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Nechipurenko YD, Buchelnikov AS. Ligand Binding to Nucleic Acids in Solution and on Microchips. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922030162] [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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Abstract
Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery plays a regulatory role in gene expression remained unclear. Here, we show that DNA indeed transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which allows a fine-tuning of the dynamic properties of genetic circuits. Most insights on DNA-mediated allostery upon transcription factor (TF) binding were either based on artificial promoters or found to be short-ranged. Here authors use single-molecule FRET and cryo-EM to show that Bacillus subtilis bacteria utilize long-range allostery in a stochastic and reversible phenotype switch.
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Morgunova E, Taipale J. Structural perspective of cooperative transcription factor binding. Curr Opin Struct Biol 2017; 47:1-8. [PMID: 28349863 DOI: 10.1016/j.sbi.2017.03.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/07/2017] [Indexed: 12/27/2022]
Abstract
In prokaryotes, individual transcription factors (TFs) can recognize long DNA motifs that are alone sufficient to define the genes that they induce or repress. In contrast, in higher organisms that have larger genomes, TFs recognize sequences that are too short to define unique genomic positions. In addition, development of multicellular organisms requires molecular systems that are capable of executing combinatorial logical operations. Co-operative recognition of DNA by multiple TFs allows both definition of unique genomic positions in large genomes, and complex information processing at the level of individual regulatory elements. The TFs can co-operate in multiple different ways, and the precise mechanism used for co-operation determines important features of the regulatory interactions. Here, we present an overview of the structural basis of the different mechanisms by which TFs can cooperate, focusing on insight from recent functional studies and structural analyses of specific TF-TF-DNA complexes.
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Affiliation(s)
- Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden; Genome-Scale Biology Research Program, P.O. Box 63, FI-00014 University of Helsinki, Finland.
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Jin J, Lian T, Gu C, Yu K, Gao YQ, Su XD. The effects of cytosine methylation on general transcription factors. Sci Rep 2016; 6:29119. [PMID: 27385050 PMCID: PMC4935894 DOI: 10.1038/srep29119] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 12/24/2022] Open
Abstract
DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.
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Affiliation(s)
- Jianshi Jin
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Tengfei Lian
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Chan Gu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kai Yu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Yi Qin Gao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiao-Dong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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Huang P, López Villar E. Possible mechanism and clinical potentials of allostery. Clin Transl Med 2014; 3:18. [PMID: 25024818 PMCID: PMC4091739 DOI: 10.1186/2001-1326-3-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/16/2014] [Indexed: 11/10/2022] Open
Abstract
Allostery is involved in the dynamic regulation of biological functions in proteins. Advances in allostery research have recently drawn great interest and brought allostery closer to the clinic. The present commentary describes the mechanism by which allostery may involve in from a cell-wide view and its contribution to the discovery of new therapeutics to diseases.
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Affiliation(s)
- Peixin Huang
- Liver Cancer Institute, Pulmonary Department, Fudan University Zhongshan Hospital, Shanghai 200032, China
| | - Elena López Villar
- Department of Oncohematology of Children, Hospital Universitario Niño Jesús, Avda. Menéndez Pelayo, NO 65, 28009 Madrid, Spain
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