1
|
Natarajan AK, Ryssy J, Kuzyk A. A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy. NANOSCALE 2023; 15:3212-3218. [PMID: 36722916 DOI: 10.1039/d2nr05366g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA-protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP-DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA-protein interactions.
Collapse
Affiliation(s)
- Ashwin Karthick Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| |
Collapse
|
2
|
Yoshua SB, Watson GD, Howard JAL, Velasco-Berrelleza V, Leake MC, Noy A. Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity. Nucleic Acids Res 2021; 49:8684-8698. [PMID: 34352078 PMCID: PMC8421141 DOI: 10.1093/nar/gkab641] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 07/02/2021] [Accepted: 07/16/2021] [Indexed: 11/29/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating genes. Vital to these activities are complex nucleoprotein structures, however, how these form remains unclear. Integration host factor (IHF) is an Escherichia coli NAP that creates very sharp bends in DNA at sequences relevant to several functions including transcription and recombination, and is also responsible for general DNA compaction when bound non-specifically. We show that IHF–DNA structural multimodality is more elaborate than previously thought, and provide insights into how this drives mechanical switching towards strongly bent DNA. Using single-molecule atomic force microscopy and atomic molecular dynamics simulations we find three binding modes in roughly equal proportions: ‘associated’ (73° of DNA bend), ‘half-wrapped’ (107°) and ‘fully-wrapped’ (147°), only the latter occurring with sequence specificity. We show IHF bridges two DNA double helices through non-specific recognition that gives IHF a stoichiometry greater than one and enables DNA mesh assembly. We observe that IHF-DNA structural multiplicity is driven through non-specific electrostatic interactions that we anticipate to be a general NAP feature for physical organization of chromosomes.
Collapse
Affiliation(s)
- Samuel B Yoshua
- Department of Physics, University of York, York YO10 5DD, UK
| | - George D Watson
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
| | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
| |
Collapse
|
3
|
Aermes C, Hayn A, Fischer T, Mierke CT. Environmentally controlled magnetic nano-tweezer for living cells and extracellular matrices. Sci Rep 2020; 10:13453. [PMID: 32778758 PMCID: PMC7417586 DOI: 10.1038/s41598-020-70428-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
The magnetic tweezer technique has become a versatile tool for unfolding or folding of individual molecules, mainly DNA. In addition to single molecule analysis, the magnetic tweezer can be used to analyze the mechanical properties of cells and extracellular matrices. We have established a magnetic tweezer that is capable of measuring the linear and non-linear viscoelastic behavior of a wide range of soft matter in precisely controlled environmental conditions, such as temperature, CO2 and humidity. The magnetic tweezer presented in this study is suitable to detect specific differences in the mechanical properties of different cell lines, such as human breast cancer cells and mouse embryonic fibroblasts, as well as collagen matrices of distinct concentrations in the presence and absence of fibronectin crosslinks. The precise calibration and control mechanism employed in the presented magnetic tweezer setup provides the ability to apply physiological force up to 5 nN on 4.5 µm superparamagnetic beads coated with fibronectin and coupled to the cells or collagen matrices. These measurements reveal specific local linear and non-linear viscoelastic behavior of the investigated samples. The viscoelastic response of cells and collagen matrices to the force application is best described by a weak power law behavior. Our results demonstrate that the stress stiffening response and the fluidization of cells is cell type specific and varies largely between differently invasive and aggressive cancer cells. Finally, we showed that the viscoelastic behavior of collagen matrices with and without fibronectin crosslinks measured by the magnetic tweezer can be related to the microstructure of these matrices.
Collapse
Affiliation(s)
- Christian Aermes
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Alexander Hayn
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Tony Fischer
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Claudia Tanja Mierke
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany.
| |
Collapse
|
4
|
Zhao X, Guo S, Lu C, Chen J, Le S, Fu H, Yan J. Single-molecule manipulation quantification of site-specific DNA binding. Curr Opin Chem Biol 2019; 53:106-117. [DOI: 10.1016/j.cbpa.2019.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/24/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
|
5
|
Abstract
![]()
Life is an emergent property of transient
interactions between
biomolecules and other organic and inorganic molecules that somehow
leads to harmony and order. Measurement and quantitation of these
biological interactions are of value to scientists and are major goals
of biochemistry, as affinities provide insight into biological processes.
In an organism, these interactions occur in the context of forces
and the need for a consideration of binding affinities in the context
of a changing mechanical landscape necessitates a new way to consider
the biochemistry of protein–protein interactions. In the past
few decades, the field of mechanobiology has exploded, as both the
appreciation of, and the technical advances required to facilitate
the study of, how forces impact biological processes have become evident.
The aim of this review is to introduce the concept of force dependence
of biomolecular interactions and the requirement to be able to measure
force-dependent binding constants. The focus of this discussion will
be on the mechanotransduction that occurs at the integrin-mediated
adhesions with the extracellular matrix and the major mechanosensors
talin and vinculin. However, the approaches that the cell uses to
sense and respond to forces can be applied to other systems, and this
therefore provides a general discussion of the force dependence of
biomolecule interactions.
Collapse
Affiliation(s)
- Yinan Wang
- Department of Physics , National University of Singapore , 117542 Singapore
| | - Jie Yan
- Department of Physics , National University of Singapore , 117542 Singapore.,Mechanobiology Institute , National University of Singapore , 117411 Singapore
| | - Benjamin T Goult
- School of Biosciences , University of Kent , Canterbury , Kent CT2 7NJ , U.K
| |
Collapse
|
6
|
Efremov AK, Yan J. Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions. Nucleic Acids Res 2018; 46:6504-6527. [PMID: 29878241 PMCID: PMC6061897 DOI: 10.1093/nar/gky478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022] Open
Abstract
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA-protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA-protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.
Collapse
Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
- Department of Physics, National University of Singapore, 117551, Singapore
| |
Collapse
|
7
|
mDia1 senses both force and torque during F-actin filament polymerization. Nat Commun 2017; 8:1650. [PMID: 29162803 PMCID: PMC5698482 DOI: 10.1038/s41467-017-01745-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/12/2017] [Indexed: 11/08/2022] Open
Abstract
Formins, an important family of force-bearing actin-polymerizing factors, function as homodimers that bind with the barbed end of actin filaments through a ring-like structure assembled from dimerized FH2 domains. It has been hypothesized that force applied to formin may facilitate transition of the FH2 ring from an inhibitory closed conformation to a permissive open conformation, speeding up actin polymerization. We confirm this hypothesis for mDia1 dependent actin polymerization by stretching a single-actin filament in the absence of profilin using magnetic tweezers, and observe that increasing force from 0.5 to 10 pN can drastically speed up the actin polymerization rate. Further, we find that this force-promoted actin polymerization requires torsionally unconstrained actin filament, suggesting that mDia1 also senses torque. As actin filaments are subject to complex mechanical constraints in living cells, these results provide important insights into how formin senses these mechanical constraints and regulates actin organization accordingly.
Collapse
|
8
|
Theoretical Methods for Studying DNA Structural Transitions under Applied Mechanical Constraints. Polymers (Basel) 2017; 9:polym9020074. [PMID: 30970752 PMCID: PMC6432069 DOI: 10.3390/polym9020074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/14/2017] [Indexed: 11/24/2022] Open
Abstract
Recent progress in single-molecule manipulation technologies has made it possible to exert force and torque on individual DNA biopolymers to probe their mechanical stability and interaction with various DNA-binding proteins. It was revealed in these experiments that the DNA structure and formation of nucleoprotein complexes by DNA-architectural proteins can be strongly modulated by an intricate interplay between the entropic elasticity of DNA and its global topology, which is closely related to the mechanical constraints applied to the DNA. Detailed understanding of the physical processes underlying the DNA behavior observed in single-molecule experiments requires the development of a general theoretical framework, which turned out to be a rather challenging task. Here, we review recent advances in theoretical methods that can be used to interpret single-molecule manipulation experiments on DNA.
Collapse
|
9
|
Efremov AK, Winardhi RS, Yan J. Transfer-matrix calculations of DNA polymer micromechanics under tension and torque constraints. Phys Rev E 2016; 94:032404. [PMID: 27739846 DOI: 10.1103/physreve.94.032404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Indexed: 06/06/2023]
Abstract
Recent development of single-molecule manipulation technologies has made it possible to exert constant force and torque on individual DNA biopolymers to probe their elastic characteristics and structural stability. It has been previously shown that depending on the nature of applied mechanical constraints, DNA can exist in several forms including B-, L-, and P-DNA. However, there is still a lack of understanding of how structural heterogeneity of DNA, which may naturally arise due to sequence-dependent DNA properties, protein binding, or DNA damage, influences local stability of the above DNA states. To provide a more complete and detailed description of the DNA mechanics, we developed a theoretical framework based on transfer-matrix calculations and demonstrated how it can be used to predict the DNA behavior upon application of a wide range of force and torque constraints. The resulting phase diagram shows DNA structural transitions that are in good agreement with previous experimental and theoretical studies. We further discuss how the constructed formalism can be extended to include local inhomogeneities in the DNA physical properties, thus making it possible to investigate the effect of DNA sequence as well as protein binding on DNA structural stability.
Collapse
Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Centre for Bioimaging Sciences, National University of Singapore, Singapore 117557
| | - Ricksen S Winardhi
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Department of Physics, National University of Singapore, Singapore 117551
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Centre for Bioimaging Sciences, National University of Singapore, Singapore 117557
- Department of Physics, National University of Singapore, Singapore 117551
| |
Collapse
|
10
|
Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF. Sci Rep 2015; 5:18146. [PMID: 26657062 PMCID: PMC4677351 DOI: 10.1038/srep18146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/12/2015] [Indexed: 02/01/2023] Open
Abstract
The bacterial nucleoid, a bacterial genome packed by nucleoid binding proteins, forms the physical basis for cellular processes such as gene transcription and DNA replication. Bacteria need to dynamically modulate their nucleoid structures at different growth phases and in response to environmental changes. At the nutrients deficient stationary phase, DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) are the two most abundant nucleoid associated proteins in E. coli. Yet, it remains unclear how the nucleoid architecture is controlled by the interplay between these two proteins, as well as the nucleoid's response to environmental changes. This question is addressed here using single DNA manipulation approach. Our results reveal that the two proteins are differentially selected for DNA binding, which can be tuned by changing environmental factors over physiological ranges including KCl (50-300 mM), MgCl2 (0-10 mM), pH (6.5-8.5) and temperature (23-37 °C). Increasing pH and MgCl2 concentrations switch from Dps-binding to IHF-binding. Stable Dps-DNA and IHF-DNA complexes are insensitive to temperature changes for the range tested. The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture.
Collapse
|
11
|
Le S, Liu R, Lim CT, Yan J. Uncovering mechanosensing mechanisms at the single protein level using magnetic tweezers. Methods 2015; 94:13-8. [PMID: 26318089 DOI: 10.1016/j.ymeth.2015.08.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/01/2015] [Accepted: 08/25/2015] [Indexed: 11/28/2022] Open
Abstract
Mechanosensing of the micro-environments has been shown to be essential for cell survival, growth, differentiation and migration. The mechanosensing pathways are mediated by a set of mechanosensitive proteins located at focal adhesion and cell-cell adherens junctions as well as in the cytoskeleton network. Here we review the applications of magnetic tweezers on elucidating the molecular mechanisms of the mechanosensing proteins. The scope of this review includes the principles of the magnetic tweezers technology, theoretical analysis of force-dependent stability and interaction of mechanosensing proteins, and recent findings obtained using magnetic tweezers.
Collapse
Affiliation(s)
- Shimin Le
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore
| | - Ruchuan Liu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore; College of Physics, Chongqing University, Chongqing 401331, China
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore 117575, Singapore; Department of Mechanical Engineering, National University of Singapore, Singapore 117575, Singapore.
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore.
| |
Collapse
|
12
|
Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction. Biochemistry 2015; 54:4142-60. [DOI: 10.1021/acs.biochem.5b00447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Apoorva Ravishankar
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
13
|
Le S, Yao M, Chen J, Efremov AK, Azimi S, Yan J. Disturbance-free rapid solution exchange for magnetic tweezers single-molecule studies. Nucleic Acids Res 2015; 43:e113. [PMID: 26007651 PMCID: PMC4787821 DOI: 10.1093/nar/gkv554] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/15/2015] [Indexed: 11/16/2022] Open
Abstract
Single-molecule manipulation technologies have been extensively applied to studies of the structures and interactions of DNA and proteins. An important aspect of such studies is to obtain the dynamics of interactions; however the initial binding is often difficult to obtain due to large mechanical perturbation during solution introduction. Here, we report a simple disturbance-free rapid solution exchange method for magnetic tweezers single-molecule manipulation experiments, which is achieved by tethering the molecules inside microwells (typical dimensions–diameter (D): 40–50 μm, height (H): 100 μm; H:D∼2:1). Our simulations and experiments show that the flow speed can be reduced by several orders of magnitude near the bottom of the microwells from that in the flow chamber, effectively eliminating the flow disturbance to molecules tethered in the microwells. We demonstrate a wide scope of applications of this method by measuring the force dependent DNA structural transitions in response to solution condition change, and polymerization dynamics of RecA on ssDNA/SSB-coated ssDNA/dsDNA of various tether lengths under constant forces, as well as the dynamics of vinculin binding to α-catenin at a constant force (< 5 pN) applied to the α-catenin protein.
Collapse
Affiliation(s)
- Shimin Le
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Mingxi Yao
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Jin Chen
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Artem K Efremov
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Sara Azimi
- Department of Physics, National University of Singapore, 117542, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore Department of Physics, National University of Singapore, 117542, Singapore Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
| |
Collapse
|
14
|
Le S, Chen H, Zhang X, Chen J, Patil KN, Muniyappa K, Yan J. Mechanical force antagonizes the inhibitory effects of RecX on RecA filament formation in Mycobacterium tuberculosis. Nucleic Acids Res 2014; 42:11992-9. [PMID: 25294832 PMCID: PMC4231760 DOI: 10.1093/nar/gku899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/08/2014] [Accepted: 09/17/2014] [Indexed: 11/13/2022] Open
Abstract
Efficient bacterial recombinational DNA repair involves rapid cycles of RecA filament assembly and disassembly. The RecX protein plays a crucial inhibitory role in RecA filament formation and stability. As the broken ends of DNA are tethered during homologous search, RecA filaments assembled at the ends are likely subject to force. In this work, we investigated the interplay between RecX and force on RecA filament formation and stability. Using magnetic tweezers, at single molecular level, we found that Mycobacterium tuberculosis (Mt) RecX could catalyze stepwise de-polymerization of preformed MtRecA filament in the presence of ATP hydrolysis at low forces (<7 pN). However, applying larger forces antagonized the inhibitory effects of MtRecX, and a partially de-polymerized MtRecA filament could re-polymerize in the presence of MtRecX, which cannot be explained by previous models. Theoretical analysis of force-dependent conformational free energies of naked ssDNA and RecA nucleoprotein filament suggests that mechanical force stabilizes RecA filament, which provides a possible mechanism for the observation. As the antagonizing effect of force on the inhibitory function of RecX takes place in a physiological range; these findings broadly suggest a potential mechanosensitive regulation during homologous recombination.
Collapse
Affiliation(s)
- Shimin Le
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore Department of Physics, Xiamen University, Xiamen 361005, China
| | - Xinghua Zhang
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, National University of Singapore, Singapore 138602, Singapore
| | - Jin Chen
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | | | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore Department of Physics, National University of Singapore, Singapore 117542, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore 117557, Singapore
| |
Collapse
|
15
|
Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction. J Biol Chem 2014; 289:34325-40. [PMID: 25324543 DOI: 10.1074/jbc.m114.608596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.
Collapse
Affiliation(s)
| | | | - Apoorva Ravishankar
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|