1
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Andrews SS, Wiley HS, Sauro HM. Design patterns of biological cells. Bioessays 2024; 46:e2300188. [PMID: 38247191 PMCID: PMC10922931 DOI: 10.1002/bies.202300188] [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: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
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Affiliation(s)
- Steven S. Andrews
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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2
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Zeitler L, Denby Wilkes C, Goldar A, Soutourina J. A quantitative modelling approach for DNA repair on a population scale. PLoS Comput Biol 2022; 18:e1010488. [PMID: 36094963 PMCID: PMC9499311 DOI: 10.1371/journal.pcbi.1010488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/22/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The great advances of sequencing technologies allow the in vivo measurement of nuclear processes-such as DNA repair after UV exposure-over entire cell populations. However, data sets usually contain only a few samples over several hours, missing possibly important information in between time points. We developed a data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we understand them as the superposition of signals from independent cells. By motivating repair as a stochastic process, we derive a minimal model for which the parameters can be conveniently estimated. We correlate repair parameters to a variety of genomic features that are assumed to influence repair, including transcription rate and nucleosome density. The clearest link was found for the transcription unit length, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.
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Affiliation(s)
- Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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3
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Modulating binding affinity, specificity and configurations by multivalent interactions. Biophys J 2022; 121:1868-1880. [PMID: 35450827 DOI: 10.1016/j.bpj.2022.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/20/2021] [Accepted: 04/14/2022] [Indexed: 11/22/2022] Open
Abstract
Biological functions of proteins rely on their specific interactions with binding partners. Many proteins contain multiple domains, which can bind to their targets that often have more than one binding site, resulting in multivalent interactions. While it has been shown that multivalent interactions play an crucial role in modulating binding affinity and specificity, other potential effects of multivalent interactions are less explored. Here, we developed a broadly applicable transfer matrix formalism and used it to investigate the binding of two-domain ligands to targets with multiple binding sites. We show that 1) ligands with two specific binding domains can drastically boost both the binding affinity and specificity and down-shift the working concentration range, compared to single-domain ligands, 2) the presence of a positive domain-domain cooperativity or containing a non-specific binding domain can down-shift the working concentration range of ligands by increasing the binding affinity without compromising the binding specificity, 3) the configuration of the bound ligands has a strong concentration dependence, providing important insights into the physical origin of phase-separation processes taking place in living cells. In line with previous studies, our results suggest that multivalent interactions are utilized by cells for highly efficient regulation of target binding involved in a diverse range of cellular processes such as signal transduction, gene transcription, antibody-antigen recognition.
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4
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Chakraborty P, Ghosh S. Emergent correlations in gene expression dynamics as footprints of resource competition. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:131. [PMID: 34694511 DOI: 10.1140/epje/s10189-021-00122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions, all gene circuits draw resources in the form of RNA polymerases, ribosomes, and tRNAs. Recent experiments pointed out that the role of resource competition on synthetic circuit outputs could be immense. However, the effect of complexity of the circuit architecture on resource sharing dynamics is yet unexplored. In this paper, we employ mathematical modelling and in-silico experiments to identify the sources of resource trade-off and to quantify its impact on the function of a genetic circuit, keeping our focus on regulation of immediate downstream proteins, which are often used as protein read-outs. We show that estimating gene expression dynamics from readings of downstream protein data might be unreliable when the resource is limited and ribosome affinities are asymmetric. We focus on the impact of mRNA copy number and ribosome binding site (RBS) strength on the nonlinear isocline that emerges with two regimes, prominently separated by a tipping point, and study how correlation and competition dominate each other depending on various circuit parameters. Focusing further on genetic toggle circuit, we have identified major effects of resource competition in this model motif and quantified the observations. The observations are testable in wet-lab experiments, as all the parameters chosen are experimentally relevant.
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Affiliation(s)
- Priya Chakraborty
- Department of Physics, National Institute of Technology, Durgapur, 713209, India
| | - Sayantari Ghosh
- Department of Physics, National Institute of Technology, Durgapur, 713209, India.
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5
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Kim J, Ahn D, Park CJ. FOXO4 Transactivation Domain Interaction with Forkhead DNA Binding Domain and Effect on Selective DNA Recognition for Transcription Initiation. J Mol Biol 2021; 433:166808. [PMID: 33450250 DOI: 10.1016/j.jmb.2021.166808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 11/25/2022]
Abstract
Forkhead box O4 (FOXO4) is a human transcription factor (TF) that participates in cell homeostasis. While the structure and DNA binding properties of the conserved forkhead domain (FHD) have been thoroughly investigated, how the transactivation domain (TAD) regulates the DNA binding properties of the protein remains elusive. Here, we investigated the role of TAD in modulating the DNA binding properties of FOXO4 using solution NMR. We found that TAD and FHD form an intramolecular complex mainly governed by hydrophobic interaction. Remarkably, TAD and DNA share the same surface of FHD for binding. While FHD did not differentiate binding to target and non-target DNA, the FHD-TAD complex showed different behaviors depending on the DNA sequence. In the presence of TAD, free and DNA-bound FHD exhibited a slow exchange with target DNA and a fast exchange with non-target DNA. The interaction of the two domains affected the kinetic function of FHD depending on the type of DNA. Based on these findings, we suggest a transcription initiation model by which TAD modulates FOXO4 recognition of its target promoter DNA sequences. This study describes the function of TAD in FOXO4 and provides a new kinetic perspective on target sequence selection by TFs.
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Affiliation(s)
- Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Dabin Ahn
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea.
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6
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Iwahara J, Kolomeisky AB. Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications. Biophys Chem 2020; 269:106521. [PMID: 33338872 PMCID: PMC7855466 DOI: 10.1016/j.bpc.2020.106521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022]
Abstract
To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other factors such as molecular crowding. These theoretical models not only offer explanations on the relation of microscopic processes to macroscopic behavior of proteins, but also facilitate the analysis and interpretation of experimental data. In this review article, we provide an overview on discrete-state stochastic kinetic models and explain how these models can be applied to experimental investigations using stopped-flow, single-molecule, nuclear magnetic resonance (NMR), and other biophysical and biochemical methods.
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Affiliation(s)
- Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Anatoly B Kolomeisky
- Department of Chemistry, Department of Chemical and Biomolecular Engineering, Department of Physics and Astronomy and Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
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7
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Transient binding and jumping dynamics of p53 along DNA revealed by sub-millisecond resolved single-molecule fluorescence tracking. Sci Rep 2020; 10:13697. [PMID: 32792545 PMCID: PMC7426816 DOI: 10.1038/s41598-020-70763-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022] Open
Abstract
Characterization of the target search dynamics of DNA-binding proteins along DNA has been hampered by the time resolution of a standard single-molecule fluorescence microscopy. Here, we achieved the time resolution of 0.5 ms in the fluorescence microscopy measurements by optimizing the fluorescence excitation based on critical angle illumination and by utilizing the time delay integration mode of the electron-multiplying charge coupled device. We characterized the target search dynamics of the tumor suppressor p53 along nonspecific DNA at physiological salt concentrations. We identified a short-lived encounter intermediate before the formation of the long-lived p53–DNA complex. Both the jumps and the one-dimensional diffusion of p53 along DNA were accelerated at higher salt concentrations, suggesting the rotation-uncoupled movement of p53 along DNA grooves and conformational changes in the p53/DNA complex. This method can be used to clarify the unresolved dynamics of DNA-binding proteins previously hidden by time averaging.
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8
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Sabi R, Tuller T. Modelling and measuring intracellular competition for finite resources during gene expression. J R Soc Interface 2020; 16:20180887. [PMID: 31113334 DOI: 10.1098/rsif.2018.0887] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dissecting the competition between genes for shared expressional resources is of fundamental importance for understanding the interplay between cellular components. Owing to the relationship between gene expression and cellular fitness, genomes are shaped by evolution to improve resource allocation. Whereas experimental approaches to investigate intracellular competition require technical resources and human expertise, computational models and in silico simulations allow vast numbers of experiments to be carried out and controlled easily, and with significantly reduced costs. Thus, modelling competition has a pivotal role in understanding the effects of competition on the biophysics of the cell. In this article, we review various computational models proposed to describe the different types of competition during gene expression. We also present relevant synthetic biology experiments and their biotechnological implications, and discuss the open questions in the field.
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Affiliation(s)
- Renana Sabi
- 1 Department of Biomedical Engineering, Tel Aviv University , Israel
| | - Tamir Tuller
- 1 Department of Biomedical Engineering, Tel Aviv University , Israel.,2 The Sagol School of Neuroscience, Tel Aviv University , Israel
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9
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Andrews SS. Effects of surfaces and macromolecular crowding on bimolecular reaction rates. Phys Biol 2020; 17:045001. [DOI: 10.1088/1478-3975/ab7f51] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Kamagata K, Itoh Y, Subekti DRG. How p53 Molecules Solve the Target DNA Search Problem: A Review. Int J Mol Sci 2020; 21:E1031. [PMID: 32033163 PMCID: PMC7037437 DOI: 10.3390/ijms21031031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/11/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
Interactions between DNA and DNA-binding proteins play an important role in many essential cellular processes. A key function of the DNA-binding protein p53 is to search for and bind to target sites incorporated in genomic DNA, which triggers transcriptional regulation. How do p53 molecules achieve "rapid" and "accurate" target search in living cells? The search dynamics of p53 were expected to include 3D diffusion in solution, 1D diffusion along DNA, and intersegmental transfer between two different DNA strands. Single-molecule fluorescence microscopy enabled the tracking of p53 molecules on DNA and the characterization of these dynamics quantitatively. Recent intensive single-molecule studies of p53 succeeded in revealing each of these search dynamics. Here, we review these studies and discuss the target search mechanisms of p53.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Dwiky Rendra Graha Subekti
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; (Y.I.); (D.R.G.S.)
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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11
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Stoof R, Wood A, Goñi-Moreno Á. A Model for the Spatiotemporal Design of Gene Regulatory Circuits †. ACS Synth Biol 2019; 8:2007-2016. [PMID: 31429541 DOI: 10.1021/acssynbio.9b00022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mathematical modeling assists the design of synthetic regulatory networks by providing a detailed mechanistic understanding of biological systems. Models that can predict the performance of a design are fundamental for synthetic biology since they minimize iterations along the design-build-test lifecycle. Such predictability depends crucially on what assumptions (i.e., biological simplifications) the model considers. Here, we challenge a common assumption when it comes to the modeling of bacterial-based gene regulation: considering negligible the effects of intracellular physical space. It is commonly assumed that molecules, such as transcription factors (TF), are homogeneously distributed inside a cell, so there is no need to model their diffusion. We describe a mathematical model that accounts for molecular diffusion and show how simulations of network performance are decisively affected by the distance between its components. Specifically, the model focuses on the search by a TF for its target promoter. The combination of local searches, via one-dimensional sliding along the chromosome, and global searches, via three-dimensional diffusion through the cytoplasm, determine TF-promoter interplay. Previous experimental results with engineered bacteria in which the distance between TF source and target was minimized or enlarged were successfully reproduced by the spatially resolved model we introduce here. This suggests that the spatial specification of the circuit alone can be exploited as a design parameter in synthetic biology to select programmable output levels.
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Affiliation(s)
- Ruud Stoof
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Alexander Wood
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, U.K
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12
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Itoh Y, Murata A, Takahashi S, Kamagata K. Intrinsically disordered domain of tumor suppressor p53 facilitates target search by ultrafast transfer between different DNA strands. Nucleic Acids Res 2019; 46:7261-7269. [PMID: 29986056 PMCID: PMC6101536 DOI: 10.1093/nar/gky586] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/19/2018] [Indexed: 01/23/2023] Open
Abstract
Intersegmental transfer (IST) is an important strategy in the target search used by sequence-specific DNA-binding proteins (DBPs), enabling DBPs to search for targets between multiple DNA strands without dissociation. We examined the IST of the tumor suppressor p53 using ensemble stopped-flow and single-molecule fluorescence measurements. The ensemble measurements demonstrated that p53 exhibits very fast IST, whose rate constant was ∼108 M-1 s-1. To determine the domains of p53 responsible for IST, two mutants with deletions of one of its two DNA binding domains were generated. The mutant lacking the disordered C-terminal (CT) domain (the CoreTet mutant) abolished IST, whereas the mutant lacking the structured core domain (the TetCT mutant) maintained IST, clearly demonstrating the importance of the CT domain. Single-molecule fluorescence measurements further demonstrated the transfer of p53 between two tethered DNA strands. The pseudo-wild-type p53 and the TetCT mutant showed significant transfer efficiencies, whereas the transfer efficiency for the CoreTet mutant was zero. These results suggest that ultrafast IST might be promoted by four copies of the CT domain, by binding to two DNA strands simultaneously. Such ultrafast IST might be important to avoid nearby-bound DBPs during the target search process of p53 in nucleus.
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Affiliation(s)
- Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Agato Murata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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13
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Wollman AJM, Hedlund EG, Shashkova S, Leake MC. Towards mapping the 3D genome through high speed single-molecule tracking of functional transcription factors in single living cells. Methods 2019; 170:82-89. [PMID: 31252059 PMCID: PMC6971689 DOI: 10.1016/j.ymeth.2019.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022] Open
Abstract
How genomic DNA is organized in the nucleus is a long-standing question. We describe a single-molecule bioimaging method utilizing super-localization precision coupled to fully quantitative image analysis tools, towards determining snapshots of parts of the 3D genome architecture of model eukaryote budding yeast Saccharomyces cerevisiae with exceptional millisecond time resolution. We employ astigmatism imaging to enable robust extraction of 3D position data on genomically encoded fluorescent protein reporters that bind to DNA. Our relatively straightforward method enables snippets of 3D architectures of likely single genome conformations to be resolved captured via DNA-sequence specific binding proteins in single functional living cells.
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Affiliation(s)
- Adam J M Wollman
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Erik G Hedlund
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Sviatlana Shashkova
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Mark C Leake
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
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14
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Leake MC. Transcription factors in eukaryotic cells can functionally regulate gene expression by acting in oligomeric assemblies formed from an intrinsically disordered protein phase transition enabled by molecular crowding. Transcription 2018; 9:298-306. [PMID: 29895219 PMCID: PMC6150617 DOI: 10.1080/21541264.2018.1475806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
High-speed single-molecule fluorescence microscopy in vivo shows that transcription factors in eukaryotes can act in oligomeric clusters mediated by molecular crowding and intrinsically disordered protein. This finding impacts on the longstanding puzzle of how transcription factors find their gene targets so efficiently in the complex, heterogeneous environment of the cell. Abbreviations CDF - cumulative distribution function; FRAP - fluorescence recovery after photobleaching; GFP - Green fluorescent protein; STORM - stochastic optical reconstruction microscopy; TF - Transcription factor; YFP - Yellow fluorescent protein
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Affiliation(s)
- Mark C Leake
- a Departments of Physics and Biology , Biological Physical Sciences Institute, University of York , York , UK
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15
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Andrews SS. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 2017; 33:710-717. [PMID: 28365760 DOI: 10.1093/bioinformatics/btw700] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022] Open
Abstract
Motivation Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Results Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface. Availability and Implementation Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org . Contact steven.s.andrews@gmail.com.
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Affiliation(s)
- Steven S Andrews
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Isaac Newton Institute for Mathematical Sciences, Cambridge CB3 0EH, UK
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16
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Howard MJ, Wilson SH. Processive searching ability varies among members of the gap-filling DNA polymerase X family. J Biol Chem 2017; 292:17473-17481. [PMID: 28893909 DOI: 10.1074/jbc.m117.801860] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA repair proteins must locate rare damaged sites within the genome. DNA polymerase β (Pol β), a member of the DNA polymerase X family that is involved in base excision repair, uses a processive hopping search mechanism to locate substrates. This effectively enhances its search footprint on DNA, increasing the probability of locating damaged sites. Processive searching has been reported or proposed for many DNA-binding proteins, raising the question of how widespread or specific to certain enzymes the ability to perform this function is. To provide insight into this question, we compared the ability of three homologous DNA Pol X family members to perform a processive search for 1-nucleotide gaps in DNA using a previously developed biochemical assay. We found that at near-predicted physiological ionic strengths, the intramolecular searching ability of Pol β is at least 4-fold higher than that of Pol μ and ∼2-fold higher than that of Pol λ. Pol β also was able to perform intersegmental transfer with the intersegmental searching ability of Pol β being at least 6- and ∼2-fold higher than that of Pols μ and λ, respectively. Mutational analysis suggested that differences in the N-terminal domains of these polymerases are responsible for the varying degrees of searching competence. Of note, the differences in processive searching ability observed among the DNA Pol X family members correlated with their proposed biological functions in base excision repair and nonhomologous end joining.
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Affiliation(s)
- Michael J Howard
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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17
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Wollman AJ, Shashkova S, Hedlund EG, Friemann R, Hohmann S, Leake MC. Transcription factor clusters regulate genes in eukaryotic cells. eLife 2017; 6:27451. [PMID: 28841133 PMCID: PMC5602325 DOI: 10.7554/elife.27451] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/24/2017] [Indexed: 01/07/2023] Open
Abstract
Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway, supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression.
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Affiliation(s)
- Adam Jm Wollman
- Biological Physical Sciences Institute, University of York, York, United Kingdom
| | - Sviatlana Shashkova
- Biological Physical Sciences Institute, University of York, York, United Kingdom.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Erik G Hedlund
- Biological Physical Sciences Institute, University of York, York, United Kingdom
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Mark C Leake
- Biological Physical Sciences Institute, University of York, York, United Kingdom
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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Sewitz SA, Fahmi Z, Lipkow K. Higher order assembly: folding the chromosome. Curr Opin Struct Biol 2017; 42:162-168. [DOI: 10.1016/j.sbi.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/13/2017] [Indexed: 11/28/2022]
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Igarashi C, Murata A, Itoh Y, Subekti DRG, Takahashi S, Kamagata K. DNA Garden: A Simple Method for Producing Arrays of Stretchable DNA for Single-Molecule Fluorescence Imaging of DNA-Binding Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160298] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chihiro Igarashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Agato Murata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Yuji Itoh
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Dwiky Rendra Graha Subekti
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Satoshi Takahashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Kiyoto Kamagata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
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Wang D, Miyazono KI, Tanokura M. Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA. Sci Rep 2016; 6:35197. [PMID: 27731370 PMCID: PMC5059719 DOI: 10.1038/srep35197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023] Open
Abstract
R.PabI is a type II restriction enzyme that recognizes the 5′-GTAC-3′ sequence and belongs to the HALFPIPE superfamily. Although most restriction enzymes cleave phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes the N-glycosidic bond of the flipped adenine in a similar manner to DNA glycosylases. In this study, we determined the structure of R.PabI in complex with double-stranded DNA without the R.PabI recognition sequence by X-ray crystallography. The 1.9 Å resolution structure of the complex showed that R.PabI forms a tetrameric structure to sandwich the double-stranded DNA and the tetrameric structure is stabilized by four salt bridges. DNA binding and DNA glycosylase assays of the R.PabI mutants showed that the residues that form the salt bridges (R70 and D71) are essential for R.PabI to find the recognition sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide along it to find the recognition sequence.
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Affiliation(s)
- Delong Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Itoh Y, Murata A, Sakamoto S, Nanatani K, Wada T, Takahashi S, Kamagata K. Activation of p53 Facilitates the Target Search in DNA by Enhancing the Target Recognition Probability. J Mol Biol 2016; 428:2916-30. [DOI: 10.1016/j.jmb.2016.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/23/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
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