1
|
Zhao X, Vogirala VK, Liu M, Zhou Y, Rhodes D, Sandin S, Yan J. Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies. Commun Biol 2024; 7:148. [PMID: 38310140 PMCID: PMC10838314 DOI: 10.1038/s42003-024-05838-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/20/2024] [Indexed: 02/05/2024] Open
Abstract
TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2's interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2's preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2's binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2's interaction with telomeric DNA.
Collapse
Affiliation(s)
- Xiaodan Zhao
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore
| | - Vinod Kumar Vogirala
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Meihan Liu
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore
| | - Yu Zhou
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore
| | - Daniela Rhodes
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technology University, 636921, Singapore, Singapore
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technology University, 636921, Singapore, Singapore.
- Umeå university, KBC-huset (KB), Linnaeus väg 10, Umeå, 90187, Sweden.
| | - Jie Yan
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore.
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China.
| |
Collapse
|
2
|
Wang Y, Wang H, Zhang S, Yang Z, Shi X, Zhang L. Exploration of the Character Representation of DNA Chiral Conformations and Deformations via a Curved Surface Discrete Frenet Frame. Int J Mol Sci 2023; 25:4. [PMID: 38203177 PMCID: PMC10778681 DOI: 10.3390/ijms25010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
While undergoing structural deformation, DNA experiences changes in the interactions between its internal base pairs, presenting challenges to conventional elastic methods. To address this, we propose the Discrete Critical State (DCS) model in this paper. This model combines surface discrete frame theory with gauge theory and Landau phase transition theory to investigate DNA's structural deformation, phase transitions, and chirality. Notably, the DCS model considers both the internal interactions within DNA and formulates an overall equation using unified physical and geometric parameters. By employing the discrete frame, we derive the evolution of physical quantities along the helical axis of DNA, including geodesic curvature, geodesic torsion, and others. Our findings indicate that B-DNA has a significantly lower free energy density compared to Z-DNA, which is in agreement with experimental observations. This research reveals that the direction of base pairs is primarily governed by the geodesic curve within the helical plane, aligning closely with the orientation of the base pairs. Moreover, the geodesic curve has a profound influence on the arrangement of base pairs at the microscopic level and effectively regulates the configuration and geometry of DNA through macroscopic-level free energy considerations.
Collapse
Affiliation(s)
- Ying Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Xuguang Shi
- College of Science, Beijing Forestry University, Beijing 100083, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| |
Collapse
|
3
|
Efremov AK, Hovan L, Yan J. Nucleus size and its effect on nucleosome stability in living cells. Biophys J 2022; 121:4189-4204. [PMID: 36146936 PMCID: PMC9675033 DOI: 10.1016/j.bpj.2022.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/15/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
DNA architectural proteins play a major role in organization of chromosomal DNA in living cells by packaging it into chromatin, whose spatial conformation is determined by an intricate interplay between the DNA-binding properties of architectural proteins and physical constraints applied to the DNA by a tight nuclear space. Yet, the exact effects of the nucleus size on DNA-protein interactions and chromatin structure currently remain obscure. Furthermore, there is even no clear understanding of molecular mechanisms responsible for the nucleus size regulation in living cells. To find answers to these questions, we developed a general theoretical framework based on a combination of polymer field theory and transfer-matrix calculations, which showed that the nucleus size is mainly determined by the difference between the surface tensions of the nuclear envelope and the endoplasmic reticulum membrane as well as the osmotic pressure exerted by cytosolic macromolecules on the nucleus. In addition, the model demonstrated that the cell nucleus functions as a piezoelectric element, changing its electrostatic potential in a size-dependent manner. This effect has been found to have a profound impact on stability of nucleosomes, revealing a previously unknown link between the nucleus size and chromatin structure. Overall, our study provides new insights into the molecular mechanisms responsible for regulation of the nucleus size, as well as the potential role of nuclear organization in shaping the cell response to environmental cues.
Collapse
Affiliation(s)
- Artem K Efremov
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
| | - Ladislav Hovan
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| |
Collapse
|
4
|
Chen X, Tsai MY, Wolynes PG. The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout. J Am Chem Soc 2022; 144:1835-1845. [DOI: 10.1021/jacs.1c11911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Xun Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Min-Yeh Tsai
- Department of Chemistry, Tamkang University, New Taipei City, 251301, Taiwan (R.O.C.)
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
5
|
McCormack LS, Efremov AK, Yan J. Effects of size, cooperativity, and competitive binding on protein positioning on DNA. Biophys J 2021; 120:2040-2053. [PMID: 33771470 DOI: 10.1016/j.bpj.2021.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/26/2021] [Accepted: 03/18/2021] [Indexed: 11/24/2022] Open
Abstract
Accurate positioning of proteins on chromosomal DNA is crucial for its proper organization as well as gene transcription regulation. Recent experiments revealed existence of periodic patterns of nucleoprotein complexes on DNA, which frequently cannot be explained by sequence-dependent binding of proteins. Previous theoretical studies suggest that such patterns typically emerge as a result of the proteins' volume-exclusion effect. However, the role of other physical factors in patterns' formation, such as the length of DNA, its sequence heterogeneity, and protein binding cooperativity/binding competition to DNA, remains unclear. To address these less understood yet important aspects, we investigated potential effects of these factors on protein positioning on finite-size DNA by using transfer-matrix calculations. It has been found that upon binding to DNA, proteins form oscillatory patterns that span over the length of up to ∼10 times the size of the protein binding site, with the shape of the patterns being strongly dependent on the length of DNA and the proteins' binding cooperativity to DNA. Furthermore, calculations showed that small variations in the proteins' affinity to DNA due to its sequence heterogeneity do not much change the main geometric characteristics of the observed protein patterns. Finally, competition between two different types of proteins for binding to DNA has been found to lead to formation of highly diverse and complex alternating positioning of the two proteins. Altogether, these results provide new insights into the roles of physicochemical properties of proteins, the DNA length, and DNA-binding competition between proteins in formation of protein positioning patterns on DNA.
Collapse
Affiliation(s)
- Leo S McCormack
- Department of Physics, Imperial College London, London, United Kingdom; Mechanobiology InstituteNational University of Singapore, Singapore, Singapore
| | - Artem K Efremov
- Mechanobiology InstituteNational University of Singapore, Singapore, Singapore.
| | - Jie Yan
- Mechanobiology InstituteNational University of Singapore, Singapore, Singapore; Department of Physics, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
6
|
Martis B S, Forquet R, Reverchon S, Nasser W, Meyer S. DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria? Comput Struct Biotechnol J 2019; 17:1047-1055. [PMID: 31452857 PMCID: PMC6700405 DOI: 10.1016/j.csbj.2019.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/28/2022] Open
Abstract
DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.
Collapse
Affiliation(s)
- Shiny Martis B
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| |
Collapse
|
7
|
Abstract
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here, we show that trends in the interaction energy of ligands binding to DNA can be explained within an elastic birod model, which accounts for the deformation of each strand as well as the change in stacking energy due to perturbations in position and orientation of the bases caused by the binding of ligands. The strain fields produced by the ligands decay with distance from the binding site. The interaction energy of two ligands decays exponentially with the distance between them and oscillates with the periodicity of the double helix in quantitative agreement with experimental measurements. The trend in the computed interaction energy is similar to that in the perturbation of groove width produced by the binding of a single ligand, which is consistent with molecular simulations. Our analysis provides a new framework to understand allosteric interactions in DNA and can be extended to other rod-like macromolecules whose elasticity plays a role in biological functions.
Collapse
Affiliation(s)
- Jaspreet Singh
- Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| |
Collapse
|