1
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Becker NA, Peters JP, James Maher L. High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria. Methods Mol Biol 2024; 2819:103-123. [PMID: 39028504 DOI: 10.1007/978-1-0716-3930-6_6] [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: 07/20/2024]
Abstract
The occurrence of DNA looping is ubiquitous. This process plays a well-documented role in the regulation of prokaryotic gene expression, such as in regulation of the Escherichia coli lactose (lac) operon. Here we present two complementary methods for high-resolution in vivo detection of DNA/protein binding within the bacterial nucleoid by using either chromatin immunoprecipitation combined with phage λ exonuclease digestion (ChIP-exo) or chromatin endogenous cleavage (ChEC), coupled with ligation-mediated polymerase chain reaction (LM-PCR) and Southern blot analysis. As an example, we apply these in vivo protein-mapping methods to E. coli to show direct binding of architectural proteins in the Lac repressor-mediated DNA repression loop.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, IA, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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2
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Starr CH, Bryant Z, Spakowitz AJ. Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics. Biophys J 2022; 121:1949-1962. [PMID: 35421389 PMCID: PMC9199097 DOI: 10.1016/j.bpj.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/19/2021] [Accepted: 04/06/2022] [Indexed: 11/02/2022] Open
Abstract
Measurements of protein-mediated DNA looping reveal that in vivo conditions favor the formation of loops shorter than those that occur in vitro, yet the precise physical mechanisms underlying this shift remain unclear. To understand the extent to which in vivo supercoiling may explain these shifts, we develop a theoretical model based on coarse-grained molecular simulation and analytical transition state theory, enabling us to map out looping energetics and kinetics as a function of two key biophysical parameters: superhelical density and loop length. We show that loops on the scale of a persistence length respond to supercoiling over a much wider range of superhelical densities and to a larger extent than longer loops. This effect arises from a tendency for loops to be centered on the plectonemic end region, which bends progressively more tightly with superhelical density. This trend reveals a mechanism by which supercoiling favors shorter loop lengths. In addition, our model predicts a complex kinetic response to supercoiling for a given loop length, governed by a competition between an enhanced rate of looping due to torsional buckling and a reduction in looping rate due to chain straightening as the plectoneme tightens at higher superhelical densities. Together, these effects lead to a flattening of the kinetic response to supercoiling within the physiological range for all but the shortest loops. Using experimental estimates for in vivo superhelical densities, we discuss our model's ability to explain available looping data, highlighting both the importance of supercoiling as a regulatory force in genetics and the additional complexities of looping phenomena in vivo.
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Affiliation(s)
- Charles H Starr
- Biophysics Program, Stanford University, Stanford, California
| | - Zev Bryant
- Biophysics Program, Stanford University, Stanford, California; Department of Bioengineering, Stanford University, Stanford, California
| | - Andrew J Spakowitz
- Biophysics Program, Stanford University, Stanford, California; Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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3
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Tse DH, Becker NA, Young RT, Olson WK, Peters JP, Schwab TL, Clark KJ, Maher LJ. Designed architectural proteins that tune DNA looping in bacteria. Nucleic Acids Res 2021; 49:10382-10396. [PMID: 34478548 PMCID: PMC8501960 DOI: 10.1093/nar/gkab759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/28/2022] Open
Abstract
Architectural proteins alter the shape of DNA. Some distort the double helix by introducing sharp kinks. This can serve to relieve strain in tightly-bent DNA structures. Here, we design and test artificial architectural proteins based on a sequence-specific Transcription Activator-like Effector (TALE) protein, either alone or fused to a eukaryotic high mobility group B (HMGB) DNA-bending domain. We hypothesized that TALE protein binding would stiffen DNA to bending and twisting, acting as an architectural protein that antagonizes the formation of small DNA loops. In contrast, fusion to an HMGB domain was hypothesized to generate a targeted DNA-bending architectural protein that facilitates DNA looping. We provide evidence from Escherichia coli Lac repressor gene regulatory loops supporting these hypotheses in living bacteria. Both data fitting to a thermodynamic DNA looping model and sophisticated molecular modeling support the interpretation of these results. We find that TALE protein binding inhibits looping by stiffening DNA to bending and twisting, while the Nhp6A domain enhances looping by bending DNA without introducing twisting flexibility. Our work illustrates artificial approaches to sculpt DNA geometry with functional consequences. Similar approaches may be applicable to tune the stability of small DNA loops in eukaryotes.
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Affiliation(s)
- David H Tse
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Robert T Young
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Center for Quantitative Biology, Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Center for Quantitative Biology, Piscataway, NJ 08854, USA
| | - Justin P Peters
- Department of Chemistry and Biochemistry, University of Northern Iowa, 1227 West 27th Street, Cedar Falls, IA 50614, USA
| | - Tanya L Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
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4
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Garruss AS, Collins KM, Church GM. Deep representation learning improves prediction of LacI-mediated transcriptional repression. Proc Natl Acad Sci U S A 2021; 118:e2022838118. [PMID: 34187888 PMCID: PMC8271634 DOI: 10.1073/pnas.2022838118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of the Escherichia coli LacI protein. We analyze structural and evolutionary aspects that relate to how the function of this protein is maintained, including an in-depth look at the C-terminal domain. We develop a deep neural network to predict transcriptional repression mediated by the lac repressor of Escherichia coli using experimental measurements of variant function. When measured across 10 separate training and validation splits using 5,009 single mutations of the lac repressor, our best-performing model achieved a median Pearson correlation of 0.79, exceeding any previous model. We demonstrate that deep representation learning approaches, first trained in an unsupervised manner across millions of diverse proteins, can be fine-tuned in a supervised fashion using lac repressor experimental datasets to more effectively predict a variant's effect on repression. These findings suggest a deep representation learning model may improve the prediction of other important properties of proteins.
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Affiliation(s)
- Alexander S Garruss
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Program in Bioinformatics and Integrative Genomics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Katherine M Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Boston, MA 02139
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138
- Program in Bioinformatics and Integrative Genomics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
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5
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Guo H, Xu N, Prell M, Königs H, Hermanns-Sachweh B, Lüscher B, Kappes F. Bacterial Growth Inhibition Screen (BGIS): harnessing recombinant protein toxicity for rapid and unbiased interrogation of protein function. FEBS Lett 2021; 595:1422-1437. [PMID: 33704777 DOI: 10.1002/1873-3468.14072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
In two proof-of-concept studies, we established and validated the Bacterial Growth Inhibition Screen (BGIS), which explores recombinant protein toxicity in Escherichia coli as a largely overlooked and alternative means for basic characterization of functional eukaryotic protein domains. By applying BGIS, we identified an unrecognized RNA-interacting domain in the DEK oncoprotein (this study) and successfully combined BGIS with random mutagenesis as a screening tool for loss-of-function mutants of the DNA modulating domain of DEK [1]. Collectively, our findings shed new light on the phenomenon of recombinant protein toxicity in E. coli. Given the easy and rapid implementation and wide applicability, BGIS will extend the repertoire of basic methods for the identification, analysis and unbiased manipulation of proteins.
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Affiliation(s)
- Haihong Guo
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Nengwei Xu
- Department of Biological Sciences, Suzhou Dushu Lake Science and Education Innovation District, Suzhou Industrial Park, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Malte Prell
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Hiltrud Königs
- Institute of Pathology, Medical School, RWTH Aachen University, Germany
| | | | - Bernhard Lüscher
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Ferdinand Kappes
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
- Department of Biological Sciences, Suzhou Dushu Lake Science and Education Innovation District, Suzhou Industrial Park, Xi'an Jiaotong-Liverpool University, Suzhou, China
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6
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Kamagata K, Ouchi K, Tan C, Mano E, Mandali S, Wu Y, Takada S, Takahashi S, Johnson RC. The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA. Nucleic Acids Res 2020; 48:10820-10831. [PMID: 32997109 PMCID: PMC7641734 DOI: 10.1093/nar/gkaa799] [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: 04/30/2020] [Revised: 08/13/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes: mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.
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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.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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7
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Becker NA, Peters JP, Schwab TL, Phillips WJ, Wallace JP, Clark KJ, Maher LJ. Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins. Biophys J 2020; 119:2045-2054. [PMID: 33091377 PMCID: PMC7732741 DOI: 10.1016/j.bpj.2020.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 11/18/2022] Open
Abstract
Gene regulation by control of transcription initiation is a fundamental property of living cells. Much of our understanding of gene repression originated from studies of the Escherichia coli lac operon switch, in which DNA looping plays an essential role. To validate and generalize principles from lac for practical applications, we previously described artificial DNA looping driven by designed transcription activator-like effector dimer (TALED) proteins. Because TALE monomers bind the idealized symmetrical lac operator sequence in two orientations, our prior studies detected repression due to multiple DNA loops. We now quantitatively characterize gene repression in living E. coli by a collection of individual TALED loops with systematic loop length variation. Fitting of a thermodynamic model allows unequivocal demonstration of looping and comparison of the engineered TALED repression system with the natural lac repressor system.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Justin P Peters
- Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, Iowa
| | - Tanya L Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - William J Phillips
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jordan P Wallace
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
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8
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Sarangi MK, Zvoda V, Holte MN, Becker NA, Peters JP, Maher LJ, Ansari A. Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A. Nucleic Acids Res 2019; 47:2871-2883. [PMID: 30698746 PMCID: PMC6451137 DOI: 10.1093/nar/gkz022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 01/17/2023] Open
Abstract
The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.
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Affiliation(s)
- Manas Kumar Sarangi
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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9
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Clark DP, Pazdernik NJ, McGehee MR. Transcription of Genes. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Becker NA, Peters JP, Maher LJ. High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria. Methods Mol Biol 2018; 1837:95-115. [PMID: 30109607 DOI: 10.1007/978-1-4939-8675-0_6] [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: 06/08/2023]
Abstract
The occurrence of DNA looping is ubiquitous. This process plays a well-documented role in the regulation of prokaryotic gene expression, such as the Escherichia coli lactose (lac) operon. Here, we present two complementary methods for high-resolution in vivo detection of DNA/protein binding within the bacterial nucleoid by using either chromatin immunoprecipitation combined with phage λ exonuclease digestion (ChIP-exo) or chromatin endogenous cleavage (ChEC), coupled with ligation-mediated polymerase chain reaction (LM-PCR) and Southern blot analysis. As an example we apply these in vivo protein-mapping methods to E. coli to show direct binding of architectural proteins in the Lac repressor-mediated DNA repression loop.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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11
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:145-155. [PMID: 28035245 PMCID: PMC5153831 DOI: 10.1007/s12551-016-0241-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 01/09/2023] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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12
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:233-243. [PMID: 27738452 PMCID: PMC5039213 DOI: 10.1007/s12551-016-0208-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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13
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Tan C, Terakawa T, Takada S. Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics. J Am Chem Soc 2016; 138:8512-22. [DOI: 10.1021/jacs.6b03729] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Cheng Tan
- Department
of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tsuyoshi Terakawa
- Department
of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Shoji Takada
- Department
of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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14
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Bondos SE, Swint-Kruse L, Matthews KS. Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins. J Biol Chem 2015; 290:24669-77. [PMID: 26342073 DOI: 10.1074/jbc.r115.685032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To modulate transcription, a variety of input signals must be sensed by genetic regulatory proteins. In these proteins, flexibility and disorder are emerging as common themes. Prokaryotic regulators generally have short, flexible segments, whereas eukaryotic regulators have extended regions that lack predicted secondary structure (intrinsic disorder). Two examples illustrate the impact of flexibility and disorder on gene regulation: the prokaryotic LacI/GalR family, with detailed information from studies on LacI, and the eukaryotic family of Hox proteins, with specific insights from investigations of Ultrabithorax (Ubx). The widespread importance of structural disorder in gene regulatory proteins may derive from the need for flexibility in signal response and, particularly in eukaryotes, in protein partner selection.
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Affiliation(s)
- Sarah E Bondos
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Liskin Swint-Kruse
- the Department of Biochemistry and Molecular Biology, the University of Kansas Medical Center, Kansas City, Kansas 66160, and
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