1
|
Chang S, Laureti L, Thrall ES, Kay MS, Philippin G, Jergic S, Pagès V, Loparo JJ. A bipartite interaction with the processivity clamp potentiates Pol IV-mediated TLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596738. [PMID: 38853898 PMCID: PMC11160790 DOI: 10.1101/2024.05.30.596738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Processivity clamps mediate polymerase switching for translesion synthesis (TLS). All three E. coli TLS polymerases interact with the β2 processivity clamp through a conserved clamp-binding motif (CBM), which is indispensable for TLS. Notably, Pol IV also makes a unique secondary contact with the clamp through non-CBM residues. However, the role of this "rim contact" in Pol IV-mediated TLS remains poorly understood. Here we show that the rim contact is critical for TLS past strong replication blocks. In in vitro reconstituted Pol IV-mediated TLS, ablating the rim contact compromises TLS past 3-methyl dA, a strong block, while barely affecting TLS past N2-furfuryl dG, a weak block. Similar observations are also made in E. coli cells bearing a single copy of these lesions in the genome. Within lesion-stalled replication forks, the rim interaction and ssDNA binding protein cooperatively poise Pol IV to better compete with Pol III for binding to a cleft through its CBM. We propose that this bipartite clamp interaction enables Pol IV to rapidly resolve lesion-stalled replication through TLS at the fork, which reduces damage induced mutagenesis.
Collapse
Affiliation(s)
- Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Luisa Laureti
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Elizabeth S. Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marguerite S Kay
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gaëlle Philippin
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Slobodan Jergic
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, NSW, Australia
| | - Vincent Pagès
- Cancer Research Center of Marseille: Team DNA Damage and Genome Instability | CNRS, Aix Marseille Univ, Inserm, Institut Paoli-Calmettes, Marseille, France
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Pipalović G, Filić Ž, Ćehić M, Paradžik T, Zahradka K, Crnolatac I, Vujaklija D. Impact of C-terminal domains of paralogous single-stranded DNA binding proteins from Streptomyces coelicolor on their biophysical properties and biological functions. Int J Biol Macromol 2024; 268:131544. [PMID: 38614173 DOI: 10.1016/j.ijbiomac.2024.131544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Single-stranded DNA-binding proteins (SSB) are crucial in DNA metabolism. While Escherichia coli SSB is extensively studied, the significance of its C-terminal domain has only recently emerged. This study explored the significance of C-domains of two paralogous Ssb proteins in S. coelicolor. Mutational analyses of C-domains uncovered a novel role of SsbA during sporulation-specific cell division and demonstrated that the C-tip is non-essential for survival. In vitro methods revealed altered biophysical and biochemical properties of Ssb proteins with modified C-domains. Determined hydrodynamic properties suggested that the C-domains of SsbA and SsbB occupy a globular position proposed to mediate cooperative binding. Only SsbA was found to form biomolecular condensates independent of the C-tip. Interestingly, the truncated C-domain of SsbA increased the molar enthalpy of unfolding. Additionally, calorimetric titrations revealed that C-domain mutations affected ssDNA binding. Moreover, this analysis showed that the SsbA C-tip aids binding most likely by regulating the position of the flexible C-domain. It also highlighted ssDNA-induced conformational mobility restrictions of all Ssb variants. Finally, the gel mobility shift assay confirmed that the intrinsically disordered linker is essential for cooperative binding of SsbA. These findings highlight the important role of the C-domain in the functioning of SsbA and SsbB proteins.
Collapse
Affiliation(s)
- Goran Pipalović
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Želimira Filić
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Mirsada Ćehić
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Tina Paradžik
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Ksenija Zahradka
- Division of Molecular Biology, Institute Ruđer Bošković, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Institute Ruđer Bošković, Zagreb, Croatia.
| | - Dušica Vujaklija
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia.
| |
Collapse
|
3
|
Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
Collapse
Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
4
|
Wilkinson EM, Spenkelink LM, van Oijen AM. Observing protein dynamics during DNA-lesion bypass by the replisome. Front Mol Biosci 2022; 9:968424. [PMID: 36213113 PMCID: PMC9534484 DOI: 10.3389/fmolb.2022.968424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Faithful DNA replication is essential for all life. A multi-protein complex called the replisome contains all the enzymatic activities required to facilitate DNA replication, including unwinding parental DNA and synthesizing two identical daughter molecules. Faithful DNA replication can be challenged by both intrinsic and extrinsic factors, which can result in roadblocks to replication, causing incomplete replication, genomic instability, and an increased mutational load. This increased mutational load can ultimately lead to a number of diseases, a notable example being cancer. A key example of a roadblock to replication is chemical modifications in the DNA caused by exposure to ultraviolet light. Protein dynamics are thought to play a crucial role to the molecular pathways that occur in the presence of such DNA lesions, including potential damage bypass. Therefore, many assays have been developed to study these dynamics. In this review, we discuss three methods that can be used to study protein dynamics during replisome–lesion encounters in replication reactions reconstituted from purified proteins. Specifically, we focus on ensemble biochemical assays, single-molecule fluorescence, and cryo-electron microscopy. We discuss two key model DNA replication systems, derived from Escherichia coli and Saccharomyces cerevisiae. The main methods of choice to study replication over the last decades have involved biochemical assays that rely on ensemble averaging. While these assays do not provide a direct readout of protein dynamics, they can often be inferred. More recently, single-molecule techniques including single-molecule fluorescence microscopy have been used to visualize replisomes encountering lesions in real time. In these experiments, individual proteins can be fluorescently labeled in order to observe the dynamics of specific proteins during DNA replication. Finally, cryo-electron microscopy can provide detailed structures of individual replisome components, which allows functional data to be interpreted in a structural context. While classic cryo-electron microscopy approaches provide static information, recent developments such as time-resolved cryo-electron microscopy help to bridge the gap between static structures and dynamic single-molecule techniques by visualizing sequential steps in biochemical pathways. In combination, these techniques will be capable of visualizing DNA replication and lesion encounter dynamics in real time, whilst observing the structural changes that facilitate these dynamics.
Collapse
Affiliation(s)
- Elise M. Wilkinson
- 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
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
| | - 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
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
| |
Collapse
|
5
|
Kaur G, Spenkelink LM, Lewis JS, Jergic S, Dixon NE, van Oijen AM. Production of long linear DNA substrates with site-specific chemical lesions for single-molecule replisome studies. Methods Enzymol 2022; 672:299-315. [PMID: 35934481 DOI: 10.1016/bs.mie.2022.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Single-molecule imaging studies using long linear DNA substrates have revealed unanticipated insights into the dynamics of multi-protein systems. The use of long DNA substrates allows for the study of protein-DNA interactions with observation of the movement and behavior of proteins over distances accessible by fluorescence microscopy. Generalized methods can be exploited to generate and optimize a variety of linear DNA substrates with plasmid DNA as a simple starting point using standard biochemical techniques. Here, we present protocols to produce high-quality plasmid-based 36-kb linear DNA substrates that support DNA replication by the Escherichia coli replisome and that contain chemical lesions at well-defined positions. These substrates can be used to visualize replisome-lesion encounters at the single-molecule level, providing mechanistic details of replisome stalling and dynamics occurring during replication rescue and restart.
Collapse
Affiliation(s)
- Gurleen Kaur
- 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
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Slobodan Jergic
- 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.
| |
Collapse
|
6
|
Spinks RR, Spenkelink LM, Stratmann SA, Xu ZQ, Stamford NPJ, Brown SE, Dixon NE, Jergic S, van Oijen AM. DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies. Nucleic Acids Res 2021; 49:6804-6816. [PMID: 34139009 PMCID: PMC8266626 DOI: 10.1093/nar/gkab493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 01/09/2023] Open
Abstract
In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.
Collapse
Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Sarah A Stratmann
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - N Patrick J Stamford
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Susan E Brown
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Thangaraj SK, James S, Rouvinen J, Jänis J. Thermokinetic Analysis of Protein Subunit Exchange by Variable-Temperature Native Mass Spectrometry. Biochemistry 2019; 58:5025-5029. [PMID: 31790206 DOI: 10.1021/acs.biochem.9b00911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many protein complexes are assembled from a varying number of subunits, which are continuously exchanging with diverse time scales. This structural dynamics is considered to be important for many regulatory and sensory adaptation processes that occur in vivo. We have developed an accurate method for monitoring protein subunit exchange by using native electrospray ionization mass spectrometry (ESI-MS), exemplified here for an extremely stable Rad50 zinc hook (Hk) dimer assembly, Zn(Hk)2. The method has two steps: appropriate protein/peptide mutation and native ESI-MS analysis using a variable-temperature sample inlet. In this work, two Hk mutants were produced, mixed with wild-type Hk, and measured at three different temperatures. A thermokinetic analysis of heterodimer formation allowed us to determine the enthalpy, entropy, and Gibbs free energy of activation for subunit exchange, showing that the reaction is slow and associated with a high enthalpic barrier, consistent with the exceptionally high stability of the Zn(Hk)2 assembly.
Collapse
Affiliation(s)
- Senthil K Thangaraj
- Department of Chemistry , University of Eastern Finland , P.O. Box 111, FI-801101 Joensuu , Finland
| | - Salman James
- Department of Chemistry , University of Eastern Finland , P.O. Box 111, FI-801101 Joensuu , Finland
| | - Juha Rouvinen
- Department of Chemistry , University of Eastern Finland , P.O. Box 111, FI-801101 Joensuu , Finland
| | - Janne Jänis
- Department of Chemistry , University of Eastern Finland , P.O. Box 111, FI-801101 Joensuu , Finland
| |
Collapse
|
9
|
Spenkelink LM, Lewis JS, Jergic S, Xu ZQ, Robinson A, Dixon NE, van Oijen AM. Recycling of single-stranded DNA-binding protein by the bacterial replisome. Nucleic Acids Res 2019; 47:4111-4123. [PMID: 30767010 PMCID: PMC6486552 DOI: 10.1093/nar/gkz090] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/30/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the replisome that is much more complex in how it retains or recycles protein components. Here, we visualize how an in vitro reconstituted Escherichia coli replisome recruits SSB by relying on two different molecular mechanisms. Not only does it recruit new SSB molecules from solution to coat newly formed single-stranded DNA on the lagging strand, but it also internally recycles SSB from one Okazaki fragment to the next. We show that this internal transfer mechanism is balanced against recruitment from solution in a manner that is concentration dependent. By visualizing SSB dynamics in live cells, we show that both internal transfer and external exchange mechanisms are physiologically relevant.
Collapse
Affiliation(s)
- Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG, the Netherlands
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Andrew Robinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
10
|
Whinn KS, Kaur G, Lewis JS, Schauer GD, Mueller SH, Jergic S, Maynard H, Gan ZY, Naganbabu M, Bruchez MP, O'Donnell ME, Dixon NE, van Oijen AM, Ghodke H. Nuclease dead Cas9 is a programmable roadblock for DNA replication. Sci Rep 2019; 9:13292. [PMID: 31527759 PMCID: PMC6746809 DOI: 10.1038/s41598-019-49837-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/31/2019] [Indexed: 01/19/2023] Open
Abstract
Limited experimental tools are available to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct as a generic, novel, targetable protein-DNA roadblock for studying mechanisms underlying enzymatic activities on DNA substrates in vitro. We illustrate the broad utility of this tool by demonstrating replication fork arrest by the specifically bound dCas9-guideRNA complex to arrest viral, bacterial and eukaryotic replication forks in vitro.
Collapse
Affiliation(s)
- Kelsey S Whinn
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Gurleen Kaur
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Jacob S Lewis
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Grant D Schauer
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Stefan H Mueller
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Slobodan Jergic
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Hamish Maynard
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Zhong Yan Gan
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Matharishwan Naganbabu
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Nicholas E Dixon
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| | - Harshad Ghodke
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| |
Collapse
|
11
|
Lewis JS, Spenkelink LM, Jergic S, Wood EA, Monachino E, Horan NP, Duderstadt KE, Cox MM, Robinson A, Dixon NE, van Oijen AM. Single-molecule visualization of fast polymerase turnover in the bacterial replisome. eLife 2017; 6. [PMID: 28432790 PMCID: PMC5419744 DOI: 10.7554/elife.23932] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli DNA replication machinery has been used as a road map to uncover design rules that enable DNA duplication with high efficiency and fidelity. Although the enzymatic activities of the replicative DNA Pol III are well understood, its dynamics within the replisome are not. Here, we test the accepted view that the Pol III holoenzyme remains stably associated within the replisome. We use in vitro single-molecule assays with fluorescently labeled polymerases to demonstrate that the Pol III* complex (holoenzyme lacking the β2 sliding clamp), is rapidly exchanged during processive DNA replication. Nevertheless, the replisome is highly resistant to dilution in the absence of Pol III* in solution. We further show similar exchange in live cells containing labeled clamp loader and polymerase. These observations suggest a concentration-dependent exchange mechanism providing a balance between stability and plasticity, facilitating replacement of replisomal components dependent on their availability in the environment. DOI:http://dx.doi.org/10.7554/eLife.23932.001
Collapse
Affiliation(s)
- Jacob S Lewis
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Lisanne M Spenkelink
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Enrico Monachino
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Nicholas P Horan
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technishche Universität München, Garching, Germany
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Andrew Robinson
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Antoine M van Oijen
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| |
Collapse
|
12
|
Tan HY, Wilczek LA, Pottinger S, Manosas M, Yu C, Nguyenduc T, Bianco PR. The intrinsically disordered linker of E. coli SSB is critical for the release from single-stranded DNA. Protein Sci 2017; 26:700-717. [PMID: 28078720 DOI: 10.1002/pro.3115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022]
Abstract
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, they have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target. In this study, they examine the role of the linker region in SSB function in a variety of DNA metabolic processes in vitro. Using the same linker mutants, the results show that in addition to association reactions (either DNA or protein), the IDL is critical for the release of SSB from DNA. This release can be under conditions of ssDNA competition or active displacement by a DNA helicase or recombinase. Consistent with their previous work these results indicate that SSB linker mutants are defective for SSB-SSB interactions, and when the IDL is removed a terminal SSB-DNA complex results. Formation of this complex inhibits downstream processing of DNA by helicases such as RecG or PriA as well as recombination, mediated by RecA. A model, based on the evidence herein, is presented to explain how the IDL acts in SSB function.
Collapse
Affiliation(s)
- Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Luke A Wilczek
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Maria Manosas
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028, Barcelona, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Cong Yu
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| |
Collapse
|
13
|
Bianco PR. The tale of SSB. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:111-118. [PMID: 27838363 DOI: 10.1016/j.pbiomolbio.2016.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/04/2016] [Indexed: 01/07/2023]
Abstract
The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions. It does this by binding, via PXXP motifs, to the OB-fold (aka SH3 domain) of a nearby protein. When the nearby protein is another SSB tetramer, this leads to a highly efficient ssDNA binding reaction that rapidly and cooperatively covers and protects the exposed nucleic acid from degradation. Alternatively, when the nearby protein is a member of the SSB interactome, loading of the enzyme onto the DNA takes places.
Collapse
Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA; Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Åberg C, Duderstadt KE, van Oijen AM. Stability versus exchange: a paradox in DNA replication. Nucleic Acids Res 2016; 44:4846-54. [PMID: 27112565 PMCID: PMC4889951 DOI: 10.1093/nar/gkw296] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/11/2016] [Indexed: 11/14/2022] Open
Abstract
Multi-component biological machines, comprising individual proteins with specialized functions, perform a variety of essential processes in cells. Once assembled, most such complexes are considered very stable, retaining individual constituents as long as required. However, rapid and frequent exchange of individual factors in a range of critical cellular assemblies, including DNA replication machineries, DNA transcription regulators and flagellar motors, has recently been observed. The high stability of a multi-protein complex may appear mutually exclusive with rapid subunit exchange. Here, we describe a multisite competitive exchange mechanism, based on simultaneous binding of a protein to multiple low-affinity sites. It explains how a component can be stably integrated into a complex in the absence of competing factors, while able to rapidly exchange in the presence of competing proteins. We provide a mathematical model for the mechanism and give analytical expressions for the stability of a pre-formed complex, in the absence and presence of competitors. Using typical binding kinetic parameters, we show that the mechanism is operational under physically realistic conditions. Thus, high stability and rapid exchange within a complex can be reconciled and this framework can be used to rationalize previous observations, qualitatively as well as quantitatively.
Collapse
Affiliation(s)
- Christoffer Åberg
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands School of Chemistry, University of Wollongong, NSW 2522, Australia
| |
Collapse
|
16
|
Dannatt HRW, Felletti M, Jehle S, Wang Y, Emsley L, Dixon NE, Lesage A, Pintacuda G. Weak and Transient Protein Interactions Determined by Solid‐State NMR. Angew Chem Int Ed Engl 2016; 55:6638-41. [DOI: 10.1002/anie.201511609] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Hugh R. W. Dannatt
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Michele Felletti
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Stefan Jehle
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Yao Wang
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| |
Collapse
|
17
|
Dannatt HRW, Felletti M, Jehle S, Wang Y, Emsley L, Dixon NE, Lesage A, Pintacuda G. Weak and Transient Protein Interactions Determined by Solid‐State NMR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511609] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hugh R. W. Dannatt
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Michele Felletti
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Stefan Jehle
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Yao Wang
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| |
Collapse
|
18
|
Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res 2015; 44:1681-90. [PMID: 26657641 PMCID: PMC4770218 DOI: 10.1093/nar/gkv1375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli has three DNA polymerases implicated in the bypass of DNA damage, a process called translesion synthesis (TLS) that alleviates replication stalling. Although these polymerases are specialized for different DNA lesions, it is unclear if they interact differently with the replication machinery. Of the three, DNA polymerase (Pol) II remains the most enigmatic. Here we report a stable ternary complex of Pol II, the replicative polymerase Pol III core complex and the dimeric processivity clamp, β. Single-molecule experiments reveal that the interactions of Pol II and Pol III with β allow for rapid exchange during DNA synthesis. As with another TLS polymerase, Pol IV, increasing concentrations of Pol II displace the Pol III core during DNA synthesis in a minimal reconstitution of primer extension. However, in contrast to Pol IV, Pol II is inefficient at disrupting rolling-circle synthesis by the fully reconstituted Pol III replisome. Together, these data suggest a β-mediated mechanism of exchange between Pol II and Pol III that occurs outside the replication fork.
Collapse
Affiliation(s)
- James E Kath
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle K Scotland
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Johannes H Wilbertz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Slobodan Jergic
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Mark D Sutton
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Genetics, Genomics and Bioinformatics Program, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
19
|
Deng L, Chen X, Li W, Wang Z, Wong YE, Chan TWD. Sensitivity and Robustness Enhancements by Using a V-Shape Ion Funnel in FTICR-MS. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b01828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liulin Deng
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiangfeng Chen
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
- Shandong Academy of Sciences, Jinan, Shandong, 250014, P. R. China
| | - Wan Li
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| | - Ze Wang
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| | - Yiling Elaine Wong
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| | - T.-W. Dominic Chan
- Department
of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, P. R. China
| |
Collapse
|
20
|
Yin Z, Whittell LR, Wang Y, Jergic S, Ma C, Lewis PJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J Med Chem 2015; 58:4693-702. [PMID: 25970224 DOI: 10.1021/acs.jmedchem.5b00232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.
Collapse
Affiliation(s)
- Zhou Yin
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Louise R Whittell
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Yao Wang
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Cong Ma
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J Lewis
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas E Dixon
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jennifer L Beck
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael J Kelso
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Aaron J Oakley
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
21
|
Yin Z, Wang Y, Whittell L, Jergic S, Liu M, Harry E, Dixon N, Kelso M, Beck J, Oakley A. DNA Replication Is the Target for the Antibacterial Effects of Nonsteroidal Anti-Inflammatory Drugs. ACTA ACUST UNITED AC 2014; 21:481-487. [DOI: 10.1016/j.chembiol.2014.02.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/03/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
|
22
|
Su XC, Wang Y, Yagi H, Shishmarev D, Mason CE, Smith PJ, Vandevenne M, Dixon NE, Otting G. Bound or free: interaction of the C-terminal domain of Escherichia coli single-stranded DNA-binding protein (SSB) with the tetrameric core of SSB. Biochemistry 2014; 53:1925-34. [PMID: 24606314 DOI: 10.1021/bi5001867] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-stranded DNA (ssDNA)-binding protein (SSB) protects ssDNA from degradation and recruits other proteins for DNA replication and repair. Escherichia coli SSB is the prototypical eubacterial SSB in a family of tetrameric SSBs. It consists of a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain). The eight-residue C-terminal segment of SSB (C-peptide) mediates the binding of SSB to many different SSB-binding proteins. Previously published nuclear magnetic resonance (NMR) data of the monomeric state at pH 3.4 showed that the C-peptide binds to the OB-domain at a site that overlaps with the ssDNA binding site, but investigating the protein at neutral pH is difficult because of the high molecular mass and limited solubility of the tetramer. Here we show that the C-domain is highly mobile in the SSB tetramer at neutral pH and that binding of the C-peptide to the OB-domain is so weak that most of the C-peptides are unbound even in the absence of ssDNA. We address the problem of determining intramolecular binding affinities in the situation of fast exchange between two states, one of which cannot be observed by NMR and cannot be fully populated. The results were confirmed by electron paramagnetic resonance spectroscopy and microscale thermophoresis. The C-peptide-OB-domain interaction is shown to be driven primarily by electrostatic interactions, so that binding of 1 equiv of (dT)35 releases practically all C-peptides from the OB-domain tetramer. The interaction is much more sensitive to NaCl than to potassium glutamate, which is the usual osmolyte in E. coli. As the C-peptide is predominantly in the unbound state irrespective of the presence of ssDNA, long-range electrostatic effects from the C-peptide may contribute more to regulating the activity of SSB than any engagement of the C-peptide by the OB-domain.
Collapse
Affiliation(s)
- Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, China
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Yin Z, Whittell LR, Wang Y, Jergic S, Liu M, Harry EJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J Med Chem 2014; 57:2799-806. [PMID: 24592885 DOI: 10.1021/jm500122r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.
Collapse
Affiliation(s)
- Zhou Yin
- School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery. Proc Natl Acad Sci U S A 2014; 111:4073-8. [PMID: 24591606 DOI: 10.1073/pnas.1402010111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replication of DNA plays a central role in transmitting hereditary information from cell to cell. To achieve reliable DNA replication, multiple proteins form a stable complex, known as the replisome, enabling them to act together in a highly coordinated fashion. Over the past decade, the roles of the various proteins within the replisome have been determined. Although many of their interactions have been characterized, it remains poorly understood how replication proteins enter and leave the replisome. In this study, we visualize fluorescently labeled bacteriophage T7 DNA polymerases within the replisome while we simultaneously observe the kinetics of the replication process. This combination of observables allows us to monitor both the activity and dynamics of individual polymerases during coordinated leading- and lagging-strand synthesis. Our data suggest that lagging-strand polymerases are exchanged at a frequency similar to that of Okazaki fragment synthesis and that two or more polymerases are present in the replisome during DNA replication. Our studies imply a highly dynamic picture of the replisome with lagging-strand DNA polymerases residing at the fork for the synthesis of only a few Okazaki fragments. Further, new lagging-strand polymerases are readily recruited from a pool of polymerases that are proximally bound to the replisome and continuously replenished from solution.
Collapse
|
25
|
Shishmarev D, Wang Y, Mason CE, Su XC, Oakley AJ, Graham B, Huber T, Dixon NE, Otting G. Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy. Nucleic Acids Res 2013; 42:2750-7. [PMID: 24288378 PMCID: PMC3936761 DOI: 10.1093/nar/gkt1238] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron density of the C-peptide. Here we show that SSB forms a monomer at pH 3.4, which is suitable for studies by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The OB-domain retains its 3D structure in the monomer, and the C-peptide is shown by nuclear Overhauser effects and lanthanide-induced pseudocontact shifts to bind to the OB-domain at a site that harbors ssDNA in the crystal structure of the SSB–ssDNA complex. 15N relaxation data demonstrate high flexibility of the polypeptide segment linking the C-peptide to the OB-domain and somewhat increased flexibility of the C-peptide compared with the OB-domain, suggesting that the C-peptide either retains high mobility in the bound state or is in a fast equilibrium with an unbound state.
Collapse
Affiliation(s)
- Dmitry Shishmarev
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia, Centre for Medical and Molecular Bioscience and School of Chemistry, University of Wollongong, New South Wales 2522, Australia and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville Victoria 3052, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein. J Mol Biol 2013; 425:4790-801. [PMID: 23583780 DOI: 10.1016/j.jmb.2013.04.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/14/2013] [Accepted: 04/03/2013] [Indexed: 01/26/2023]
Abstract
DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit clamp loader complex, is responsible for loading the sliding clamp (β2) onto DNA. Here, we use structural information derived from ion mobility mass spectrometry (IM-MS) to build three-dimensional models of one form of the full clamp loader complex, γ3δδ'ψχ (254 kDa). By probing the interaction between the clamp loader and a single-stranded DNA (ssDNA) binding protein (SSB4) and by identifying two distinct conformational states, with and without ssDNA, we assemble models of ψχ-SSB4 (108 kDa) and the clamp loader-SSB4 (340 kDa) consistent with IM data. A significant increase in measured collision cross-section (~10%) of the clamp loader-SSB4 complex upon DNA binding suggests large conformational rearrangements. This DNA bound conformation represents the active state and, along with the presence of ψχ, stabilises the clamp loader-SSB4 complex. Overall, this study of a large heteromeric complex analysed by IM-MS, coupled with integrative modelling, highlights the potential of such an approach to reveal structural features of previously unknown complexes of high biological importance.
Collapse
|
27
|
Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JMH, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM, Dixon NE. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode. EMBO J 2013; 32:1322-33. [PMID: 23435564 DOI: 10.1038/emboj.2012.347] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/07/2012] [Indexed: 02/08/2023] Open
Abstract
Processive DNA synthesis by the αεθ core of the Escherichia coli Pol III replicase requires it to be bound to the β2 clamp via a site in the α polymerase subunit. How the ε proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of ε. Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in ε that, in conjunction with the site in α, maintains a closed state of the αεθ-β2 replicase in the polymerization mode of DNA synthesis. The ε-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states.
Collapse
Affiliation(s)
- Slobodan Jergic
- School of Chemistry, University of Wollongong, Wollongong, New South Wales, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|