1
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Lüking M, Elf J, Levy Y. Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study. J Phys Chem B 2022; 126:9971-9984. [PMID: 36416228 PMCID: PMC9743208 DOI: 10.1021/acs.jpcb.2c05006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In a process known as facilitated diffusion, DNA-binding proteins find their target sites by combining three-dimensional diffusion and one-dimensional scanning of the DNA. Following the trade-off between speed and stability, agile exploration of DNA requires loose binding, whereas, at the DNA target site, the searching protein needs to establish tight interactions with the DNA. To enable both efficient search and stable binding, DNA-binding proteins and DNA often switch conformations upon recognition. Here, we study the one-dimensional diffusion and DNA binding of the dimeric lac repressor (LacI), which was reported to adopt two different conformations when binding different conformations of DNA. Using coarse-grained molecular dynamic simulations, we studied the diffusion and the sequence-specific binding of these conformations of LacI, as well as their truncated or monomeric variants, with two DNA conformations: straight and bent. The simulations were compared to experimental observables. This study supports that linear diffusion along DNA combines tight rotation-coupled groove tracking and rotation-decoupled hopping, where the protein briefly dissociates and reassociates just a few base pairs away. Tight groove tracking is crucial for target-site recognition, while hopping speeds up the overall search process. We investigated the diffusion of different LacI conformations on DNA and show how the flexibility of LacI's hinge regions ensures agility on DNA as well as faithful groove tracking. If the hinge regions instead form α-helices at the protein-DNA interface, tight groove tracking is not possible. On the contrary, the helical hinge region is essential for tight binding to bent, specific DNA, for the formation of the specific complex. Based on our study of different encounter complexes, we argue that the conformational change in LacI and DNA bending are somewhat coupled. Our findings underline the importance of two distinct protein conformations for facilitated diffusion and specific binding, respectively.
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Affiliation(s)
- Malin Lüking
- Department
of Cell- and Molecular Biology-ICM, Uppsala
University, Uppsala, Uppsala County751 24, Sweden
| | - Johan Elf
- Department
of Cell- and Molecular Biology-ICM, Uppsala
University, Uppsala, Uppsala County751 24, Sweden
| | - Yaakov Levy
- Department
of Chemical and Structural Biology, Weizmann
Institute of Science, Rehovot, Central District76100, Israel,. Tel.: 972-8-9344587
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2
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Vazquez-Rivera E, Rojas B, Parrott JC, Shen AL, Xing Y, Carney PR, Bradfield CA. The aryl hydrocarbon receptor as a model PAS sensor. Toxicol Rep 2021; 9:1-11. [PMID: 34950569 PMCID: PMC8671103 DOI: 10.1016/j.toxrep.2021.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins containing PER-ARNT-SIM (PAS) domains are commonly associated with environmental adaptation in a variety of organisms. The PAS domain is found in proteins throughout Archaea, Bacteria, and Eukarya and often binds small-molecules, supports protein-protein interactions, and transduces input signals to mediate an adaptive physiological response. Signaling events mediated by PAS sensors can occur through induced phosphorelays or genomic events that are often dependent upon PAS domain interactions. In this perspective, we briefly discuss the diversity of PAS domain containing proteins, with particular emphasis on the prototype member, the aryl hydrocarbon receptor (AHR). This ligand-activated transcription factor acts as a sensor of the chemical environment in humans and many chordates. We conclude with the idea that since mammalian PAS proteins often act through PAS-PAS dimers, undocumented interactions of this type may link biological processes that we currently think of as independent. To support this idea, we present a framework to guide future experiments aimed at fully elucidating the spectrum of PAS-PAS interactions with an eye towards understanding how they might influence environmental sensing in human and wildlife populations.
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Affiliation(s)
- Emmanuel Vazquez-Rivera
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Brenda Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Jessica C. Parrott
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Anna L. Shen
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Yongna Xing
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Patrick R. Carney
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
| | - Christopher A. Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
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3
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Purtov YA, Tishchenko SV, Nikulin AD. Modeling the Interaction of the UxuR–ExuR Heterodimer with the Components of the Metabolic Pathway of Escherichia coli for Hexuronate Utilization. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921050201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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4
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Pogenberg V, Ballesteros-Álvarez J, Schober R, Sigvaldadóttir I, Obarska-Kosinska A, Milewski M, Schindl R, Ögmundsdóttir MH, Steingrímsson E, Wilmanns M. Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif. Nucleic Acids Res 2020; 48:934-948. [PMID: 31777941 PMCID: PMC6954422 DOI: 10.1093/nar/gkz1104] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/01/2019] [Accepted: 11/25/2019] [Indexed: 12/01/2022] Open
Abstract
Interrupted dimeric coiled coil segments are found in a broad range of proteins and generally confer selective functional properties such as binding to specific ligands. However, there is only one documented case of a basic-helix–loop–helix leucine zipper transcription factor—microphthalmia-associated transcription factor (MITF)—in which an insertion of a three-residue stammer serves as a determinant of conditional partner selectivity. To unravel the molecular principles of this selectivity, we have analyzed the high-resolution structures of stammer-containing MITF and an engineered stammer-less MITF variant, which comprises an uninterrupted symmetric coiled coil. Despite this fundamental difference, both MITF structures reveal identical flanking in-phase coiled coil arrangements, gained by helical over-winding and local asymmetry in wild-type MITF across the stammer region. These conserved structural properties allow the maintenance of a proper functional readout in terms of nuclear localization and binding to specific DNA-response motifs regardless of the presence of the stammer. By contrast, MITF heterodimer formation with other bHLH-Zip transcription factors is only permissive when both factors contain either the same type of inserted stammer or no insert. Our data illustrate a unique principle of conditional partner selectivity within the wide arsenal of transcription factors with specific partner-dependent functional readouts.
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Affiliation(s)
| | - Josué Ballesteros-Álvarez
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Romana Schober
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Gruberstraße 40, A-4020 Linz, Austria
| | - Ingibjörg Sigvaldadóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Agnieszka Obarska-Kosinska
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany.,Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Morlin Milewski
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rainer Schindl
- Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstrasse 6, A-8010 Graz, Austria
| | - Margrét Helga Ögmundsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Matthias Wilmanns
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany.,University Hamburg Clinical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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5
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Popa SC, Shin JA. The Intrinsically Disordered Loop in the USF1 bHLHZ Domain Modulates Its DNA-Binding Sequence Specificity in Hereditary Asthma. J Phys Chem B 2019; 123:9862-9871. [PMID: 31670516 DOI: 10.1021/acs.jpcb.9b06719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1, a basic region/helix-loop-helix/leucine zipper (bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen activator inhibitor) promoter. Two alleles containing the E-box control PAI-1 transcription; these alleles are termed "4G" and "5G" based on the G tract flanking E-box. USF1-governed transcription of PAI-1 is elevated in heritable asthma sufferers: the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1 uses its basic region to bind E-box, we found that it uses its 12 amino-acid loop to recognize the flanking sequence and discern the single-nucleotide difference between the alleles. We used the bacterial one-hybrid and electrophoretic mobility shift assays to assess protein-DNA recognition, and circular dichroism to examine protein secondary structure. We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1 bHLHZ Kd values 4.1 ± 0.3 nM and 7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in stimulated human mast cells showed a preference for 4G. We replaced the 8 amino-acid loop of transcription factor Max bHLHZ with the 12 amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphism-while Max bHLHZ does not-confirming that USF1 differentiation of the 4G/5G is driven by the loop.
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Affiliation(s)
- Serban C Popa
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
| | - Jumi A Shin
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
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6
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Zhao L, Lai L, Zhang Z. How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain—an atomic level characterization. Phys Chem Chem Phys 2019; 21:19795-19804. [DOI: 10.1039/c9cp03917a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Ca2+binding and triggering conformation transition of nCaM were detected in unbiased molecular dynamics simulations.
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Affiliation(s)
- Likun Zhao
- College of Life Science
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Luhua Lai
- BNLMS, and Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
- Center for Quantitative Biology
| | - Zhuqing Zhang
- College of Life Science
- University of Chinese Academy of Sciences
- Beijing
- China
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7
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Xu JS, Hewitt MN, Gulati JS, Cruz MA, Zhan H, Liu S, Matthews KS. Lactose repressor hinge domain independently binds DNA. Protein Sci 2018; 27:839-847. [PMID: 29318690 PMCID: PMC5866929 DOI: 10.1002/pro.3372] [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] [Received: 11/19/2017] [Revised: 01/02/2018] [Accepted: 01/02/2018] [Indexed: 12/29/2022]
Abstract
The short 8-10 amino acid "hinge" sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer-binding domains. Structural studies of full-length or truncated LacI-operator DNA complexes demonstrate insertion of the dimeric helical "hinge" structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi-symmetric DNA sites for optimal contact by the N-terminal helix-turn-helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1-50 to remove the HtH DNA binding domain or residues 1-58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix-turn-helix domain with its highly positive charge. LacI missing residues 1-50 binds to DNA with ∼4-fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1-58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.
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Affiliation(s)
- Joseph S Xu
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Madeleine N Hewitt
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Jaskeerat S Gulati
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Matthew A Cruz
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Hongli Zhan
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
| | - Shirley Liu
- Department of BioSciences, MS-140, Rice University, Houston, Texas, 77251
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8
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Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP. The herpes viral transcription factor ICP4 forms a novel DNA recognition complex. Nucleic Acids Res 2017; 45:8064-8078. [PMID: 28505309 PMCID: PMC5737704 DOI: 10.1093/nar/gkx419] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
The transcription factor ICP4 from herpes simplex virus has a central role in regulating the gene expression cascade which controls viral infection. Here we present the crystal structure of the functionally essential ICP4 DNA binding domain in complex with a segment from its own promoter, revealing a novel homo-dimeric fold. We also studied the complex in solution by small angle X-Ray scattering, nuclear magnetic resonance and surface-plasmon resonance which indicated that, in addition to the globular domain, a flanking intrinsically disordered region also recognizes DNA. Together the data provides a rationale for the bi-partite nature of the ICP4 DNA recognition consensus sequence as the globular and disordered regions bind synergistically to adjacent DNA motifs. Therefore in common with its eukaryotic host, the viral transcription factor ICP4 utilizes disordered regions to enhance the affinity and tune the specificity of DNA interactions in tandem with a globular domain.
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Affiliation(s)
- Richard B Tunnicliffe
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK
| | - Michael P Lockhart-Cairns
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0QX, UK
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK
| | - A Paul Mould
- Biomolecular Analysis Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK
| | - Thomas A Jowitt
- Biomolecular Analysis Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK
| | - Hilary Sito
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK
| | - Clair Baldock
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK
| | - Rozanne M Sandri-Goldin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Alexander P Golovanov
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK
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9
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Wang J, Custer G, Beckett D, Matysiak S. Long Distance Modulation of Disorder-to-Order Transitions in Protein Allostery. Biochemistry 2017; 56:4478-4488. [PMID: 28718281 DOI: 10.1021/acs.biochem.7b00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP. The effector acts by promoting BirA dimerization, which is a prerequisite for sequence-specific binding to the biotin biosynthetic operon operator sequence. A 30 Å distance separates the effector binding and dimerization surfaces in BirA, and previous studies indicate that allostery is mediated, in part, by disorder-to-order transitions on the two coupled sites. In this work, combined experimental and computational methods have been applied to investigate the molecular basis of allosteric communication in BirA. Double-mutant cycle analysis coupled with thermodynamic measurements indicates functional coupling between residues in disordered loops on the two distant surfaces. All atom molecular dynamics simulations reveal that this coupling occurs through long distance reciprocal modulation of the structure and dynamics of disorder-to-order transitions on the two surfaces.
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Affiliation(s)
- Jingheng Wang
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory Custer
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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10
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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11
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Grove A. Regulation of Metabolic Pathways by MarR Family Transcription Factors. Comput Struct Biotechnol J 2017; 15:366-371. [PMID: 28694934 PMCID: PMC5487221 DOI: 10.1016/j.csbj.2017.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved sophisticated mechanisms for regulation of metabolic pathways. Such regulatory circuits ensure that anabolic pathways remain repressed unless final products are in short supply and that catabolic enzymes are not produced in absence of their substrates. The precisely tuned gene activity underlying such circuits is in the purview of transcription factors that may bind pathway intermediates, which in turn modulate transcription factor function and therefore gene expression. This review focuses on the role of ligand-responsive MarR family transcription factors in controlling expression of genes encoding metabolic enzymes and the mechanisms by which such control is exerted. Prospects for exploiting these transcription factors for optimization of gene expression for metabolic engineering and for the development of biosensors are considered.
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Affiliation(s)
- Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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12
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Schreier HI, Soen Y, Brenner N. Exploratory adaptation in large random networks. Nat Commun 2017; 8:14826. [PMID: 28429717 PMCID: PMC5413947 DOI: 10.1038/ncomms14826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/02/2017] [Indexed: 02/06/2023] Open
Abstract
The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demonstrate the feasibility of exploratory adaptation in a high-dimensional network model of gene regulation. Exploration is initiated by failure to comply with a constraint and is implemented by random sampling of network configurations. It ceases if and when the network reaches a stable state satisfying the constraint. We find that successful convergence (adaptation) in high dimensions requires outgoing network hubs and is enhanced by their auto-regulation. The ability of these empirically validated features of gene regulatory networks to support exploratory adaptation without fine-tuning, makes it plausible for biological implementation. Recent works suggest that cellular networks may respond to novel challenges on the time-scale of cellular lifetimes through large-scale perturbation of gene expression and convergence to a new state. Here, the authors demonstrate the theoretical feasibility of exploratory adaptation in cellular networks by showing that convergence to new states depends on known features of these networks.
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Affiliation(s)
- Hallel I Schreier
- Network Biology Research Laboratories, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Interdisciplinary Program for Applied Mathematics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yoav Soen
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Brenner
- Network Biology Research Laboratories, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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13
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Minde D, Dunker AK, Lilley KS. Time, space, and disorder in the expanding proteome universe. Proteomics 2017; 17:1600399. [PMID: 28145059 PMCID: PMC5573936 DOI: 10.1002/pmic.201600399] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 12/31/2022]
Abstract
Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms.
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Affiliation(s)
- David‐Paul Minde
- Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - A. Keith Dunker
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisINUSA
| | - Kathryn S. Lilley
- Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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14
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Ortiz-Lombardia M, Foos N, Maurel-Zaffran C, Saurin AJ, Graba Y. Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction. Bioessays 2017; 39. [PMID: 28092121 DOI: 10.1002/bies.201600246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.
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Affiliation(s)
- Miguel Ortiz-Lombardia
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France.,Aix-Marseille-Université, CNRS UMR 7256, AFMB, Marseille, France
| | - Nicolas Foos
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France
| | | | - Andrew J Saurin
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
| | - Yacine Graba
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
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15
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Smith NC, Matthews JM. Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors. Curr Opin Struct Biol 2016; 38:68-74. [PMID: 27295424 DOI: 10.1016/j.sbi.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ability to discriminate target and variant non-target DNA sequences. Here, we summarise established mechanisms of protein-DNA recognition, as specified by both macromolecules. We also review recent advances in the fields of genome binding, molecular dynamics and biomolecular interaction studies that bring us close to a full understanding of how eukaryotic transcription factors find and target DNA in vivo to form functional centres of gene regulation through networks of protein-protein and protein-DNA interactions.
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Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia.
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16
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Abstract
Metazoans encode clusters of paralogous Hox genes that are critical for proper development of the body plan. However, there are a number of unresolved issues regarding how paralogous Hox factors achieve specificity to control distinct cell fates. First, how do Hox paralogs, which have very similar DNA binding preferences in vitro, drive different transcriptional programs in vivo? Second, the number of potential Hox binding sites within the genome is vast compared to the number of sites bound. Hence, what determines where in the genome Hox factors bind? Third, what determines whether a Hox factor will activate or repress a specific target gene? Here, we review the current evidence that is beginning to shed light onto these questions. In particular, we highlight how cooperative interactions with other transcription factors (especially PBC and HMP proteins) and the sequences of cis-regulatory modules provide a basis for the mechanisms of Hox specificity. We conclude by integrating a number of the concepts described throughout the review in a case study of a highly interrogated Drosophila cis-regulatory module named “The Distal-less Conserved Regulatory Element” (DCRE).
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Affiliation(s)
- Arya Zandvakili
- Molecular and Developmental Biology Graduate Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-636-3366
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17
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Choudhury S, Naiya G, Singh P, Lemmens P, Roy S, Pal SK. Modulation of Ultrafast Conformational Dynamics in Allosteric Interaction of Gal Repressor Protein with Different Operator DNA Sequences. Chembiochem 2016; 17:605-13. [DOI: 10.1002/cbic.201500657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
| | - Gitashri Naiya
- Division of Structural Biology and Bioinformatics; Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Priya Singh
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
| | - Peter Lemmens
- Institute for Condensed Matter Physics and Laboratory for Emerging Nanometrology; TU Braunschweig; Mendelssohnstrasse 3 38106 Braunschweig Germany
| | - Siddhartha Roy
- Division of Structural Biology and Bioinformatics; Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences; S. N. Bose National Centre for Basic Sciences; Block JD Sector III Salt Lake Kolkata 700 098 India
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