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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, 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
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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2
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Xu L, Halma MTJ, Wuite GJL. Mapping fast DNA polymerase exchange during replication. Nat Commun 2024; 15:5328. [PMID: 38909023 PMCID: PMC11193749 DOI: 10.1038/s41467-024-49612-3] [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: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Despite extensive studies on DNA replication, the exchange mechanisms of DNA polymerase during replication remain unclear. Existing models propose that this exchange is facilitated by protein partners like helicase. Here we present data, employing a combination of mechanical DNA manipulation and single fluorescent protein observation, that reveal DNA polymerase undergoing rapid and autonomous exchange during replication not coordinated by other proteins. The DNA polymerase shows fast unbinding and rebinding dynamics, displaying a preference for either exonuclease or polymerase activity, or pausing events, during each brief binding event. We also observed a 'memory effect' in DNA polymerase rebinding, i.e., the enzyme tends to preserve its prior activity upon reassociation. This effect, potentially linked to the ssDNA/dsDNA junction's conformation, might play a role in regulating binding preference enabling high processivity amidst rapid protein exchange. Taken together, our findings support an autonomous replication model that includes rapid protein exchange, burst of activity, and a 'memory effect' while moving processively forward.
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Affiliation(s)
- Longfu Xu
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Matthew T J Halma
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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3
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Schiopu I, Dragomir I, Asandei A. Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability. RSC Adv 2024; 14:5449-5460. [PMID: 38352678 PMCID: PMC10862658 DOI: 10.1039/d3ra07746b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.
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Affiliation(s)
- Irina Schiopu
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Isabela Dragomir
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Alina Asandei
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
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4
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Bonde NJ, Kozlov AG, Cox MM, Lohman TM, Keck JL. Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. Crit Rev Biochem Mol Biol 2024; 59:99-127. [PMID: 38770626 PMCID: PMC11209772 DOI: 10.1080/10409238.2024.2330372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 05/22/2024]
Abstract
The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ssDNA and transfers rapidly between different segments of ssDNA. SSB interacts with many other proteins involved in DNA metabolism, with 22 such SSB-interacting proteins, or SIPs, defined to date. These interactions chiefly involve the disordered and conserved C-terminal residues of SSB. When not bound to ssDNA, SSB can aggregate to form a phase-separated biomolecular condensate. Current understanding of the properties of SSB and the functional significance of its many intermolecular interactions are summarized in this review.
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Affiliation(s)
- Nina J. Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander G. Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Whinn KS, Sharma N, van Oijen AM, Ghodke H. Single-Molecule Fluorescence Imaging of DNA Replication Stalling at Sites of Nucleoprotein Complexes. Methods Mol Biol 2024; 2694:215-234. [PMID: 37824007 DOI: 10.1007/978-1-0716-3377-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
DNA replication in cells occurs on crowded and often damaged template DNA, forming potentially deleterious roadblocks to the progressing replication fork. Numerous tools have been developed to investigate the mechanisms of DNA replication and the fate of stalled replication forks. Here, we describe single-molecule fluorescence imaging methods to visualize processive DNA replication and replication fork stalling at site-specific nucleoprotein complexes. Using dCas9 as a protein barrier and rolling-circle DNA templates, we visualize effective, stable, and site-specific blocking of the Escherichia coli replisome. Additionally, we present a protocol to produce an 18-kb rolling-circle DNA template that provides increased spatial resolution in imaging the interplay between replisomes and roadblocks. These methods can be used to investigate encounters of the replisome with nucleoprotein complexes at the single-molecule level, providing important mechanistic details of replisome stalling and downstream rescue or restart pathways.
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Affiliation(s)
- Kelsey S Whinn
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Nischal Sharma
- 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.
| | - Harshad Ghodke
- 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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6
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Xiao Y, Jiang Z, Zhang M, Zhang X, Gan Q, Yang Y, Wu P, Feng X, Ni J, Dong X, She Q, Huang Q, Shen Y. The canonical single-stranded DNA-binding protein is not an essential replication factor but an RNA chaperon in Saccharolobus islandicus. iScience 2023; 26:108389. [PMID: 38034349 PMCID: PMC10684826 DOI: 10.1016/j.isci.2023.108389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/28/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) have been regarded as indispensable replication factors. Herein, we report that the genes encoding the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in Saccharolobus islandicus REY15A are not essential for cell viability. Interestingly, at a lower temperature (55°C), the protein level of SisSSB increases and the growth of ΔSisssb and ΔSisssbΔSisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and is able to melt RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of cold-shock proteins in E. coli. Importantly, these activities are conserved in the canonical SSBs from Crenarchaeota species that lack bacterial Csp homologs. Overall, our study has clarified the function of the archaeal canonical SSBs which do not function as a DNA-processing factor, but play a role in the processes requiring melting of dsRNA or DNA/RNA hybrid.
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Affiliation(s)
- Yuanxi Xiao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Zhichao Jiang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Mengqi Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xuemei Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qi Gan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yunfeng Yang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
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7
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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.
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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
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8
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [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: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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9
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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10
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Chung ES, Kar P, Kamkaew M, Amir A, Aldridge BB. Mycobacterium tuberculosis grows linearly at the single-cell level with larger variability than model organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541183. [PMID: 37292927 PMCID: PMC10245742 DOI: 10.1101/2023.05.17.541183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability of bacterial pathogens to regulate growth is crucial to control homeostasis, virulence, and drug response. Yet, we do not understand the growth and cell cycle behaviors of Mycobacterium tuberculosis (Mtb), a slow-growing pathogen, at the single-cell level. Here, we use time-lapse imaging and mathematical modeling to characterize these fundamental properties of Mtb. Whereas most organisms grow exponentially at the single-cell level, we find that Mtb exhibits a unique linear growth mode. Mtb growth characteristics are highly variable from cell-to-cell, notably in their growth speeds, cell cycle timing, and cell sizes. Together, our study demonstrates that growth behavior of Mtb diverges from what we have learned from model bacteria. Instead, Mtb generates a heterogeneous population while growing slowly and linearly. Our study provides a new level of detail into how Mtb grows and creates heterogeneity, and motivates more studies of growth behaviors in bacterial pathogens.
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11
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Radford HM, Toft CJ, Sorenson AE, Schaeffer PM. Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins. Int J Mol Sci 2023; 24:ijms24108802. [PMID: 37240152 DOI: 10.3390/ijms24108802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Over 1.2 million deaths are attributed to multi-drug-resistant (MDR) bacteria each year. Persistence of MDR bacteria is primarily due to the molecular mechanisms that permit fast replication and rapid evolution. As many pathogens continue to build resistance genes, current antibiotic treatments are being rendered useless and the pool of reliable treatments for many MDR-associated diseases is thus shrinking at an alarming rate. In the development of novel antibiotics, DNA replication is still a largely underexplored target. This review summarises critical literature and synthesises our current understanding of DNA replication initiation in bacteria with a particular focus on the utility and applicability of essential initiation proteins as emerging drug targets. A critical evaluation of the specific methods available to examine and screen the most promising replication initiation proteins is provided.
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Affiliation(s)
- Holly M Radford
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Casey J Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Alanna E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Patrick M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
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12
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Bonde NJ, Henry C, Wood EA, Cox MM, Keck J. Interaction with the carboxy-terminal tip of SSB is critical for RecG function in E. coli. Nucleic Acids Res 2023; 51:3735-3753. [PMID: 36912097 PMCID: PMC10164576 DOI: 10.1093/nar/gkad162] [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: 12/21/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
In Escherichia coli, the single-stranded DNA-binding protein (SSB) acts as a genome maintenance organizational hub by interacting with multiple DNA metabolism proteins. Many SSB-interacting proteins (SIPs) form complexes with SSB by docking onto its carboxy-terminal tip (SSB-Ct). An alternative interaction mode in which SIPs bind to PxxP motifs within an intrinsically-disordered linker (IDL) in SSB has been proposed for the RecG DNA helicase and other SIPs. Here, RecG binding to SSB and SSB peptides was measured in vitro and the RecG/SSB interface was identified. The results show that RecG binds directly and specifically to the SSB-Ct, and not the IDL, through an evolutionarily conserved binding site in the RecG helicase domain. Mutations that block RecG binding to SSB sensitize E. coli to DNA damaging agents and induce the SOS DNA-damage response, indicating formation of the RecG/SSB complex is important in vivo. The broader role of the SSB IDL is also investigated. E. coli ssb mutant strains encoding SSB IDL deletion variants lacking all PxxP motifs retain wildtype growth and DNA repair properties, demonstrating that the SSB PxxP motifs are not major contributors to SSB cellular functions.
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Affiliation(s)
- Nina J Bonde
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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13
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Mueller SH, Fitschen LJ, Shirbini A, Hamdan SM, Spenkelink L, van Oijen A. Rapid single-molecule characterisation of enzymes involved in nucleic-acid metabolism. Nucleic Acids Res 2022; 51:e5. [PMID: 36321650 PMCID: PMC9841422 DOI: 10.1093/nar/gkac949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/12/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
The activity of enzymes is traditionally characterised through bulk-phase biochemical methods that only report on population averages. Single-molecule methods are advantageous in elucidating kinetic and population heterogeneity but are often complicated, time consuming, and lack statistical power. We present a highly-generalisable and high-throughput single-molecule assay to rapidly characterise proteins involved in DNA metabolism. The assay exclusively relies on changes in total fluorescence intensity of surface-immobilised DNA templates as a result of DNA synthesis, unwinding or digestion. Combined with an automated data-analysis pipeline, our method provides enzymatic activity data of thousands of molecules in less than an hour. We demonstrate our method by characterising three fundamentally different enzyme activities: digestion by the phage λ exonuclease, synthesis by the phage Phi29 polymerase, and unwinding by the E. coli UvrD helicase. We observe the previously unknown activity of the UvrD helicase to remove neutravidin bound to 5'-, but not 3'-ends of biotinylated DNA.
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Affiliation(s)
- Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lucy J Fitschen
- 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
| | - Afnan Shirbini
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Samir M Hamdan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lisanne M Spenkelink
- Correspondence may also be addressed to Lisanne M. Spenkelink. Tel: +61 2 4239 2371;
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14
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Replication stalling activates SSB for recruitment of DNA damage tolerance factors. Proc Natl Acad Sci U S A 2022; 119:e2208875119. [PMID: 36191223 PMCID: PMC9565051 DOI: 10.1073/pnas.2208875119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translesion synthesis (TLS) polymerases bypass DNA lesions that block replicative polymerases, allowing cells to tolerate DNA damage encountered during replication. It is well known that most bacterial TLS polymerases must interact with the sliding-clamp processivity factor to carry out TLS, but recent work in Escherichia coli has revealed that single-stranded DNA-binding protein (SSB) plays a key role in enriching the TLS polymerase Pol IV at stalled replication forks in the presence of DNA damage. It remains unclear how this interaction with SSB enriches Pol IV in a stalling-dependent manner given that SSB is always present at the replication fork. In this study, we use single-molecule imaging in live E. coli cells to investigate this SSB-dependent enrichment of Pol IV. We find that Pol IV is enriched through its interaction with SSB in response to a range of different replication stresses and that changes in SSB dynamics at stalled forks may explain this conditional Pol IV enrichment. Finally, we show that other SSB-interacting proteins are likewise selectively enriched in response to replication perturbations, suggesting that this mechanism is likely a general one for enrichment of repair factors near stalled replication forks.
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15
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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.
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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,
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16
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Sale JE. Focus and persistence: how Pol IV unblocks stalled DNA synthesis. Nat Struct Mol Biol 2022; 29:846-847. [PMID: 36127467 DOI: 10.1038/s41594-022-00825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK.
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17
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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.
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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.
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18
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Brown JWP, Alford RG, Walsh JC, Spinney RE, Xu SY, Hertel S, Berengut JF, Spenkelink LM, van Oijen AM, Böcking T, Morris RG, Lee LK. Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor. ACS NANO 2022; 16:6455-6467. [PMID: 35316035 DOI: 10.1021/acsnano.2c00699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
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Affiliation(s)
- James W P Brown
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rokiah G Alford
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - James C Walsh
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Chemistry, University of Sydney, Sydney 2006, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, 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
| | - Till Böcking
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney 2052, Australia
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19
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How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein. J Mol Biol 2022; 434:167562. [PMID: 35351518 PMCID: PMC9400470 DOI: 10.1016/j.jmb.2022.167562] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 01/01/2023]
Abstract
E. coli single-stranded-DNA binding protein (EcSSB) displays nearest-neighbor (NN) and non-nearest-neighbor (NNN)) cooperativity in binding ssDNA during genome maintenance. NNN cooperativity requires the intrinsically-disordered linkers (IDL) of the C-terminal tails. Potassium glutamate (KGlu), the primary E. coli salt, promotes NNN-cooperativity, while KCl inhibits it. We find that KGlu promotes compaction of a single polymeric SSB-coated ssDNA beyond what occurs in KCl, indicating a link of compaction to NNN-cooperativity. EcSSB also undergoes liquid-liquid phase separation (LLPS), inhibited by ssDNA binding. We find that LLPS, like NNN-cooperativity, is promoted by increasing [KGlu] in the physiological range, while increasing [KCl] and/or deletion of the IDL eliminate LLPS, indicating similar interactions in both processes. From quantitative determinations of interactions of KGlu and KCl with protein model compounds, we deduce that the opposing effects of KGlu and KCl on SSB LLPS and cooperativity arise from their opposite interactions with amide groups. KGlu interacts unfavorably with the backbone (especially Gly) and side chain amide groups of the IDL, promoting amide-amide interactions in LLPS and NNN-cooperativity. By contrast, KCl interacts favorably with these amide groups and therefore inhibits LLPS and NNN-cooperativity. These results highlight the importance of salt interactions in regulating the propensity of proteins to undergo LLPS.
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20
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Maritan M, Autin L, Karr J, Covert MW, Olson AJ, Goodsell DS. Building Structural Models of a Whole Mycoplasma Cell. J Mol Biol 2022; 434:167351. [PMID: 34774566 PMCID: PMC8752489 DOI: 10.1016/j.jmb.2021.167351] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023]
Abstract
Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.
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Affiliation(s)
- Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA. https://twitter.com/MartinaMaritan
| | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA. https://twitter.com/grinche
| | - Jonathan Karr
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
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21
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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22
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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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23
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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.
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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
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24
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Single-Molecule Fluorescence Methods to Study Protein Exchange Kinetics in Supramolecular Complexes. Methods Mol Biol 2021; 2281:49-65. [PMID: 33847951 DOI: 10.1007/978-1-0716-1290-3_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Recent single-molecule studies have demonstrated that the composition of multi-protein complexes can strike a balance between stability and dynamics. Proteins can dynamically exchange in and out of the complex depending on their concentration in solution. These exchange dynamics are a key determinant of the molecular pathways available to multi-protein complexes. It is therefore important that we develop robust and reproducible assays to study protein exchange. Using DNA replication as an example, we describe three single-molecule fluorescence assays used to study protein exchange dynamics. In the chase exchange assay, fluorescently labeled proteins are challenged by unlabeled proteins, where exchange results in the disappearance of the fluorescence signal. In the FRAP exchange assay, fluorescently labeled proteins are photobleached before exchange is measured by an increase in fluorescence as non-bleached proteins exchange into the complex. Finally, in the two-color exchange assay, proteins are labeled with two different fluorophores and exchange is visualized by detecting changes in color. All three assays compliment in their ability to elucidate the dynamic behavior of proteins in large biological systems.
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25
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Silvestre I, Nunes A, Borges V, Isidro J, Silva C, Vieira L, Gomes JP, Borrego MJ. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. INFECTION GENETICS AND EVOLUTION 2021; 93:104969. [PMID: 34147652 DOI: 10.1016/j.meegid.2021.104969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.
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Affiliation(s)
- Inês Silvestre
- Department of Life Sciences, UCIBIO, Nova School of Science and Technology, 2829-516 Caparica, Portugal; National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; CBIOS - Research Center for Biosciences & Health Technologies, Lusófona University of Humanities and Technologies, Campo Grande 376, 1749-024 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Catarina Silva
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Nova Medical School
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Nova Medical School
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 1169-056 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal.
| | - Maria José Borrego
- National Reference Laboratory for Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal.
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26
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Bianco PR, Lu Y. Single-molecule insight into stalled replication fork rescue in Escherichia coli. Nucleic Acids Res 2021; 49:4220-4238. [PMID: 33744948 PMCID: PMC8096234 DOI: 10.1093/nar/gkab142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 01/05/2023] Open
Abstract
DNA replication forks stall at least once per cell cycle in Escherichia coli. DNA replication must be restarted if the cell is to survive. Restart is a multi-step process requiring the sequential action of several proteins whose actions are dictated by the nature of the impediment to fork progression. When fork progress is impeded, the sequential actions of SSB, RecG and the RuvABC complex are required for rescue. In contrast, when a template discontinuity results in the forked DNA breaking apart, the actions of the RecBCD pathway enzymes are required to resurrect the fork so that replication can resume. In this review, we focus primarily on the significant insight gained from single-molecule studies of individual proteins, protein complexes, and also, partially reconstituted regression and RecBCD pathways. This insight is related to the bulk-phase biochemical data to provide a comprehensive review of each protein or protein complex as it relates to stalled DNA replication fork rescue.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yue Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
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27
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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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28
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Kozlov AG, Lohman TM. Probing E. coli SSB protein-DNA topology by reversing DNA backbone polarity. Biophys J 2021; 120:1522-1533. [PMID: 33636169 PMCID: PMC8105733 DOI: 10.1016/j.bpj.2021.02.025] [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: 12/07/2020] [Revised: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli single-strand (ss) DNA binding protein (SSB) is an essential protein that binds ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in two major modes, differing in occluded site size and cooperativity. The (SSB)35 mode in which ssDNA wraps, on average, around two subunits is favored at low [NaCl] and high SSB/DNA ratios and displays high unlimited, nearest-neighbor cooperativity forming long protein clusters. The (SSB)65 mode, in which ssDNA wraps completely around four subunits of the tetramer, is favored at higher [NaCl] (>200 mM) and displays limited low cooperativity. Crystal structures of E. coli SSB and Plasmodium falciparum SSB show ssDNA bound to the SSB subunits (OB folds) with opposite polarities of the sugar phosphate backbones. To investigate whether SSB subunits show a polarity preference for binding ssDNA, we examined EcSSB and PfSSB binding to a series of (dT)70 constructs in which the backbone polarity was switched in the middle of the DNA by incorporating a reverse-polarity (RP) phosphodiester linkage, either 3'-3' or 5'-5'. We find only minor effects on the DNA binding properties for these RP constructs, although (dT)70 with a 3'-3' polarity switch shows decreased affinity for EcSSB in the (SSB)65 mode and lower cooperativity in the (SSB)35 mode. However, (dT)70 in which every phosphodiester linkage is reversed does not form a completely wrapped (SSB)65 mode but, rather, binds EcSSB in the (SSB)35 mode with little cooperativity. In contrast, PfSSB, which binds ssDNA only in an (SSB)65 mode and with opposite backbone polarity and different topology, shows little effect of backbone polarity on its DNA binding properties. We present structural models suggesting that strict backbone polarity can be maintained for ssDNA binding to the individual OB folds if there is a change in ssDNA wrapping topology of the RP ssDNA.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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29
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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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30
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Naufer MN, Morse M, Möller GB, McIsaac J, Rouzina I, Beuning PJ, Williams MC. Multiprotein E. coli SSB-ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions. Nucleic Acids Res 2021; 49:1532-1549. [PMID: 33434279 PMCID: PMC7897507 DOI: 10.1093/nar/gkaa1267] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli SSB (EcSSB) is a model single-stranded DNA (ssDNA) binding protein critical in genome maintenance. EcSSB forms homotetramers that wrap ssDNA in multiple conformations to facilitate DNA replication and repair. Here we measure the binding and wrapping of many EcSSB proteins to a single long ssDNA substrate held at fixed tensions. We show EcSSB binds in a biphasic manner, where initial wrapping events are followed by unwrapping events as ssDNA-bound protein density passes critical saturation and high free protein concentration increases the fraction of EcSSBs in less-wrapped conformations. By destabilizing EcSSB wrapping through increased substrate tension, decreased substrate length, and protein mutation, we also directly observe an unstable bound but unwrapped state in which ∼8 nucleotides of ssDNA are bound by a single domain, which could act as a transition state through which rapid reorganization of the EcSSB-ssDNA complex occurs. When ssDNA is over-saturated, stimulated dissociation rapidly removes excess EcSSB, leaving an array of stably-wrapped complexes. These results provide a mechanism through which otherwise stably bound and wrapped EcSSB tetramers are rapidly removed from ssDNA to allow for DNA maintenance and replication functions, while still fully protecting ssDNA over a wide range of protein concentrations.
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Affiliation(s)
- M Nabuan Naufer
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - James McIsaac
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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31
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Lin M, Malik FK, Guo JT. A comparative study of protein-ssDNA interactions. NAR Genom Bioinform 2021; 3:lqab006. [PMID: 33655206 PMCID: PMC7902235 DOI: 10.1093/nargab/lqab006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fareeha K Malik
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Research Center of Modeling and Simulation, National University of Science and Technology, Islamabad, 44000, Pakistan
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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32
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Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions. Proc Natl Acad Sci U S A 2020; 117:26206-26217. [PMID: 33020264 PMCID: PMC7584906 DOI: 10.1073/pnas.2000761117] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells must rapidly and efficiently react to DNA damage to avoid its harmful consequences. Here we report a molecular mechanism that gives rise to a model of how bacterial cells mobilize DNA repair proteins for timely response to genomic stress and initiation of DNA repair upon exposure of single-stranded DNA. We found that bacterial single-stranded DNA binding protein (SSB), a central player in genome metabolism, can undergo dynamic phase separation under physiological conditions. SSB condensates can store a wide array of DNA repair proteins that specifically interact with SSB. However, elevated levels of single-stranded DNA during genomic stress can dissolve SSB condensates, enabling rapid mobilization of SSB and SSB-interacting proteins to sites of DNA damage. Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that the Escherichia coli SSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
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33
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Myka KK, Marians KJ. Two components of DNA replication-dependent LexA cleavage. J Biol Chem 2020; 295:10368-10379. [PMID: 32513870 PMCID: PMC7383369 DOI: 10.1074/jbc.ra120.014224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA-RecA filament supported LexA cleavage. Surprisingly, replication of an undamaged template supported levels of LexA cleavage like that induced by a template carrying two site-specific cyclobutane pyrimidine dimers. We found that two processes generate ssDNA that could support LexA cleavage. 1) During unperturbed replication, single-stranded regions formed because of stochastic uncoupling of the leading-strand DNA polymerase from the replication fork DNA helicase, and 2) on the damaged template, nascent leading-strand gaps were generated by replisome lesion skipping. The two pathways differed in that RecF stimulated LexA cleavage during replication of the damaged template, but not normal replication. RecF appears to facilitate RecA filament formation on the leading-strand ssDNA gaps generated by replisome lesion skipping.
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Affiliation(s)
- Kamila K Myka
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
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34
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Dubiel K, Henry C, Spenkelink LM, Kozlov AG, Wood EA, Jergic S, Dixon NE, van Oijen AM, Cox MM, Lohman TM, Sandler SJ, Keck JL. Development of a single-stranded DNA-binding protein fluorescent fusion toolbox. Nucleic Acids Res 2020; 48:6053-6067. [PMID: 32374866 PMCID: PMC7293020 DOI: 10.1093/nar/gkaa320] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/15/2020] [Accepted: 05/04/2020] [Indexed: 01/13/2023] Open
Abstract
Bacterial single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA and help to recruit heterologous proteins to their sites of action. SSBs perform these essential functions through a modular structural architecture: the N-terminal domain comprises a DNA binding/tetramerization element whereas the C-terminus forms an intrinsically disordered linker (IDL) capped by a protein-interacting SSB-Ct motif. Here we examine the activities of SSB-IDL fusion proteins in which fluorescent domains are inserted within the IDL of Escherichia coli SSB. The SSB-IDL fusions maintain DNA and protein binding activities in vitro, although cooperative DNA binding is impaired. In contrast, an SSB variant with a fluorescent protein attached directly to the C-terminus that is similar to fusions used in previous studies displayed dysfunctional protein interaction activity. The SSB-IDL fusions are readily visualized in single-molecule DNA replication reactions. Escherichia coli strains in which wildtype SSB is replaced by SSB-IDL fusions are viable and display normal growth rates and fitness. The SSB-IDL fusions form detectible SSB foci in cells with frequencies mirroring previously examined fluorescent DNA replication fusion proteins. Cells expressing SSB-IDL fusions are sensitized to some DNA damaging agents. The results highlight the utility of SSB-IDL fusions for biochemical and cellular studies of genome maintenance reactions.
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Affiliation(s)
- Katarzyna Dubiel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - 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
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - 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
| | - 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
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Sandler
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, MA 01003, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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35
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Hwang J, Kim JY, Kim C, Park S, Joo S, Kim SK, Lee NK. Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans. eLife 2020; 9:50945. [PMID: 32297860 PMCID: PMC7200156 DOI: 10.7554/elife.50945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, a protein that is essential for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA-binding protein (drSSB) for binding to the freely exposed ssDNA, and efficiently displaces drSSB from ssDNA without consuming ATP. drRecO replaces drSSB and dissociates it completely from ssDNA even though drSSB binds to ssDNA approximately 300 times more strongly than drRecO does. We suggest that drRecO facilitates the loading of RecA onto drSSB-coated ssDNA by utilizing a small drSSB-free space on ssDNA that is generated by the fast diffusion of drSSB on ssDNA.
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Affiliation(s)
- Jihee Hwang
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, United States
| | - Cheolhee Kim
- Daegu National Science Museum, Daegu, Republic of Korea
| | - Soojin Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
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36
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Mishra G, Bigman LS, Levy Y. ssDNA diffuses along replication protein A via a reptation mechanism. Nucleic Acids Res 2020; 48:1701-1714. [PMID: 31919510 PMCID: PMC7038930 DOI: 10.1093/nar/gkz1202] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/23/2019] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Affiliation(s)
- Garima Mishra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Lavi S Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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37
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Design of customizable long linear DNA substrates with controlled end modifications for single-molecule studies. Anal Biochem 2020; 592:113541. [DOI: 10.1016/j.ab.2019.113541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 01/15/2023]
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38
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Lewis JS, Spenkelink LM, Schauer GD, Yurieva O, Mueller SH, Natarajan V, Kaur G, Maher C, Kay C, O'Donnell ME, van Oijen AM. Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication. Mol Cell 2019; 77:17-25.e5. [PMID: 31704183 DOI: 10.1016/j.molcel.2019.10.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/25/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022]
Abstract
Structural and biochemical studies have revealed the basic principles of how the replisome duplicates genomic DNA, but little is known about its dynamics during DNA replication. We reconstitute the 34 proteins needed to form the S. cerevisiae replisome and show how changing local concentrations of the key DNA polymerases tunes the ability of the complex to efficiently recycle these proteins or to dynamically exchange them. Particularly, we demonstrate redundancy of the Pol α-primase DNA polymerase activity in replication and show that Pol α-primase and the lagging-strand Pol δ can be re-used within the replisome to support the synthesis of large numbers of Okazaki fragments. This unexpected malleability of the replisome might allow it to deal with barriers and resource challenges during replication of large genomes.
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Affiliation(s)
- Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olga Yurieva
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Varsha Natarajan
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Gurleen Kaur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Claire Maher
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Callum Kay
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Michael E O'Donnell
- Laboratory of DNA Replication, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Cambridge, MA 02138, USA.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia.
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39
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Regulation of Nearest-Neighbor Cooperative Binding of E. coli SSB Protein to DNA. Biophys J 2019; 117:2120-2140. [PMID: 31708161 DOI: 10.1016/j.bpj.2019.09.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022] Open
Abstract
Escherichia coli single-strand (ss) DNA-binding protein (SSB) is an essential protein that binds ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in several modes differing in occluded site size and cooperativity. The 35-site-size ((SSB)35) mode favored at low [NaCl] and high SSB/DNA ratios displays high "unlimited" nearest-neighbor cooperativity (ω35), forming long protein clusters, whereas the 65-site-size ((SSB)65) mode in which ssDNA wraps completely around the tetramer is favored at higher [NaCl] (>200 mM) and displays "limited" cooperativity (ω65), forming only dimers of tetramers. In addition, a non-nearest-neighbor high cooperativity can also occur in the (SSB)65 mode on long ssDNA even at physiological salt concentrations in the presence of glutamate and requires its intrinsically disordered C-terminal linker (IDL) region. However, whether cooperativity exists between the different modes and the role of the IDL in nearest-neighbor cooperativity has not been probed. Here, we combine sedimentation velocity and fluorescence titration studies to examine nearest-neighbor cooperativity in each binding mode and between binding modes using (dT)70 and (dT)140. We find that the (SSB)35 mode always shows extremely high "unlimited" cooperativity that requires the IDL. At high salt, wild-type SSB and a variant without the IDL, SSB-ΔL, bind in the (SSB)65 mode but show little cooperativity, although cooperativity increases at lower [NaCl] for wild-type SSB. We also find significant intermode nearest-neighbor cooperativity (ω65/35), with ω65 ≪ ω65/35 <ω35. The intrinsically disordered region of SSB is required for all cooperative interactions; however, in contrast to the non-nearest-neighbor cooperativity observed on longer ssDNA, glutamate does not enhance these nearest-neighbor cooperativities. Therefore, we show that SSB possesses four types of cooperative interactions, with clear differences in the forces stabilizing nearest-neighbor versus non-nearest-neighbor cooperativity.
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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Mueller SH, Spenkelink LM, van Oijen AM. When proteins play tag: the dynamic nature of the replisome. Biophys Rev 2019; 11:641-651. [PMID: 31273608 PMCID: PMC6682189 DOI: 10.1007/s12551-019-00569-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication, or the copying of DNA, is a fundamental process to all life. The system of proteins that carries out replication, the replisome, encounters many roadblocks on its way. An inability of the replisome to properly overcome these roadblocks will negatively affect genomic integrity which in turn can lead to disease. Over the past decades, efforts by many researchers using a broad array of approaches have revealed roles for many different proteins during the initial response of the replisome upon encountering roadblocks. Here, we revisit what is known about DNA replication and the effect of roadblocks during DNA replication across different organisms. We also address how advances in single-molecule techniques have changed our view of the replisome from a highly stable machine with behavior dictated by deterministic principles to a dynamic system that is controlled by stochastic processes. We propose that these dynamics will play crucial roles in roadblock bypass. Further single-molecule studies of this bypass will, therefore, be essential to facilitate the in-depth investigation of multi-protein complexes that is necessary to understand complicated collisions on the DNA.
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Affiliation(s)
- Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
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