1
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Łazowski K, Woodgate R, Fijalkowska IJ. Escherichia coli DNA replication: the old model organism still holds many surprises. FEMS Microbiol Rev 2024; 48:fuae018. [PMID: 38982189 PMCID: PMC11253446 DOI: 10.1093/femsre/fuae018] [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: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.
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Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, United States
| | - Iwona J Fijalkowska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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2
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. Nat Commun 2023; 14:4396. [PMID: 37474605 PMCID: PMC10359460 DOI: 10.1038/s41467-023-40106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer length is defined are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates. We show that gp41 alone is an open spiral, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the ring closure and activates the helicase. Helicase activation exposes a cryptic hydrophobic surface to recruit the gp61 primase. The primase binds the helicase in a bipartite mode in which the N-terminal Zn-binding domain and the C-terminal RNA polymerase domain each contain a helicase-interacting motif that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Our study reveals the T4 primosome assembly process and sheds light on the RNA primer synthesis mechanism.
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Affiliation(s)
- Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michelle M Spiering
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | | | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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3
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539249. [PMID: 37205424 PMCID: PMC10187150 DOI: 10.1101/2023.05.03.539249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 Å. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.
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4
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Xu L, Halma MTJ, Wuite GJL. Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches. Int J Mol Sci 2023; 24:ijms24032806. [PMID: 36769124 PMCID: PMC9917605 DOI: 10.3390/ijms24032806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins' activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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5
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Ding F, Cocco S, Raj S, Manosas M, Nguyen T, Spiering M, Bensimon D, Allemand JF, Croquette V. Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain. Nucleic Acids Res 2022; 50:12082-12093. [PMID: 36478056 PMCID: PMC9757040 DOI: 10.1093/nar/gkac1113] [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: 06/20/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.
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Affiliation(s)
- Fangyuan Ding
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
- Center for Synthetic Biology, Chao Family Comprehensive Cancer Center, Department of Developmental and Cell Biology, and Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Simona Cocco
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Saurabh Raj
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, 110016, India
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Thao Thi Thu Nguyen
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Michelle M Spiering
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - David Bensimon
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS, Inserm, École Normale Supérieure, PSL Research University, F-75005, Paris, France
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jean-François Allemand
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS, Inserm, École Normale Supérieure, PSL Research University, F-75005, Paris, France
| | - Vincent Croquette
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS, Inserm, École Normale Supérieure, PSL Research University, F-75005, Paris, France
- ESPCI Paris, Université PSL, Paris, France
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6
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Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
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7
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Spinks RR, Spenkelink LM, Dixon NE, van Oijen AM. Single-Molecule Insights Into the Dynamics of Replicative Helicases. Front Mol Biosci 2021; 8:741718. [PMID: 34513934 PMCID: PMC8426354 DOI: 10.3389/fmolb.2021.741718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Helicases are molecular motors that translocate along single-stranded DNA and unwind duplex DNA. They rely on the consumption of chemical energy from nucleotide hydrolysis to drive their translocation. Specialized helicases play a critically important role in DNA replication by unwinding DNA at the front of the replication fork. The replicative helicases of the model systems bacteriophages T4 and T7, Escherichia coli and Saccharomyces cerevisiae have been extensively studied and characterized using biochemical methods. While powerful, their averaging over ensembles of molecules and reactions makes it challenging to uncover information related to intermediate states in the unwinding process and the dynamic helicase interactions within the replisome. Here, we describe single-molecule methods that have been developed in the last few decades and discuss the new details that these methods have revealed about replicative helicases. Applying methods such as FRET and optical and magnetic tweezers to individual helicases have made it possible to access the mechanistic aspects of unwinding. It is from these methods that we understand that the replicative helicases studied so far actively translocate and then passively unwind DNA, and that these hexameric enzymes must efficiently coordinate the stepping action of their subunits to achieve unwinding, where the size of each step is prone to variation. Single-molecule fluorescence microscopy methods have made it possible to visualize replicative helicases acting at replication forks and quantify their dynamics using multi-color colocalization, FRAP and FLIP. These fluorescence methods have made it possible to visualize helicases in replication initiation and dissect this intricate protein-assembly process. In a similar manner, single-molecule visualization of fluorescent replicative helicases acting in replication identified that, in contrast to the replicative polymerases, the helicase does not exchange. Instead, the replicative helicase acts as the stable component that serves to anchor the other replication factors to the replisome.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
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8
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Zhang S, Xiao X, Kong J, Lu K, Dou SX, Wang PY, Ma L, Liu Y, Li G, Li W, Zhang H. DNA polymerase Gp90 activities and regulations on strand displacement DNA synthesis revealed at single-molecule level. FASEB J 2021; 35:e21607. [PMID: 33908664 DOI: 10.1096/fj.202100033rr] [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: 01/07/2021] [Revised: 03/18/2021] [Accepted: 04/05/2021] [Indexed: 11/11/2022]
Abstract
Strand displacement DNA synthesis (SDDS) is an essential step in DNA replication. With magnetic tweezers, we investigated SDDS kinetics of wild-type gp90 and its exonuclease-deficient polymerase gp90 exo- at single-molecule level. A novel binding state of gp90 to the fork flap was confirmed prior to SDDS, suggesting an intermediate in the initiation of SDDS. The rate and processivity of SDDS by gp90 exo- or wt-gp90 are increased with force and dNTP concentration. The rate and processivity of exonuclease by wt-gp90 are decreased with force. High GC content decreases SDDS and exonuclease processivity but increases exonuclease rate for wt-gp90. The high force and dNTP concentration and low GC content facilitate the successive SDDS but retard the successive exonuclease for wt-gp90. Furthermore, increasing GC content accelerates the transition from SDDS or exonuclease to exonuclease. This work reveals the kinetics of SDDS in detail and offers a broader cognition on the regulation of various factors on SDDS at single-polymerase level.
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Affiliation(s)
- Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ke Lu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuru Liu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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9
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Magnetic Tweezers-Based Single-Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase. Methods Mol Biol 2021; 2281:93-115. [PMID: 33847954 DOI: 10.1007/978-1-0716-1290-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ability of magnetic tweezers to apply forces and measure molecular displacements has resulted in its extensive use to study the activity of enzymes involved in various aspects of nucleic acid metabolism. These studies have led to the discovery of key aspects of protein-protein and protein-nucleic acid interaction, uncovering dynamic heterogeneities that are lost to ensemble averaging in bulk experiments. The versatility of magnetic tweezers lies in the possibility and ease of tracking multiple parallel single-molecule events to yield statistically relevant single-molecule data. Moreover, they allow tracking both fast millisecond dynamics and slow processes (spanning several hours). In this chapter, we present the protocols used to study the interaction between E. coli SSB, single-stranded DNA (ssDNA), and E. coli RecQ helicase using magnetic tweezers. In particular, we propose constant force and force modulation assays to investigate SSB binding to DNA, as well as to characterize various facets of RecQ helicase activity stimulation by SSB.
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10
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Benkovic SJ. From Bioorganic Models to Cells. Annu Rev Biochem 2021; 90:57-76. [PMID: 34153218 DOI: 10.1146/annurev-biochem-062320-062929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
I endeavor to share how various choices-some deliberate, some unconscious-and the unmistakable influence of many others shaped my scientific pursuits. I am fascinated by how two long-term, major streams of my research, DNA replication and purine biosynthesis, have merged with unexpected interconnections. If I have imparted to many of the talented individuals who have passed through my lab a degree of my passion for uncloaking the mysteries hidden in scientific research and an understanding of the honesty and rigor it demands and its impact on the world community, then my mentorship has been successful.
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Affiliation(s)
- Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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11
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Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
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12
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Biology on track: single-molecule visualisation of protein dynamics on linear DNA substrates. Essays Biochem 2021; 65:5-16. [PMID: 33236762 DOI: 10.1042/ebc20200019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Single-molecule fluorescence imaging techniques have become important tools in biological research to gain mechanistic insights into cellular processes. These tools provide unique access to the dynamic and stochastic behaviour of biomolecules. Single-molecule tools are ideally suited to study protein-DNA interactions in reactions reconstituted from purified proteins. The use of linear DNA substrates allows for the study of protein-DNA interactions with observation of the movement and behaviour of DNA-translocating proteins over long distances. Single-molecule studies using long linear DNA substrates have revealed unanticipated insights on the dynamics of multi-protein systems. In this review, we provide an overview of recent methodological advances, including the construction of linear DNA substrates. We highlight the versatility of these substrates by describing their application in different single-molecule fluorescence techniques, with a focus on in vitro reconstituted systems. We discuss insights from key experiments on DNA curtains, DNA-based molecular motor proteins, and multi-protein systems acting on DNA that relied on the use of long linear substrates and single-molecule visualisation. The quality and customisability of linear DNA substrates now allows the insertion of modifications, such as nucleosomes, to create conditions mimicking physiologically relevant crowding and complexity. Furthermore, the current technologies will allow future studies on the real-time visualisation of the interfaces between DNA maintenance processes such as replication and transcription.
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13
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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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14
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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15
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Raj S, Bagchi D, Orero JV, Banroques J, Tanner NK, Croquette V. Mechanistic characterization of the DEAD-box RNA helicase Ded1 from yeast as revealed by a novel technique using single-molecule magnetic tweezers. Nucleic Acids Res 2019; 47:3699-3710. [PMID: 30993346 PMCID: PMC6468243 DOI: 10.1093/nar/gkz057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
DEAD-box helicases are involved in all steps of RNA metabolism. They are ATP-dependent RNA binding proteins and RNA-dependent ATPases. They can displace short duplexes, but they lack processivity. Their mechanism and functioning are not clearly understood; classical or bulk biochemical assays are not sufficient to answer these questions. Single-molecule techniques provide useful tools, but they are limited in cases where the proteins are nonprocessive and give weak signals. We present here a new, magnetic-tweezers-based, single-molecule assay that is simple and that can sensitively measure the displacement time of a small, hybridized, RNA oligonucleotide. Tens of molecules can be analyzed at the same time. Comparing the displacement times with and without a helicase gives insights into the enzymatic activity of the protein. We used this assay to study yeast Ded1, which is orthologous to human DDX3. Although Ded1 acts on a variety of substrates, we find that Ded1 requires an RNA substrate for its ATP-dependent unwinding activity and that ATP hydrolysis is needed to see this activity. Further, we find that only intramolecular single-stranded RNA extensions enhance this activity. We propose a model where ATP-bound Ded1 stabilizes partially unwound duplexes and where multiple binding events may be needed to see displacement.
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Affiliation(s)
- Saurabh Raj
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Debjani Bagchi
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Jessica Valle Orero
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Josette Banroques
- Laboratoire d'Expression Génétique Microbienne, CNRS UMR8261/Université Paris 7-Diderot, Sorbonne Paris Cité Universités, 13 rue Pierre et Marie Curie, Paris, France.,Institut de Biologie Physico-Chimique, PSL Research University, 75005 Paris, France
| | - N Kyle Tanner
- Laboratoire d'Expression Génétique Microbienne, CNRS UMR8261/Université Paris 7-Diderot, Sorbonne Paris Cité Universités, 13 rue Pierre et Marie Curie, Paris, France.,Institut de Biologie Physico-Chimique, PSL Research University, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,ESPCI Paris, PSL University, 10 rue Vauquelin, 75005 Paris, France
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16
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Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure. Methods 2019; 169:46-56. [PMID: 31351926 DOI: 10.1016/j.ymeth.2019.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/01/2019] [Accepted: 07/22/2019] [Indexed: 01/05/2023] Open
Abstract
Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.
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17
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Gowravaram M, Bonneau F, Kanaan J, Maciej VD, Fiorini F, Raj S, Croquette V, Le Hir H, Chakrabarti S. A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner. Nucleic Acids Res 2019; 46:2648-2659. [PMID: 29378013 PMCID: PMC5861435 DOI: 10.1093/nar/gky040] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
The RNA helicase UPF1 is a key component of the nonsense mediated mRNA decay (NMD) pathway. Previous X-ray crystal structures of UPF1 elucidated the molecular mechanisms of its catalytic activity and regulation. In this study, we examine features of the UPF1 core and identify a structural element that adopts different conformations in the various nucleotide- and RNA-bound states of UPF1. We demonstrate, using biochemical and single molecule assays, that this structural element modulates UPF1 catalytic activity and thereby refer to it as the regulatory loop. Interestingly, there are two alternatively spliced isoforms of UPF1 in mammals which differ only in the lengths of their regulatory loops. The loop in isoform 1 (UPF11) is 11 residues longer than that of isoform 2. We find that this small insertion in UPF11 leads to a two-fold increase in its translocation and ATPase activities. To determine the mechanistic basis of this differential catalytic activity, we have determined the X-ray crystal structure of the helicase core of UPF11 in its apo-state. Our results point toward a novel mechanism of regulation of RNA helicases, wherein alternative splicing leads to subtle structural rearrangements within the protein that are critical to modulate enzyme movements and catalytic activity.
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Affiliation(s)
- Manjeera Gowravaram
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Joanne Kanaan
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Vincent D Maciej
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Francesca Fiorini
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Saurabh Raj
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,LPS, 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, F-75005 Paris, France
| | - Vincent Croquette
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,LPS, 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, F-75005 Paris, France
| | - Hervé Le Hir
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Sutapa Chakrabarti
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
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18
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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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19
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Wasserman MR, Liu S. A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines. Biochemistry 2019; 58:4667-4676. [PMID: 31251042 DOI: 10.1021/acs.biochem.9b00346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA is both a fundamental building block of life and a fascinating natural polymer. The advent of single-molecule manipulation tools made it possible to exert controlled force on individual DNA molecules and measure their mechanical response. Such investigations elucidated the elastic properties of DNA and revealed its distinctive structural configurations across force regimes. In the meantime, a detailed understanding of DNA mechanics laid the groundwork for single-molecule studies of DNA-binding proteins and DNA-processing enzymes that bend, stretch, and twist DNA. These studies shed new light on the metabolism and transactions of nucleic acids, which constitute a major part of the cell's operating system. Furthermore, the marriage of single-molecule fluorescence visualization and force manipulation has enabled researchers to directly correlate the applied tension to changes in the DNA structure and the behavior of DNA-templated complexes. Overall, experimental exploitation of DNA mechanics has been and will continue to be a unique and powerful strategy for understanding how molecular machineries recognize and modify the physical state of DNA to accomplish their biological functions.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
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20
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Schlierf M, Wang G, Chen XS, Ha T. Hexameric helicase G40P unwinds DNA in single base pair steps. eLife 2019; 8:42001. [PMID: 30688211 PMCID: PMC6370340 DOI: 10.7554/elife.42001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Most replicative helicases are hexameric, ring-shaped motor proteins that translocate on and unwind DNA. Despite extensive biochemical and structural investigations, how their translocation activity is utilized chemo-mechanically in DNA unwinding is poorly understood. We examined DNA unwinding by G40P, a DnaB-family helicase, using a single-molecule fluorescence assay with a single base pair resolution. The high-resolution assay revealed that G40P by itself is a very weak helicase that stalls at barriers as small as a single GC base pair and unwinds DNA with the step size of a single base pair. Binding of a single ATPγS could stall unwinding, demonstrating highly coordinated ATP hydrolysis between six identical subunits. We observed frequent slippage of the helicase, which is fully suppressed by the primase DnaG. We anticipate that these findings allow a better understanding on the fine balance of thermal fluctuation activation and energy derived from hydrolysis. Living cells store their genetic code written in molecules of DNA, with two strands of DNA twisted together to form the familiar double helix. When a cell prepares to divide, it must unwind its DNA so that the individual strands can be copied. Enzymes known as DNA helicases play a vital role in this unwinding process; yet, it is not completely clear how these enzymes move along the DNA. Schlierf et al. have now developed a new approach to see how an individual DNA helicase called G40P unwinds the DNA double helix. The experiments used a molecular ruler to measure the DNA unwinding and showed that the helicase opened the double helix one letter of genetic code at a time. Also, specific sequence of letters within the DNA molecules could slow down and stop G40P or even cause it to move backwards. DNA helicases work closely with other proteins inside cells to perform their task. DNA primases, for example, are enzymes that create the starting points for making new strands of DNA. Schlierf et al. found that the primase DnaG could also prevent G40P from moving backwards on the DNA, a new and unexpected function of DnaG. These findings contribute to an ongoing debate among researchers with partially contradictory models for how DNA helicases unwind the DNA double helix. Although originally from a virus, G40P is similar to a helicase enzyme found in bacteria. Therefore, a better understanding of this helicase may lead to new ways to stop bacteria copying their DNA, which might one day become new antibiotics to treat bacterial infections.
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Affiliation(s)
- Michael Schlierf
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Ganggang Wang
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Taekjip Ha
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,Howard Hughes Medical Institute, Baltimore, United States.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States.,Department of Biophysics, Johns Hopkins University, Baltimore, United States
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21
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Ostrofet E, Papini FS, Dulin D. Correction-free force calibration for magnetic tweezers experiments. Sci Rep 2018; 8:15920. [PMID: 30374099 PMCID: PMC6206022 DOI: 10.1038/s41598-018-34360-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Magnetic tweezers are a powerful technique to perform high-throughput and high-resolution force spectroscopy experiments at the single-molecule level. The camera-based detection of magnetic tweezers enables the observation of hundreds of magnetic beads in parallel, and therefore the characterization of the mechanochemical behavior of hundreds of nucleic acids and enzymes. However, magnetic tweezers experiments require an accurate force calibration to extract quantitative data, which is limited to low forces if the deleterious effect of the finite camera open shutter time (τsh) is not corrected. Here, we provide a simple method to perform correction-free force calibration for high-throughput magnetic tweezers at low image acquisition frequency (fac). By significantly reducing τsh to at least 4-fold the characteristic times of the tethered magnetic bead, we accurately evaluated the variance of the magnetic bead position along the axis parallel to the magnetic field, estimating the force with a relative error of ~10% (standard deviation), being only limited by the bead-to-bead difference. We calibrated several magnets - magnetic beads configurations, covering a force range from ~50 fN to ~60 pN. In addition, for the presented configurations, we provide a table with the mathematical expressions that describe the force as a function of the magnets position.
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Affiliation(s)
- Eugen Ostrofet
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany
| | - Flávia Stal Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany.
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22
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Buchachenko AL, Breslavskaya NN. An Insight into the Helicase Functioning Through the Hydrogen Isotope Effects. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2018. [DOI: 10.1134/s1990793117060185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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HTLV-1 Tax plugs and freezes UPF1 helicase leading to nonsense-mediated mRNA decay inhibition. Nat Commun 2018; 9:431. [PMID: 29382845 PMCID: PMC5789848 DOI: 10.1038/s41467-017-02793-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 12/28/2017] [Indexed: 12/19/2022] Open
Abstract
Up-Frameshift Suppressor 1 Homolog (UPF1) is a key factor for nonsense-mediated mRNA decay (NMD), a cellular process that can actively degrade mRNAs. Here, we study NMD inhibition during infection by human T-cell lymphotropic virus type I (HTLV-1) and characterise the influence of the retroviral Tax factor on UPF1 activity. Tax interacts with the central helicase core domain of UPF1 and might plug the RNA channel of UPF1, reducing its affinity for nucleic acids. Furthermore, using a single-molecule approach, we show that the sequential interaction of Tax with a RNA-bound UPF1 freezes UPF1: this latter is less sensitive to the presence of ATP and shows translocation defects, highlighting the importance of this feature for NMD. These mechanistic insights reveal how HTLV-1 hijacks the central component of NMD to ensure expression of its own genome. UPF1 is a central protein in nonsense-mediated mRNA decay (NMD), but contribution of its RNA processivity to NMD is unclear. Here, the authors show how the retroviral Tax protein interacts with and inhibits UPF1, and demonstrate that UPF1’s translocase activity contributes to NMD.
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24
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Scherr MJ, Safaric B, Duderstadt KE. Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication. Bioessays 2017; 40. [PMID: 29282758 DOI: 10.1002/bies.201700159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/01/2017] [Indexed: 11/07/2022]
Abstract
The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined by a uniform sequence of events. Instead, multiple exchange pathways, pauses, and DNA loop types appear to dominate replisome function. These observations suggest we must rethink our fundamental assumptions and acknowledge that each replication cycle may involve sampling of alternative, sometimes parallel, pathways. Here, we review our current mechanistic understanding of DNA replication while highlighting findings that exemplify multi-pathway aspects of replisome function and considering the broader implications.
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Affiliation(s)
- Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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25
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Lu X, Soto F, Li J, Li T, Liang Y, Wang J. Topographical Manipulation of Microparticles and Cells with Acoustic Microstreaming. ACS APPLIED MATERIALS & INTERFACES 2017; 9:38870-38876. [PMID: 29028308 DOI: 10.1021/acsami.7b15237] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Precise and reproducible manipulation of synthetic and biological microscale objects in complex environments is essential for many practical biochip and microfluidic applications. Here, we present an attractive acoustic topographical manipulation (ATM) method to achieve efficient and reproducible manipulation of diverse microscale objects. This new guidance method relies on the acoustically induced localized microstreaming forces generated around microstructures, which are capable of trapping nearby microobjects and manipulating them along a determined trajectory based on local topographic features. This unique phenomenon is investigated by numerical simulations examining the local microstreaming in the presence of microscale boundaries under the standing acoustic wave. This method can be used to manipulate a single microobject around a complex structure as well as collectively manipulate multiple objects moving synchronously along complicated shapes. Furthermore, the ATM can serve for automated maze solving by autonomously manipulating microparticles with diverse geometries and densities, including live cells, through complex maze-like topographical features without external feedback, particle modification, or adjustment of operational parameters.
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Affiliation(s)
- Xiaolong Lu
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
- State Key Laboratory of Mechanics and Control of Mechanical Structures, Nanjing University of Aeronautics and Astronautics , Nanjing 210016, China
| | - Fernando Soto
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
| | - Jinxing Li
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
| | - Tianlong Li
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
| | - Yuyan Liang
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego , La Jolla, California 92093, United States
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26
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Benkovic SJ, Spiering MM. Understanding DNA replication by the bacteriophage T4 replisome. J Biol Chem 2017; 292:18434-18442. [PMID: 28972188 DOI: 10.1074/jbc.r117.811208] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The T4 replisome has provided a unique opportunity to investigate the intricacies of DNA replication. We present a comprehensive review of this system focusing on the following: its 8-protein composition, their individual and synergistic activities, and assembly in vitro and in vivo into a replisome capable of coordinated leading/lagging strand DNA synthesis. We conclude with a brief comparison with other replisomes with emphasis on how coordinated DNA replication is achieved.
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Affiliation(s)
- Stephen J Benkovic
- From the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michelle M Spiering
- From the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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27
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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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RNA primer-primase complexes serve as the signal for polymerase recycling and Okazaki fragment initiation in T4 phage DNA replication. Proc Natl Acad Sci U S A 2017; 114:5635-5640. [PMID: 28507156 DOI: 10.1073/pnas.1620459114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The opposite strand polarity of duplex DNA necessitates that the leading strand is replicated continuously whereas the lagging strand is replicated in discrete segments known as Okazaki fragments. The lagging-strand polymerase sometimes recycles to begin the synthesis of a new Okazaki fragment before finishing the previous fragment, creating a gap between the Okazaki fragments. The mechanism and signal that initiate this behavior-that is, the signaling mechanism-have not been definitively identified. We examined the role of RNA primer-primase complexes left on the lagging ssDNA from primer synthesis in initiating early lagging-strand polymerase recycling. We show for the T4 bacteriophage DNA replication system that primer-primase complexes have a residence time similar to the timescale of Okazaki fragment synthesis and the ability to block a holoenzyme synthesizing DNA and stimulate the dissociation of the holoenzyme to trigger polymerase recycling. The collision with primer-primase complexes triggering the early termination of Okazaki fragment synthesis has distinct advantages over those previously proposed because this signal requires no transmission to the lagging-strand polymerase through protein or DNA interactions, the mechanism for rapid dissociation of the holoenzyme is always collision, and no unique characteristics need to be assigned to either identical polymerase in the replisome. We have modeled repeated cycles of Okazaki fragment initiation using a collision with a completed Okazaki fragment or primer-primase complexes as the recycling mechanism. The results reproduce experimental data, providing insights into events related to Okazaki fragment initiation and the overall functioning of DNA replisomes.
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Timonen JVI, Grzybowski BA. Tweezing of Magnetic and Non-Magnetic Objects with Magnetic Fields. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1603516. [PMID: 28198579 DOI: 10.1002/adma.201603516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
Although strong magnetic fields cannot be conveniently "focused" like light, modern microfabrication techniques enable preparation of microstructures with which the field gradients - and resulting magnetic forces - can be localized to very small dimensions. This ability provides the foundation for magnetic tweezers which in their classical variant can address magnetic targets. More recently, the so-called negative magnetophoretic tweezers have also been developed which enable trapping and manipulations of completely nonmagnetic particles provided that they are suspended in a high-magnetic-susceptibility liquid. These two modes of magnetic tweezing are complimentary techniques tailorable for different types of applications. This Progress Report provides the theoretical basis for both modalities and illustrates their specific uses ranging from the manipulation of colloids in 2D and 3D, to trapping of living cells, control of cell function, experiments with single molecules, and more.
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Affiliation(s)
- Jaakko V I Timonen
- Department of Applied Physics, Aalto University School of Science, Espoo, 02150, Finland
| | - Bartosz A Grzybowski
- Center for Soft and Living Matter, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
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30
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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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31
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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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32
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Kemmerich FE, Kasaciunaite K, Seidel R. Modular magnetic tweezers for single-molecule characterizations of helicases. Methods 2016; 108:4-13. [PMID: 27402355 DOI: 10.1016/j.ymeth.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/09/2023] Open
Abstract
Magnetic tweezers provide a versatile toolkit supporting the mechanistic investigation of helicases. In the present article, we show that custom magnetic tweezers setups are straightforward to construct and can easily be extended to provide adaptable platforms, capable of addressing a multitude of enquiries regarding the functions of these fascinating molecular machines. We first address the fundamental components of a basic magnetic tweezers scheme and review some previous results to demonstrate the versatility of this instrument. We then elaborate on several extensions to the basic magnetic tweezers scheme, and demonstrate their applications with data from ongoing research. As our methodological overview illustrates, magnetic tweezers are an extremely useful tool for the characterization of helicases and a custom built instrument can be specifically tailored to suit the experimenter's needs.
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Affiliation(s)
- Felix E Kemmerich
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Kristina Kasaciunaite
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany.
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33
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Bianco P. Stalled replication fork rescue requires a novel DNA helicase. Methods 2016; 108:40-7. [PMID: 27282357 DOI: 10.1016/j.ymeth.2016.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022] Open
Abstract
During DNA replication, forks often stall and require restart. One mechanism for restart requires that the fork be moved in a direction opposite to that of replication. This reaction is known as fork regression. For this reaction to occur, the enzyme must couple unwinding of the nascent heteroduplex fork arms to the rewinding of nascent strands ahead of itself and to the parental duplex in its wake. As the arms of the fork are complementary, this reaction is isoenergetic making it challenging to study. To overcome this, a novel adaptation of magnetic tweezers was developed by the Croquette group. Here, a 1200bp hairpin was attached at opposite ends to a flow cell surface and a magnetic bead. By manipulating the bead with the magnets, force can be applied to unwind the hairpin or alternatively, released to allow the hairpin to rewind. This adaptation was used to study fork regression by RecG. The results show that this is an efficient regression enzyme, able to work against a large opposing force. Critically, it couples DNA unwinding to duplex rewinding and in the process, can displace bound proteins from fork arms.
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Affiliation(s)
- Piero Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY 14214, USA.
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Abstract
DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the β2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads β2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.
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Affiliation(s)
- J S Lewis
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - S Jergic
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - N E Dixon
- Centre for Medical & Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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35
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Li JH, Lin WX, Zhang B, Nong DG, Ju HP, Ma JB, Xu CH, Ye FF, Xi XG, Li M, Lu Y, Dou SX. Pif1 is a force-regulated helicase. Nucleic Acids Res 2016; 44:4330-9. [PMID: 27098034 PMCID: PMC4872122 DOI: 10.1093/nar/gkw295] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 04/08/2016] [Indexed: 02/05/2023] Open
Abstract
Pif1 is a prototypical member of the 5′ to 3′ DNA helicase family conserved from bacteria to human. It has a high binding affinity for DNA, but unwinds double-stranded DNA (dsDNA) with a low processivity. Efficient DNA unwinding has been observed only at high protein concentrations that favor dimerization of Pif1. In this research, we used single-molecule fluorescence resonance energy transfer (smFRET) and magnetic tweezers (MT) to study the DNA unwinding activity of Saccharomyces cerevisiae Pif1 (Pif1) under different forces exerted on the tails of a forked dsDNA. We found that Pif1 can unwind the forked DNA repetitively for many unwinding-rezipping cycles at zero force. However, Pif1 was found to have a very limited processivity in each cycle because it loosened its strong association with the tracking strand readily, which explains why Pif1 cannot be observed to unwind DNA efficiently in bulk assays at low protein concentrations. The force enhanced the unwinding rate and the total unwinding length of Pif1 significantly. With a force of 9 pN, the rate and length were enhanced by more than 3- and 20-fold, respectively. Our results imply that the DNA unwinding activity of Pif1 can be regulated by force. The relevance of this characteristic of Pif1 to its cellular functions is discussed.
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Affiliation(s)
- Jing-Hua Li
- 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
| | - Wen-Xia Lin
- 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
| | - Bo Zhang
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Da-Guan Nong
- 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
| | - Hai-Peng Ju
- 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
| | - Jian-Bing Ma
- 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
| | - Chun-Hua Xu
- 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
| | - Fang-Fu Ye
- 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
| | - Xu Guang Xi
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Ming Li
- 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
| | - Ying Lu
- 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
| | - 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
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Fiorini F, Bagchi D, Le Hir H, Croquette V. Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities. Nat Commun 2015; 6:7581. [PMID: 26138914 PMCID: PMC4506499 DOI: 10.1038/ncomms8581] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/21/2015] [Indexed: 12/26/2022] Open
Abstract
RNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery. Upf1 is a multifunctional helicase involved in various DNA- and RNA-related processes, including nonsense-mediated mRNA decay (NMD). Here the authors demonstrate that Upf1 is a highly processive ribonucleoprotein complex remodeler—a capability likely important for Upf1's NMD function.
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Affiliation(s)
- Francesca Fiorini
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France
| | - Debjani Bagchi
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France [3] Laboratoire de Physique Statistique, Ecole Normale Supérieure, Université Pierre et Marie Curie Paris, Université Paris Diderot, CNRS, 24 rue Lhomond, Paris 75005, France
| | - Hervé Le Hir
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France
| | - Vincent Croquette
- 1] Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, Paris 75230, France [2] Institut de Biologie de l'Ecole Normale Supérieure, INSERM U1024, Paris 75230, France [3] Laboratoire de Physique Statistique, Ecole Normale Supérieure, Université Pierre et Marie Curie Paris, Université Paris Diderot, CNRS, 24 rue Lhomond, Paris 75005, France
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37
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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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38
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Beattie TR, Reyes-Lamothe R. A Replisome's journey through the bacterial chromosome. Front Microbiol 2015; 6:562. [PMID: 26097470 PMCID: PMC4456610 DOI: 10.3389/fmicb.2015.00562] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/21/2015] [Indexed: 01/03/2023] Open
Abstract
Genome duplication requires the coordinated activity of a multi-component machine, the replisome. In contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. This immutability underlines the replisome’s efficiency in copying the genome. It also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems during critical stages of DNA synthesis. Here we summarize current understanding of bacterial replisome architecture and highlight the known variations in different bacterial taxa. We then look at the mechanisms in place to ensure that the bacterial replisome is assembled appropriately on DNA, kept together during elongation, and disassembled upon termination. We put forward the idea that the architecture of the replisome may be more flexible that previously thought and speculate on elements of the replisome that maintain its stability to ensure a safe journey from origin to terminus.
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Gollnick B, Carrasco C, Zuttion F, Gilhooly NS, Dillingham MS, Moreno-Herrero F. Probing DNA helicase kinetics with temperature-controlled magnetic tweezers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:1273-84. [PMID: 25400244 PMCID: PMC4473356 DOI: 10.1002/smll.201402686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 05/04/2023]
Abstract
Motor protein functions like adenosine triphosphate (ATP) hydrolysis or translocation along molecular substrates take place at nanometric scales and consequently depend on the amount of available thermal energy. The associated rates can hence be investigated by actively varying the temperature conditions. In this article, a thermally controlled magnetic tweezers (MT) system for single-molecule experiments at up to 40 °C is presented. Its compact thermostat module yields a precision of 0.1 °C and can in principle be tailored to any other surface-coupled microscopy technique, such as tethered particle motion (TPM), nanopore-based sensing of biomolecules, or super-resolution fluorescence imaging. The instrument is used to examine the temperature dependence of translocation along double-stranded (ds)DNA by individual copies of the protein complex AddAB, a helicase-nuclease motor involved in dsDNA break repair. Despite moderately lower mean velocities measured at sub-saturating ATP concentrations, almost identical estimates of the enzymatic reaction barrier (around 21-24 k(B)T) are obtained by comparing results from MT and stopped-flow bulk assays. Single-molecule rates approach ensemble values at optimized chemical energy conditions near the motor, which can withstand opposing loads of up to 14 piconewtons (pN). Having proven its reliability, the temperature-controlled MT described herein will eventually represent a routinely applied method within the toolbox for nano-biotechnology.
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Affiliation(s)
- Benjamin Gollnick
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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40
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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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41
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Georgescu RE, Yao N, Indiani C, Yurieva O, O'Donnell ME. Replisome mechanics: lagging strand events that influence speed and processivity. Nucleic Acids Res 2014; 42:6497-510. [PMID: 24829446 PMCID: PMC4041431 DOI: 10.1093/nar/gku257] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/16/2014] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
The antiparallel structure of DNA requires lagging strand synthesis to proceed in the opposite direction of the replication fork. This imposes unique events that occur only on the lagging strand, such as primase binding to DnaB helicase, RNA synthesis, and SS B antigen (SSB) displacement during Okazaki fragment extension. Single-molecule and ensemble techniques are combined to examine the effect of lagging strand events on the Escherichia coli replisome rate and processivity. We find that primase activity lowers replisome processivity but only when lagging strand extension is inoperative. rNTPs also lower replisome processivity. However, the negative effects of primase and rNTPs on processivity are overcome by the extra grip on DNA provided by the lagging strand polymerases. Visualization of single molecules reveals that SSB accumulates at forks and may wrap extensive amounts of single-strand DNA. Interestingly SSB has an inter-strand positive effect on the rate of the leading strand based in its interaction with the replicase χ-subunit. Further, the lagging strand polymerase is faster than leading strand synthesis, indicating that replisome rate is limited by the helicase. Overall, lagging strand events that impart negative effects on the replisome are counterbalanced by the positive effects of SSB and additional sliding clamps during Okazaki fragment extension.
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Affiliation(s)
- Roxana E Georgescu
- Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, NY 10065, USA
| | - Nina Yao
- Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, NY 10065, USA
| | - Chiara Indiani
- Manhattan College, 4513 Manhattan College Pkwy, Riverdale, NY 10471, USA
| | - Olga Yurieva
- Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, NY 10065, USA
| | - Mike E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, NY 10065, USA
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42
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RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue. Nat Commun 2014; 4:2368. [PMID: 24013402 PMCID: PMC3778716 DOI: 10.1038/ncomms3368] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 07/30/2013] [Indexed: 11/09/2022] Open
Abstract
Helicases that both unwind and rewind DNA have central roles in DNA repair and genetic recombination. In contrast to unwinding, DNA rewinding by helicases has proved difficult to characterize biochemically because of its thermodynamically downhill nature. Here we use single-molecule assays to mechanically destabilize a DNA molecule and follow, in real time, unwinding and rewinding by two DNA repair helicases, bacteriophage T4 UvsW and Escherichia coli RecG. We find that both enzymes are robust rewinding enzymes, which can work against opposing forces as large as 35 pN, revealing their active character. The generation of work during the rewinding reaction allows them to couple rewinding to DNA unwinding and/or protein displacement reactions central to the rescue of stalled DNA replication forks. The overall results support a general mechanism for monomeric rewinding enzymes.
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43
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Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase. Cell Rep 2014; 6:1037-1045. [PMID: 24630993 PMCID: PMC3988844 DOI: 10.1016/j.celrep.2014.02.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/10/2014] [Accepted: 02/16/2014] [Indexed: 11/21/2022] Open
Abstract
Bacteriophage T7 gp4 serves as a model protein for replicative helicases that couples deoxythymidine triphosphate (dTTP) hydrolysis to directional movement and DNA strand separation. We employed single-molecule fluorescence resonance energy transfer methods to resolve steps during DNA unwinding by T7 helicase. We confirm that the unwinding rate of T7 helicase decreases with increasing base pair stability. For duplexes containing >35% guanine-cytosine (GC) base pairs, we observed stochastic pauses every 2–3 bp during unwinding. The dwells on each pause were distributed nonexponentially, consistent with two or three rounds of dTTP hydrolysis before each unwinding step. Moreover, we observed backward movements of the enzyme on GC-rich DNAs at low dTTP concentrations. Our data suggest a coupling ratio of 1:1 between base pairs unwound and dTTP hydrolysis, and they further support the concept that nucleic acid motors can have a hierarchy of different-sized steps or can accumulate elastic energy before transitioning to a subsequent phase. Single DNA unwinding assay recapitulates sequence-dependent unwinding High-resolution data reveal an unwinding step size of 2–3 bp Two or three hidden steps precede the unwinding step, suggesting 1:1 chemical coupling 1:1 coupling is maintained at low dNTP, but helicase often slips backward
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44
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Duderstadt KE, Reyes-Lamothe R, van Oijen AM, Sherratt DJ. Replication-fork dynamics. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a010157. [PMID: 23881939 DOI: 10.1101/cshperspect.a010157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The proliferation of all organisms depends on the coordination of enzymatic events within large multiprotein replisomes that duplicate chromosomes. Whereas the structure and function of many core replisome components have been clarified, the timing and order of molecular events during replication remains obscure. To better understand the replication mechanism, new methods must be developed that allow for the observation and characterization of short-lived states and dynamic events at single replication forks. Over the last decade, great progress has been made toward this goal with the development of novel DNA nanomanipulation and fluorescence imaging techniques allowing for the direct observation of replication-fork dynamics both reconstituted in vitro and in live cells. This article reviews these new single-molecule approaches and the revised understanding of replisome operation that has emerged.
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Affiliation(s)
- Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, Netherlands
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45
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Ribeck N, Saleh OA. DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand. PLoS One 2013; 8:e79237. [PMID: 24250825 PMCID: PMC3826741 DOI: 10.1371/journal.pone.0079237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/20/2013] [Indexed: 01/12/2023] Open
Abstract
The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, ‘occluded’ strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.
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Affiliation(s)
- Noah Ribeck
- Department of Physics, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Omar A. Saleh
- Department of Materials and Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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46
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You Z, De Falco M, Kamada K, Pisani FM, Masai H. The mini-chromosome maintenance (Mcm) complexes interact with DNA polymerase α-primase and stimulate its ability to synthesize RNA primers. PLoS One 2013; 8:e72408. [PMID: 23977294 PMCID: PMC3748026 DOI: 10.1371/journal.pone.0072408] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 07/16/2013] [Indexed: 01/14/2023] Open
Abstract
The Mini-chromosome maintenance (Mcm) proteins are essential as central components for the DNA unwinding machinery during eukaryotic DNA replication. DNA primase activity is required at the DNA replication fork to synthesize short RNA primers for DNA chain elongation on the lagging strand. Although direct physical and functional interactions between helicase and primase have been known in many prokaryotic and viral systems, potential interactions between helicase and primase have not been explored in eukaryotes. Using purified Mcm and DNA primase complexes, a direct physical interaction is detected in pull-down assays between the Mcm2∼7 complex and the hetero-dimeric DNA primase composed of the p48 and p58 subunits. The Mcm4/6/7 complex co-sediments with the primase and the DNA polymerase α-primase complex in glycerol gradient centrifugation and forms a Mcm4/6/7-primase-DNA ternary complex in gel-shift assays. Both the Mcm4/6/7 and Mcm2∼7 complexes stimulate RNA primer synthesis by DNA primase in vitro. However, primase inhibits the Mcm4/6/7 helicase activity and this inhibition is abolished by the addition of competitor DNA. In contrast, the ATP hydrolysis activity of Mcm4/6/7 complex is not affected by primase. Mcm and primase proteins mutually stimulate their DNA-binding activities. Our findings indicate that a direct physical interaction between primase and Mcm proteins may facilitate priming reaction by the former protein, suggesting that efficient DNA synthesis through helicase-primase interactions may be conserved in eukaryotic chromosomes.
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Affiliation(s)
- Zhiying You
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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47
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Zhao Y, Chen D, Yue H, French JB, Rufo J, Benkovic SJ, Huang TJ. Lab-on-a-chip technologies for single-molecule studies. LAB ON A CHIP 2013; 13:2183-98. [PMID: 23670195 PMCID: PMC3955889 DOI: 10.1039/c3lc90042h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices, such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes in the development of lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies.
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Affiliation(s)
- Yanhui Zhao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
| | - Danqi Chen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Hongjun Yue
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Jarrod B. French
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Joey Rufo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 USA
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 USA
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48
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Substrate-selective repair and restart of replication forks by DNA translocases. Cell Rep 2013; 3:1958-69. [PMID: 23746452 DOI: 10.1016/j.celrep.2013.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/15/2013] [Accepted: 05/01/2013] [Indexed: 11/19/2022] Open
Abstract
Stalled replication forks are sources of genetic instability. Multiple fork-remodeling enzymes are recruited to stalled forks, but how they work to promote fork restart is poorly understood. By combining ensemble biochemical assays and single-molecule studies with magnetic tweezers, we show that SMARCAL1 branch migration and DNA-annealing activities are directed by the single-stranded DNA-binding protein RPA to selectively regress stalled replication forks caused by blockage to the leading-strand polymerase and to restore normal replication forks with a lagging-strand gap. We unveil the molecular mechanisms by which RPA enforces SMARCAL1 substrate preference. E. coli RecG acts similarly to SMARCAL1 in the presence of E. coli SSB, whereas the highly related human protein ZRANB3 has different substrate preferences. Our findings identify the important substrates of SMARCAL1 in fork repair, suggest that RecG and SMARCAL1 are functional orthologs, and provide a comprehensive model of fork repair by these DNA translocases.
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49
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Chen D, Yue H, Spiering MM, Benkovic SJ. Insights into Okazaki fragment synthesis by the T4 replisome: the fate of lagging-strand holoenzyme components and their influence on Okazaki fragment size. J Biol Chem 2013; 288:20807-20816. [PMID: 23729670 DOI: 10.1074/jbc.m113.485961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we employed a circular replication substrate with a low priming site frequency (1 site/1.1 kb) to quantitatively examine the size distribution and formation pattern of Okazaki fragments. Replication reactions by the T4 replisome on this substrate yielded a patterned series of Okazaki fragments whose size distribution shifted through collision and signaling mechanisms as the gp44/62 clamp loader levels changed but was insensitive to changes in the gp43 polymerase concentration, as expected for a processive, recycled lagging-strand polymerase. In addition, we showed that only one gp45 clamp is continuously associated with the replisome and that no additional clamps accumulate on the DNA, providing further evidence that the clamp departs, whereas the polymerase is recycled upon completion of an Okazaki fragment synthesis cycle. We found no support for the participation of a third polymerase in Okazaki fragment synthesis.
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Affiliation(s)
- Danqi Chen
- From 414, Wartik Laboratories, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hongjun Yue
- From 414, Wartik Laboratories, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michelle M Spiering
- From 414, Wartik Laboratories, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Stephen J Benkovic
- From 414, Wartik Laboratories, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802.
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50
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Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nat Rev Microbiol 2013; 11:303-15. [DOI: 10.1038/nrmicro2994] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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