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      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

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          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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          Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.

          Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic stem (ES) cell-specific gene regulation. Here, we combine in vivo and in vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping to determine how TFs dynamically search for and assemble on their cognate DNA target sites. We find that enhanceosome assembly is hierarchically ordered with kinetically favored Sox2 engaging the target DNA first, followed by assisted binding of Oct4. Sox2/Oct4 follow a trial-and-error sampling mechanism involving 84-97 events of 3D diffusion (3.3-3.7 s) interspersed with brief nonspecific collisions (0.75-0.9 s) before acquiring and dwelling at specific target DNA (12.0-14.6 s). Sox2 employs a 3D diffusion-dominated search mode facilitated by 1D sliding along open DNA to efficiently locate targets. Our findings also reveal fundamental aspects of gene and developmental regulation by fine-tuning TF dynamics and influence of the epigenome on target search parameters. Copyright © 2014 Elsevier Inc. All rights reserved.
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            How do site-specific DNA-binding proteins find their targets?

            Essentially all the biological functions of DNA depend on site-specific DNA-binding proteins finding their targets, and therefore 'searching' through megabases of non-target DNA. In this article, we review current understanding of how this sequence searching is done. We review how simple diffusion through solution may be unable to account for the rapid rates of association observed in experiments on some model systems, primarily the Lac repressor. We then present a simplified version of the 'facilitated diffusion' model of Berg, Winter and von Hippel, showing how non-specific DNA-protein interactions may account for accelerated targeting, by permitting the protein to sample many binding sites per DNA encounter. We discuss the 1-dimensional 'sliding' motion of protein along non-specific DNA, often proposed to be the mechanism of this multiple site sampling, and we discuss the role of short-range diffusive 'hopping' motions. We then derive the optimal range of sliding for a few physical situations, including simple models of chromosomes in vivo, showing that a sliding range of approximately 100 bp before dissociation optimizes targeting in vivo. Going beyond first-order binding kinetics, we discuss how processivity, the interaction of a protein with two or more targets on the same DNA, can reveal the extent of sliding and we review recent experiments studying processivity using the restriction enzyme EcoRV. Finally, we discuss how single molecule techniques might be used to study the dynamics of DNA site-specific targeting of proteins.
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              Stoichiometry and turnover in single, functioning membrane protein complexes.

              Many essential cellular processes are carried out by complex biological machines located in the cell membrane. The bacterial flagellar motor is a large membrane-spanning protein complex that functions as an ion-driven rotary motor to propel cells through liquid media. Within the motor, MotB is a component of the stator that couples ion flow to torque generation and anchors the stator to the cell wall. Here we have investigated the protein stoichiometry, dynamics and turnover of MotB with single-molecule precision in functioning bacterial flagellar motors in Escherichia coli. We monitored motor function by rotation of a tethered cell body, and simultaneously measured the number and dynamics of MotB molecules labelled with green fluorescent protein (GFP-MotB) in the motor by total internal reflection fluorescence microscopy. Counting fluorophores by the stepwise photobleaching of single GFP molecules showed that each motor contains approximately 22 copies of GFP-MotB, consistent with approximately 11 stators each containing two MotB molecules. We also observed a membrane pool of approximately 200 GFP-MotB molecules diffusing at approximately 0.008 microm2 s(-1). Fluorescence recovery after photobleaching and fluorescence loss in photobleaching showed turnover of GFP-MotB between the membrane pool and motor with a rate constant of the order of 0.04 s(-1): the dwell time of a given stator in the motor is only approximately 0.5 min. This is the first direct measurement of the number and rapid turnover of protein subunits within a functioning molecular machine.
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                Author and article information

                Journal
                Transcription
                Transcription
                KTRN
                ktrn20
                Transcription
                Taylor & Francis
                2154-1264
                2154-1272
                2018
                9 August 2018
                9 August 2018
                : 9
                : 5
                : 298-306
                Affiliations
                Departments of Physics and Biology, Biological Physical Sciences Institute, University of York , York, UK
                Author notes
                CONTACT Mark C. Leake mark.leake@ 123456york.ac.uk
                Author information
                http://orcid.org/0000-0002-1715-1249
                Article
                1475806
                10.1080/21541264.2018.1475806
                6150617
                29895219
                6c8ebf4b-7a59-4849-bd4b-f0febdfe1f69
                © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 1 March 2018
                : 3 May 2018
                Page count
                Figures: 1, References: 80, Pages: 9
                Funding
                Funded by: Biological Physical Sciences Institute, Royal Society, MRC
                Award ID: MR/K01580X/1
                Funded by: Swedish Research Council and European Commission via Marie Curie-Network for Initial training ISOLATE
                Award ID: 289995
                Funded by: BBSRC 10.13039/501100000268
                Award ID: BB/N006453/1
                Supported by the Biological Physical Sciences Institute, Royal Society, MRC (grant MR/K01580X/1), BBSRC (grant BB/N006453/1), Swedish Research Council and European Commission via Marie Curie-Network for Initial training ISOLATE (Grant agreement nr: 289995) and the Marie Curie Alumni Association.
                Categories
                Point-of-View

                Molecular biology
                gene expression,transcription factors,single-molecule,super-resolution,cell signaling,intrinsically disordered protein,phase transition,molecular crowding,fluorescent protein

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