheless, the replisome is highly resistant to dilution in the absence of Pol III* in solution. We further show similar exchange in live cells containing labeled clamp loader and polymerase. These observations suggest a concentration-dependent exchange mechanism providing a balance between stability and plasticity, facilitating replacement of replisomal components dependent on their availability in the environment. DOI:http://dx.doi.org/10.7554/eLife.23932.001
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Affiliation(s)
- Jacob S Lewis
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Lisanne M Spenkelink
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Enrico Monachino
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Nicholas P Horan
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technishche Universität München, Garching, Germany
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Andrew Robinson
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Antoine M van Oijen
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
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10
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Monachino E, Spenkelink LM, van Oijen AM. Watching cellular machinery in action, one molecule at a time. J Cell Biol 2016; 216:41-51. [PMID: 27979907 PMCID: PMC5223611 DOI: 10.1083/jcb.201610025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 12/03/2022] Open
Abstract
Monachino et al. review recent developments in single-molecule biophysical approaches and the cell biological advances they allow. Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.
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Affiliation(s)
- Enrico Monachino
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, Netherlands
| | - Lisanne M Spenkelink
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, Netherlands
| | - Antoine M van Oijen
- Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
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11
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Duderstadt KE, Geertsema HJ, Stratmann SA, Punter CM, Kulczyk AW, Richardson CC, van Oijen AM. Simultaneous Real-Time Imaging of Leading and Lagging Strand Synthesis Reveals the Coordination Dynamics of Single Replisomes. Mol Cell 2016; 64:1035-1047. [PMID: 27889453 DOI: 10.1016/j.molcel.2016.10.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/18/2016] [Accepted: 10/20/2016] [Indexed: 11/16/2022]
Abstract
The molecular machinery responsible for DNA replication, the replisome, must efficiently coordinate DNA unwinding with priming and synthesis to complete duplication of both strands. Due to the anti-parallel nature of DNA, the leading strand is copied continuously, while the lagging strand is produced by repeated cycles of priming, DNA looping, and Okazaki-fragment synthesis. Here, we report a multidimensional single-molecule approach to visualize this coordination in the bacteriophage T7 replisome by simultaneously monitoring the kinetics of loop growth and leading-strand synthesis. We show that loops in the lagging strand predominantly occur during priming and only infrequently support subsequent Okazaki-fragment synthesis. Fluorescence imaging reveals polymerases remaining bound to the lagging strand behind the replication fork, consistent with Okazaki-fragment synthesis behind and independent of the replication complex. Individual replisomes display both looping and pausing during priming, reconciling divergent models for the regulation of primer synthesis and revealing an underlying plasticity in replisome operation.
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Affiliation(s)
- Karl E Duderstadt
- Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, 9700 AB Groningen, the Netherlands; Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Physik Department, Technische Universität München, 85748 Garching, Germany.
| | - Hylkje J Geertsema
- Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, 9700 AB Groningen, the Netherlands
| | - Sarah A Stratmann
- Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, 9700 AB Groningen, the Netherlands
| | - Christiaan M Punter
- Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, 9700 AB Groningen, the Netherlands
| | - Arkadiusz W Kulczyk
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Charles C Richardson
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, 9700 AB Groningen, the Netherlands; Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia.
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12
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Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 2016; 5. [PMID: 27723458 PMCID: PMC5056789 DOI: 10.7554/elife.17667] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes. DOI:http://dx.doi.org/10.7554/eLife.17667.001
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Raibatak Das
- Department of Integrative Biology, University of Colorado Denver, Denver, United States
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jun Lee
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Frances J Mejia
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Yang Li
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, United States
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13
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Åberg C, Duderstadt KE, van Oijen AM. Stability versus exchange: a paradox in DNA replication. Nucleic Acids Res 2016; 44:4846-54. [PMID: 27112565 PMCID: PMC4889951 DOI: 10.1093/nar/gkw296] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/11/2016] [Indexed: 11/14/2022] Open
Abstract
Multi-component biological machines, comprising individual proteins with specialized functions, perform a variety of essential processes in cells. Once assembled, most such complexes are considered very stable, retaining individual constituents as long as required. However, rapid and frequent exchange of individual factors in a range of critical cellular assemblies, including DNA replication machineries, DNA transcription regulators and flagellar motors, has recently been observed. The high stability of a multi-protein complex may appear mutually exclusive with rapid subunit exchange. Here, we describe a multisite competitive exchange mechanism, based on simultaneous binding of a protein to multiple low-affinity sites. It explains how a component can be stably integrated into a complex in the absence of competing factors, while able to rapidly exchange in the presence of competing proteins. We provide a mathematical model for the mechanism and give analytical expressions for the stability of a pre-formed complex, in the absence and presence of competitors. Using typical binding kinetic parameters, we show that the mechanism is operational under physically realistic conditions. Thus, high stability and rapid exchange within a complex can be reconciled and this framework can be used to rationalize previous observations, qualitatively as well as quantitatively.
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Affiliation(s)
- Christoffer Åberg
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands School of Chemistry, University of Wollongong, NSW 2522, Australia
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14
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Abstract
The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some "gears" of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the "replisome" machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus.
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Affiliation(s)
- Nina Y Yao
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and
| | - Mike E O'Donnell
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and.,b Howard Hughes Medical Institute, The Rockefeller University , New York , NY , USA
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15
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Zhang H, Tang Y, Lee SJ, Wei Z, Cao J, Richardson CC. Binding Affinities among DNA Helicase-Primase, DNA Polymerase, and Replication Intermediates in the Replisome of Bacteriophage T7. J Biol Chem 2015; 291:1472-80. [PMID: 26620561 DOI: 10.1074/jbc.m115.698233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/06/2022] Open
Abstract
The formation of a replication loop on the lagging strand facilitates coordinated synthesis of the leading- and lagging-DNA strands and provides a mechanism for recycling of the lagging-strand DNA polymerase. As an Okazaki fragment is completed, the loop is released, and a new loop is formed as the synthesis of a new Okazaki fragment is initiated. Loop release requires the dissociation of the complex formed by the interactions among helicase, DNA polymerase, and DNA. The completion of the Okazaki fragment may result in either a nick or a single-stranded DNA region. In the replication system of bacteriophage T7, the dissociation of the polymerase from either DNA region is faster than that observed for the dissociation of the helicase from DNA polymerase, implying that the replication loop is released more likely through the dissociation of the lagging-strand DNA from polymerase, retaining the polymerase at replication fork. Both dissociation of DNA polymerase from DNA and that of helicase from a DNA polymerase · DNA complex are much faster at a nick DNA region than the release from a ssDNA region. These results suggest that the replication loop is released as a result of the nick formed when the lagging-strand DNA polymerase encounters the previously synthesized Okazaki fragment, releasing lagging-strand DNA and retaining DNA polymerase at the replication fork for the synthesis of next Okazaki fragment.
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Affiliation(s)
- Huidong Zhang
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
| | - Yong Tang
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Seung-Joo Lee
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
| | - Zeliang Wei
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Jia Cao
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Charles C Richardson
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
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16
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Dulin D, Vilfan ID, Berghuis BA, Poranen MM, Depken M, Dekker NH. Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site. Nucleic Acids Res 2015; 43:10421-9. [PMID: 26496948 PMCID: PMC4666362 DOI: 10.1093/nar/gkv1098] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/11/2015] [Indexed: 12/02/2022] Open
Abstract
Transcription in RNA viruses is highly dynamic, with a variety of pauses interrupting nucleotide addition by RNA-dependent RNA polymerase (RdRp). For example, rare but lengthy pauses (>20 s) have been linked to backtracking for viral single-subunit RdRps. However, while such backtracking has been well characterized for multi-subunit RNA polymerases (RNAPs) from bacteria and yeast, little is known about the details of viral RdRp backtracking and its biological roles. Using high-throughput magnetic tweezers, we quantify the backtracking by RdRp from the double-stranded (ds) RNA bacteriophage Φ6, a model system for RdRps. We characterize the probability of entering long backtracks as a function of force and propose a model in which the bias toward backtracking is determined by the base paring at the dsRNA fork. We further discover that extensive backtracking provides access to a new 3′-end that allows for the de novo initiation of a second RdRp. This previously unidentified behavior provides a new mechanism for rapid RNA synthesis using coupled RdRps and hints at a possible regulatory pathway for gene expression during viral RNA transcription.
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Affiliation(s)
- David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Igor D Vilfan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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17
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Hegde PM, Dutta A, Sengupta S, Mitra J, Adhikari S, Tomkinson AE, Li GM, Boldogh I, Hazra TK, Mitra S, Hegde ML. The C-terminal Domain (CTD) of Human DNA Glycosylase NEIL1 Is Required for Forming BERosome Repair Complex with DNA Replication Proteins at the Replicating Genome: DOMINANT NEGATIVE FUNCTION OF THE CTD. J Biol Chem 2015; 290:20919-20933. [PMID: 26134572 DOI: 10.1074/jbc.m115.642918] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 12/21/2022] Open
Abstract
The human DNA glycosylase NEIL1 was recently demonstrated to initiate prereplicative base excision repair (BER) of oxidized bases in the replicating genome, thus preventing mutagenic replication. A significant fraction of NEIL1 in cells is present in large cellular complexes containing DNA replication and other repair proteins, as shown by gel filtration. However, how the interaction of NEIL1 affects its recruitment to the replication site for prereplicative repair was not investigated. Here, we show that NEIL1 binarily interacts with the proliferating cell nuclear antigen clamp loader replication factor C, DNA polymerase δ, and DNA ligase I in the absence of DNA via its non-conserved C-terminal domain (CTD); replication factor C interaction results in ∼8-fold stimulation of NEIL1 activity. Disruption of NEIL1 interactions within the BERosome complex, as observed for a NEIL1 deletion mutant (N311) lacking the CTD, not only inhibits complete BER in vitro but also prevents its chromatin association and reduced recruitment at replication foci in S phase cells. This suggests that the interaction of NEIL1 with replication and other BER proteins is required for efficient repair of the replicating genome. Consistently, the CTD polypeptide acts as a dominant negative inhibitor during in vitro repair, and its ectopic expression sensitizes human cells to reactive oxygen species. We conclude that multiple interactions among BER proteins lead to large complexes, which are critical for efficient BER in mammalian cells, and the CTD interaction could be targeted for enhancing drug/radiation sensitivity of tumor cells.
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Affiliation(s)
- Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030
| | - Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030; Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030
| | - Sanjay Adhikari
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030
| | - Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131
| | - Guo-Min Li
- Department of Toxicology and Cancer Biology and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Istvan Boldogh
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Tapas K Hazra
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030; Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555; Weill Medical College of Cornell University, New York, New York.
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030; Weill Medical College of Cornell University, New York, New York; Houston Methodist Neurological Institute, Houston, Texas 77030.
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18
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Coordinated DNA Replication by the Bacteriophage T4 Replisome. Viruses 2015; 7:3186-200. [PMID: 26102578 PMCID: PMC4488733 DOI: 10.3390/v7062766] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022] Open
Abstract
The T4 bacteriophage encodes eight proteins, which are sufficient to carry out coordinated leading and lagging strand DNA synthesis. These purified proteins have been used to reconstitute DNA synthesis in vitro and are a well-characterized model system. Recent work on the T4 replisome has yielded more detailed insight into the dynamics and coordination of proteins at the replication fork. Since the leading and lagging strands are synthesized in opposite directions, coordination of DNA synthesis as well as priming and unwinding is accomplished by several protein complexes. These protein complexes serve to link catalytic activities and physically tether proteins to the replication fork. Essential to both leading and lagging strand synthesis is the formation of a holoenzyme complex composed of the polymerase and a processivity clamp. The two holoenzymes form a dimer allowing the lagging strand polymerase to be retained within the replisome after completion of each Okazaki fragment. The helicase and primase also form a complex known as the primosome, which unwinds the duplex DNA while also synthesizing primers on the lagging strand. Future studies will likely focus on defining the orientations and architecture of protein complexes at the replication fork.
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19
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Dulin D, Vilfan ID, Berghuis BA, Hage S, Bamford DH, Poranen MM, Depken M, Dekker NH. Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase. Cell Rep 2015; 10:983-992. [PMID: 25683720 DOI: 10.1016/j.celrep.2015.01.031] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/23/2014] [Accepted: 01/10/2015] [Indexed: 02/06/2023] Open
Abstract
RNA viruses have specific mutation rates that balance the conflicting needs of an evolutionary response to host antiviral defenses and avoidance of the error catastrophe. While most mutations are known to originate in replication errors, difficulties of capturing the underlying dynamics have left the mechanochemical basis of viral mutagenesis unresolved. Here, we use multiplexed magnetic tweezers to investigate error incorporation by the bacteriophage Φ6 RNA-dependent RNA polymerase. We extract large datasets fingerprinting real-time polymerase dynamics over four magnitudes in time, in the presence of nucleotide analogs, and under varying NTP and divalent cation concentrations and fork stability. Quantitative analysis reveals a new pause state that modulates polymerase fidelity and so ties viral polymerase pausing to the biological function of optimizing virulence. Adjusting the frequency of such pauses offers a target for therapeutics and may also reflect an evolutionary strategy for virus populations to track the gradual evolution of their hosts.
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Affiliation(s)
- David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - Igor D Vilfan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - Susanne Hage
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland.
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands.
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20
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Abstract
A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules - metabolites, structural proteins, enzymes, oligonucleotides - multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or intracellular transport. By purifying single components and using them to reconstitute molecular processes in a test tube, researchers have gathered crucial knowledge about mechanistic, dynamic and structural properties of biochemical pathways. However, to sort this information into an accurate cellular road map, we need to understand reactions in their relevant context within the cellular hierarchy, which is at the individual molecule level within a crowded, cellular environment. Reactions occur in a stochastic fashion, have short-lived and not necessarily well-defined intermediates, and dynamically form functional entities. With the use of single-molecule techniques these steps can be followed and detailed kinetic information that otherwise would be hidden in ensemble averaging can be obtained. One of the first complex cellular tasks that have been studied at the single-molecule level is the replication of DNA. The replisome, the multi-protein machinery responsible for copying DNA, is built from a large number of proteins that function together in an intricate and efficient fashion allowing the complex to tolerate DNA damage, roadblocks or fluctuations in subunit concentration. In this review, we summarize advances in single-molecule studies, both in vitro and in vivo, that have contributed to our current knowledge of the mechanistic principles underlying DNA replication.
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Affiliation(s)
- S A Stratmann
- Zernike Institute for Advanced Materials, Centre for Synthetic Biology, University of Groningen, The Netherlands.
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