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Efremov AK, Qu Y, Maruyama H, Lim CJ, Takeyasu K, Yan J. Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner. J Biol Chem 2015; 290:15770-15784. [PMID: 25931116 DOI: 10.1074/jbc.m114.626705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 11/06/2022] Open
Abstract
Architectural DNA proteins play important roles in the chromosomal DNA organization and global gene regulation in living cells. However, physiological functions of some DNA-binding proteins from archaea remain unclear. Recently, several abundant DNA-architectural proteins including histones, Alba, and TrmBL2 have been identified in model euryarchaeon Thermococcus kodakarensis. Although histones and Alba proteins have been previously characterized, the DNA binding properties of TrmBL2 and its interplay with the other major architectural proteins in the chromosomal DNA organization and gene transcription regulation remain largely unexplored. Here, we report single-DNA studies showing that at low ionic strength (<300 mM KCl), TrmBL2 binds to DNA largely in non-sequence-specific manner with positive cooperativity, resulting in formation of stiff nucleoprotein filamentous patches, whereas at high ionic strength (>300 mM KCl) TrmBL2 switches to more sequence-specific interaction, suggesting the presence of high affinity TrmBL2-filament nucleation sites. Furthermore, in vitro assays indicate the existence of DNA binding competition between TrmBL2 and archaeal histones B from T. kodakarensis, which can be strongly modulated by DNA supercoiling and ionic strength of surrounding solution. Overall, these results advance our understanding of TrmBL2 DNA binding properties and provide important insights into potential functions of architectural proteins in nucleoid organization and gene regulation in T. kodakarensis.
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Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore
| | - Yuanyuan Qu
- Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; School of Physics, Shandong University, Jinan 250100, China
| | - Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan
| | - Ci J Lim
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077.
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Piili J, Marenduzzo D, Kaski K, Linna RP. Sedimentation of knotted polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012728. [PMID: 23410380 DOI: 10.1103/physreve.87.012728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/20/2012] [Indexed: 06/01/2023]
Abstract
We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R(g)(-1), more specifically with the inverse of the R(g) component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R(g)(-1) remains to a good precision linearly dependent on n(c). Therefore, R(g)(-1) is a good measure of a knot's complexity.
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Affiliation(s)
- J Piili
- Department of Biomedical Engineering and Computational Science, Aalto University, P.O. Box 12200, FI-00076 Aalto, Finland
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Wegner AS, Alexeeva S, Odijk T, Woldringh CL. Characterization of Escherichia coli nucleoids released by osmotic shock. J Struct Biol 2012; 178:260-9. [DOI: 10.1016/j.jsb.2012.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/02/2012] [Accepted: 03/03/2012] [Indexed: 10/28/2022]
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The effective hydrodynamic radius of single DNA-grafted colloids as measured by fast Brownian motion analysis. POLYMER 2011. [DOI: 10.1016/j.polymer.2011.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 2009; 43:393-418. [PMID: 19037758 DOI: 10.1080/10409230802528488] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.
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Affiliation(s)
- Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan, Amsterdam, The Netherlands
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Schlagberger X, Netz RR. Anomalous Sedimentation of Self-Avoiding Flexible Polymers. Macromolecules 2008. [DOI: 10.1021/ma070947m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xaver Schlagberger
- Physics Department, Technical University Munich, 85748 Garching, Germany
| | - Roland R. Netz
- Physics Department, Technical University Munich, 85748 Garching, Germany
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Schlagberger X, Netz RR. Anomalous polymer sedimentation far from equilibrium. PHYSICAL REVIEW LETTERS 2007; 98:128301. [PMID: 17501163 DOI: 10.1103/physrevlett.98.128301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Indexed: 05/15/2023]
Abstract
A single flexible polymer in strong sedimentation fields is investigated using hydrodynamic simulations and scaling arguments. For short chains and small fields compaction is observed. For elevated fields or long chains the chain stretches and the sedimentation coefficient decreases, in agreement with ultracentrifuge experiments on linear as well as circular DNA. For very large fields a tadpole forms consisting of a compact leading head and a trailing stretched tail.
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Affiliation(s)
- Xaver Schlagberger
- Physics Department, Technical University Munich, 85748 Garching, Germany
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Bakewell D, Morgan H. Dielectrophoresis of DNA: Time- and Frequency-Dependent Collections on Microelectrodes $^dagger$. IEEE Trans Nanobioscience 2006. [DOI: 10.1109/tnb.2005.864012] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Elmore S, Müller M, Vischer N, Odijk T, Woldringh CL. Single-particle tracking of oriC-GFP fluorescent spots during chromosome segregation in Escherichia coli. J Struct Biol 2005; 151:275-87. [PMID: 16084110 DOI: 10.1016/j.jsb.2005.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 05/19/2005] [Accepted: 06/01/2005] [Indexed: 11/19/2022]
Abstract
DNA regions close to the origin of replication were visualized by the green fluorescent protein (GFP)-Lac repressor/lac operator system. The number of oriC-GFP fluorescent spots per cell and per nucleoid in batch-cultured cells corresponded to the theoretical DNA replication pattern. A similar pattern was observed in cells growing on microscope slides used for time-lapse experiments. The trajectories of 124 oriC-GFP spots were monitored by time-lapse microscopy of 31 cells at time intervals of 1, 2, and 3 min. Spot positions were determined along the short and long axis of cells. The lengthwise movement of spots was corrected for cell elongation. The step sizes of the spots showed a Gaussian distribution with a standard deviation of approximately 110 nm. Plots of the mean square displacement versus time indicated a free diffusion regime for spot movement along the long axis of the cell, with a diffusion coefficient of 4.3+/-2.6x10(-5) microm2/s. Spot movement along the short axis showed confinement in a region of the diameter of the nucleoid ( approximately 800 nm) with an effective diffusion coefficient of 2.9+/-1.7x10(-5) microm2/s. Confidence levels for the mean square displacement analysis were obtained from numerical simulations. We conclude from the analysis that within the experimental accuracy--the limits of which are indicated and discussed--there is no evidence that spot segregation requires any other mechanism than that of cell (length) growth.
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Affiliation(s)
- Steven Elmore
- Section Molecular Cytology, Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands
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