1
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Dong HL, Zhang C, Dai L, Zhang Y, Zhang XH, Tan ZJ. The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations. Nucleic Acids Res 2024; 52:2519-2529. [PMID: 38321947 PMCID: PMC10954459 DOI: 10.1093/nar/gkae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.
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Affiliation(s)
- Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
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2
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Abdel Hakiem AF, El-Sagheir AMK, Draz ME, Mohamed NA, Aboraia AS. Assessment of binding interaction to salmon sperm DNA of two antiviral agents and ecofriendly nanoparticles: comprehensive spectroscopic study. BMC Chem 2023; 17:39. [PMID: 37076904 PMCID: PMC10114480 DOI: 10.1186/s13065-023-00952-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
The direct binding of antiviral agents; Daclatasvir and valacyclovir and green synthesized nanoparticles to salmon sperm DNA have been assessed in a comparative study. The nanoparticles were synthesized by the hydrothermal autoclave method and have been fully characterized. The interactive behavior and competitive binding of the analytes to DNA in addition to the thermodynamic properties were deeply investigated by the UV-visible spectroscopy. The binding constants were monitored in the physiological pH conditions to be 1.65 × 106, 4.92 × 105 and 3.12 × 105 for daclatasvir,valacyclovir and quantum dots, respectively. The significant changes in the spectral features of all analytes have proven intercalative binding. The competitive study has confirmed that, daclatasvir, valacyclovir, and the quantum dots have exhibited groove binding. All analytes have shown good entropy and enthalpy values indicating stable interactions. The electrostatic and non-electrostatic kinetic parameters have been determined through studying the binding interactions at different concentrations of KCl solutions. A molecular modelling study has been applied to demonstrate the binding interactions and their mechanisms. The obtained results were complementary and afforded new eras for the therapeutic applications.
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Affiliation(s)
- Ahmed Faried Abdel Hakiem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, South Valley University, Qena, 83523, Egypt.
| | | | - Mohammed E Draz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, 11152, Egypt
| | - Niveen A Mohamed
- Department of Pharmaceutical Chemistry, Unaizah College of Pharmacy, Qassim University, Unaizah, 5888, Saudi Arabia
| | - Ahmed Safwat Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71516, Egypt
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3
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Mondal A, Bhattacherjee A. Understanding protein diffusion on force-induced stretched DNA conformation. Front Mol Biosci 2022; 9:953689. [PMID: 36545509 PMCID: PMC9760818 DOI: 10.3389/fmolb.2022.953689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/22/2022] [Indexed: 12/11/2022] Open
Abstract
DNA morphology is subjected to environmental conditions and is closely coupled with its function. For example, DNA experiences stretching forces during several biological processes, including transcription and genome transactions, that significantly alter its conformation from that of B-DNA. Indeed, a well-defined 1.5 times extended conformation of dsDNA, known as Σ-DNA, has been reported in DNA complexes with proteins such as Rad51 and RecA. A striking feature in Σ-DNA is that the nucleobases are partitioned into triplets of three locally stacked bases separated by an empty rise gap of ∼ 5 Å. The functional role of such a DNA base triplet was hypothesized to be coupled with the ease of recognition of DNA bases by DNA-binding proteins (DBPs) and the physical origin of three letters (codon/anti-codon) in the genetic code. However, the underlying mechanism of base-triplet formation and the ease of DNA base-pair recognition by DBPs remain elusive. To investigate, here, we study the diffusion of a protein on a force-induced stretched DNA using coarse-grained molecular dynamics simulations. Upon pulling at the 3' end of DNA by constant forces, DNA exhibits a conformational transition from B-DNA to a ladder-like S-DNA conformation via Σ-DNA intermediate. The resulting stretched DNA conformations exhibit non-uniform base-pair clusters such as doublets, triplets, and quadruplets, of which triplets are energetically more stable than others. We find that protein favors the triplet formation compared to its unbound form while interacting non-specifically along DNA, and the relative population of it governs the ruggedness of the protein-DNA binding energy landscape and enhances the efficiency of DNA base recognition. Furthermore, we analyze the translocation mechanism of a DBP under different force regimes and underscore the significance of triplet formation in regulating the facilitated diffusion of protein on DNA. Our study, thus, provides a plausible framework for understanding the structure-function relationship between triplet formation and base recognition by a DBP and helps to understand gene regulation in complex regulatory processes.
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4
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Strzałka A, Kois-Ostrowska A, Kędra M, Łebkowski T, Bieniarz G, Szafran MJ, Jakimowicz D. Enhanced binding of an HU homologue under increased DNA supercoiling preserves chromosome organisation and sustains Streptomyces hyphal growth. Nucleic Acids Res 2022; 50:12202-12216. [PMID: 36420903 PMCID: PMC9756944 DOI: 10.1093/nar/gkac1093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
Bacterial chromosome topology is controlled by topoisomerases and nucleoid-associated proteins (NAPs). While topoisomerases regulate DNA supercoiling, NAPs introduce bends or coat DNA upon its binding, affecting DNA loop formation. Streptomyces, hyphal, multigenomic bacteria known for producing numerous clinically important compounds, use the highly processive topoisomerase I (TopA) to remove excessive negative DNA supercoils. Elongated vegetative Streptomyces cells contain multiple copies of their linear chromosome, which remain relaxed and relatively evenly distributed. Here, we explored how TopA cooperates with HupA, an HU homologue that is the most abundant Streptomyces NAP. We verified that HupA has an increased affinity for supercoiled DNA in vivo and in vitro. Analysis of mutant strains demonstrated that HupA elimination is detrimental under high DNA supercoiling conditions. The absence of HupA, combined with decreased TopA levels, disrupted chromosome distribution in hyphal cells, eventually inhibiting hyphal growth. We concluded that increased HupA binding to DNA under elevated chromosome supercoiling conditions is critical for the preservation of chromosome organisation.
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Affiliation(s)
| | - Agnieszka Kois-Ostrowska
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Magda Kędra
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Tomasz Łebkowski
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Grażyna Bieniarz
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Marcin J Szafran
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Molecular Microbiology Department, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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5
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Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
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6
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Yan Y, Xu W, Kumar S, Zhang A, Leng F, Dunlap D, Finzi L. Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time. Nucleic Acids Res 2021; 49:11550-11559. [PMID: 34723343 PMCID: PMC8599721 DOI: 10.1093/nar/gkab946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
Protein-mediated DNA looping is fundamental to gene regulation and such loops occur stochastically in purified systems. Additional proteins increase the probability of looping, but these probabilities maintain a broad distribution. For example, the probability of lac repressor-mediated looping in individual molecules ranged 0–100%, and individual molecules exhibited representative behavior only in observations lasting an hour or more. Titrating with HU protein progressively compacted the DNA without narrowing the 0–100% distribution. Increased negative supercoiling produced an ensemble of molecules in which all individual molecules more closely resembled the average. Furthermore, in only 12 min of observation, well within the doubling time of the bacterium, most molecules exhibited the looping probability of the ensemble. DNA supercoiling, an inherent feature of all genomes, appears to impose time-constrained, emergent behavior on otherwise random molecular activity.
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Affiliation(s)
- Yan Yan
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Sandip Kumar
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Alexander Zhang
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA 30322, USA
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7
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Zeng Q, Gao Y, Yu H, Zhu W, Wang Q, Long Q, Fan Z, Xiao B. Stick, stretch, and scan imaging method for DNA and filaments. RSC Adv 2021; 11:36060-36065. [PMID: 35492749 PMCID: PMC9043539 DOI: 10.1039/d1ra07067c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022] Open
Abstract
Biomolecules and organelles usually undergo changes to their structure or form as a result of mechanical stretching or stimulation. It is critical to be able to observe these changes and responses, which trigger mechano-chemical coupling or signal transduction. Advanced techniques have been developed to observe structure and form during manipulation; however, these require sophisticated methods. We have developed a simple approach to observe fine structure after stretching without fluorophore labeling. DNAs or molecules on the cell surface were bound to magnetic microbeads, followed by stretching with a magnetic field. After fixing, staining, and drying, the samples were examined by scanning electron microscopy with no need to build a functional surface with complex processes. Straight DNAs were observed rather than random-walk-like loose polymers. In our cellular experiment, the magnetic beads were bound to a Jurkat cell and formed a rosette which was later stuck to the substrate. A 41.3 μm filament on the base of a filopodium was pulled out via integrin from a cell. Therefore, our method can reveal long structures up to hundreds of micrometers at nanometer resolution after stretching or twisting. Our approach could have wide applications in structure–function studies of biomolecules, and in mechanobiology and cell biology when diffraction cannot used. Magnetic force was applied to stretch single DNAs and cells which were stuck to magnetic beads and substrates via simple conjugation methods. Scanning electron microscopy images show that the filopodia of cells were pulled to extraordinary length.![]()
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Affiliation(s)
- Qiuling Zeng
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Yuanyuan Gao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Hong Yu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Wei Zhu
- Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Qi Wang
- Artemisinin Research Center, Guangzhou University of Chinese Medicine Guangzhou Guangdong 510405 China.,Institute of Science and Technology, Guangzhou University of Chinese Medicine Guangzhou Guangdong 510006 China
| | - Quan Long
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Zhuo Fan
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
| | - Botao Xiao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China .,Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology Guangzhou 510006 China
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8
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Lin SN, Dame RT, Wuite GJL. Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions. Sci Rep 2021; 11:18492. [PMID: 34531428 PMCID: PMC8446073 DOI: 10.1038/s41598-021-97763-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.
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Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. .,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. .,LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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9
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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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10
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Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 PMCID: PMC7889641 DOI: 10.1038/s41467-021-21181-9] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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11
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Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, George-Hyslop PS, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 DOI: 10.1101/2020.05.04.076299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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Affiliation(s)
- Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Jorge R Espinosa
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Ella de Csilléry
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Akshay Sridhar
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giedre Gudiškytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jordina Guillén-Boixet
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| | - Rosana Collepardo-Guevara
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
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12
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Lin SN, Wuite GJ, Dame RT. Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU. Int J Mol Sci 2020; 21:ijms21249553. [PMID: 33334011 PMCID: PMC7765392 DOI: 10.3390/ijms21249553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out in a simple in vitro system, and to what extent these observations can be extrapolated to a living cell is unclear. In this study, we investigate the DNA binding properties of HU under conditions approximating physiological ones. We report that these properties are influenced by both macromolecular crowding and salt conditions. We use three different crowding agents (blotting grade blocker (BGB), bovine serum albumin (BSA), and polyethylene glycol 8000 (PEG8000)) as well as two different MgCl2 conditions to mimic the intracellular environment. Using tethered particle motion (TPM), we show that the transition between two binding regimes, compaction and extension of the HU protein, is strongly affected by crowding agents. Our observations suggest that magnesium ions enhance the compaction of HU–DNA and suppress filamentation, while BGB and BSA increase the local concentration of the HU protein by more than 4-fold. Moreover, BGB and BSA seem to suppress filament formation. On the other hand, PEG8000 is not a good crowding agent for concentrations above 9% (w/v), because it might interact with DNA, the protein, and/or surfaces. Together, these results reveal a complex interplay between the HU protein and the various crowding agents that should be taken into consideration when using crowding agents to mimic an in vivo system.
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Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J.L. Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Correspondence: (G.J.L.W.); (R.T.D.)
| | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Centre for Microbial Cell Biology, Leiden University, 2333 CC Leiden, The Netherlands
- Correspondence: (G.J.L.W.); (R.T.D.)
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13
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Dahlke K, Sing CE. Influence of Nucleoid-Associated Proteins on DNA Supercoiling. J Phys Chem B 2019; 123:10152-10162. [PMID: 31710235 DOI: 10.1021/acs.jpcb.9b07436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
DNA supercoiling, where the DNA strand forms a writhe to relieve torsional stress, plays a vital role in packaging the genetic material in cells. Experiment, simulation, and theory have all demonstrated how supercoiling emerges due to the over- or underwinding of the DNA strand. Nucleoid-associated proteins (NAPs) help structure DNA in prokaryotes, yet the role that they play in the supercoiling process has not been as thoroughly investigated. We develop a coarse-grained simulation to model DNA supercoiling in the presence of proteins, providing a rigorous physical understanding of how NAPs affect supercoiling behavior. Specifically, we demonstrate how the force and torque necessary to form supercoils are affected by the presence of NAPs. NAPs that bend DNA stabilize the supercoil, thus shifting the transition between extended and supercoiled DNAs. We develop a theory to explain how NAP binding affects DNA supercoiling. This provides insight into how NAPs modulate DNA compaction via a combination of supercoiling and local protein-dependent deformations.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
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14
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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15
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Marko JF, De Los Rios P, Barducci A, Gruber S. DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes. Nucleic Acids Res 2019; 47:6956-6972. [PMID: 31175837 PMCID: PMC6649773 DOI: 10.1093/nar/gkz497] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 05/20/2019] [Accepted: 06/06/2019] [Indexed: 01/08/2023] Open
Abstract
Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a 'loop extrusion' process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor 'track'-in this case DNA-are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with 'stalling' occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (Escherichia coli MukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.
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Affiliation(s)
- John F Marko
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Paolo De Los Rios
- Laboratory of Statistical Biophysics, Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Switzerland
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
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16
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Yan Y, Leng F, Finzi L, Dunlap D. Protein-mediated looping of DNA under tension requires supercoiling. Nucleic Acids Res 2019; 46:2370-2379. [PMID: 29365152 PMCID: PMC5861448 DOI: 10.1093/nar/gky021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023] Open
Abstract
Protein-mediated DNA looping is ubiquitous in chromatin organization and gene regulation, but to what extent supercoiling or nucleoid associated proteins promote looping is poorly understood. Using the lac repressor (LacI), a paradigmatic loop-mediating protein, we measured LacI-induced looping as a function of either supercoiling or the concentration of the HU protein, an abundant nucleoid protein in Escherichia coli. Negative supercoiling to physiological levels with magnetic tweezers easily drove the looping probability from 0 to 100% in single DNA molecules under slight tension that likely exists in vivo. In contrast, even saturating (micromolar) concentrations of HU could not raise the looping probability above 30% in similarly stretched DNA or 80% in DNA without tension. Negative supercoiling is required to induce significant looping of DNA under any appreciable tension.
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Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
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17
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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18
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Oliveira Paiva AM, Friggen AH, Qin L, Douwes R, Dame RT, Smits WK. The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile. J Mol Biol 2019; 431:653-672. [PMID: 30633871 DOI: 10.1016/j.jmb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022]
Abstract
The maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA and modulate its conformation, and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of Clostridium difficile have been characterized to date. Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10-kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G + C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo. The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.
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Affiliation(s)
- Ana M Oliveira Paiva
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Annemieke H Friggen
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Liang Qin
- Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Roxanne Douwes
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remus T Dame
- Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands.
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19
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Rigidification of the Escherichia coli cytoplasm by the human antimicrobial peptide LL-37 revealed by superresolution fluorescence microscopy. Proc Natl Acad Sci U S A 2018; 116:1017-1026. [PMID: 30598442 PMCID: PMC6338858 DOI: 10.1073/pnas.1814924116] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Natural antimicrobial peptides (AMPs) that exhibit broad-spectrum antibacterial activity are often highly positively charged. Fluorescence microscopy shows that after permeabilization of Escherichia coli membranes by the cationic AMP LL-37 a massive influx of peptide freezes the diffusive motion of the chromosomal DNA and a subset of ribosomes. Both are highly negatively charged. Cells cannot recover growth. We suggest that LL-37 forms noncovalent, electrostatic linkages between DNA strands and among polyribosomes, rigidifying the entire cytoplasm. While the preponderance of polyanionic biopolymers in the cytoplasm facilitates diffusion in normal growth, this same characteristic renders the bacterium highly susceptible to attack by polycationic AMPs. The results help explain why bacteria develop resistance to AMPs very slowly and may inform the design of new antibacterial agents. Superresolution, single-particle tracking reveals effects of the cationic antimicrobial peptide LL-37 on the Escherichia coli cytoplasm. Seconds after LL-37 penetrates the cytoplasmic membrane, the chromosomal DNA becomes rigidified on a length scale of ∼30 nm, evidenced by the loss of jiggling motion of specific DNA markers. The diffusive motion of a subset of ribosomes is also frozen. The mean diffusion coefficients of the DNA-binding protein HU and the nonendogenous protein Kaede decrease twofold. Roughly 108 LL-37 copies flood the cell (mean concentration ∼90 mM). Much of the LL-37 remains bound within the cell after extensive rinsing with fresh growth medium. Growth never recovers. The results suggest that the high concentration of adsorbed polycationic peptides forms a dense network of noncovalent, electrostatic linkages within the chromosomal DNA and among 70S-polysomes. The bacterial cytoplasm comprises a concentrated collection of biopolymers that are predominantly polyanionic (e.g., DNA, ribosomes, RNA, and most globular proteins). In normal cells, this provides a kind of electrostatic lubrication, enabling facile diffusion despite high biopolymer volume fraction. However, this same polyanionic nature renders the cytoplasm susceptible to massive adsorption of polycationic agents once penetration of the membranes occurs. If this phenomenon proves widespread across cationic agents and bacterial species, it will help explain why resistance to antimicrobial peptides develops only slowly. The results suggest two design criteria for polycationic peptides that efficiently kill gram-negative bacteria: facile penetration of the outer membrane and the ability to alter the cytoplasm by electrostatically linking double-stranded DNA and 70S-polysomes.
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20
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Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B 2018; 122:11519-11534. [DOI: 10.1021/acs.jpcb.8b07405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Aline Arra
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Phoebe A. Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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21
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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.
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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
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22
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Dahlke K, Sing CE. Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins. J Chem Phys 2018; 148:084902. [PMID: 29495783 DOI: 10.1063/1.5016177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.
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Affiliation(s)
- K Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - C E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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23
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Abstract
Nucleoid-associated proteins (NAPs) are important factors in shaping bacterial nucleoid and regulating global gene expression. A great deal of insights into NAPs can be obtained through studies using single DNA molecule, which has been made possible owing to recent rapid development of single-DNA manipulation techniques. These studies provide information on modes of binding to DNA, which shed light on the mechanism underlying the regulatory function of NAPs. In addition, how NAPs organize DNA and thus their contribution to chromosomal DNA packaging can be determined. In this chapter, we introduce transverse magnetic tweezers that allows for convenient manipulation of long DNA molecules, and its applications in studies of NAPs as exemplified by the E. coli H-NS protein. We describe how transverse magnetic tweezers is a powerful tool that can be used to characterize the DNA binding and organization modes of NAPs and how such information leads to better understanding of its roles in DNA packaging of bacterial nucleoid and transcription regulation.
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24
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Guttula D, Liu F, van Kan JA, Arluison V, van der Maarel JRC. Effect of HU protein on the conformation and compaction of DNA in a nanochannel. SOFT MATTER 2018; 14:2322-2328. [PMID: 29457176 DOI: 10.1039/c7sm02118f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The effect of the heat unstable nucleoid structuring protein HU on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. Pre-incubated DNA molecules contract in the longitudinal direction of the channel with increasing concentration of HU. This contraction is mainly due to HU-mediated bridging of distal DNA segments and is controlled by channel diameter as well as ionic composition and strength of the buffer. For over-threshold concentrations of HU, the DNA molecules compact into an condensed form. Divalent magnesium ions facilitate, but are not required for bridging nor condensation. The conformational response following exposure to HU was investigated with a nanofluidic device that allows an in situ change in environmental solution conditions. The stretch of the nucleoprotein complex first increases, reaches an apex in ∼20 min, and subsequently decreases to an equilibrium value pertaining to pre-incubated DNA molecules after ∼2 h. This observation is rationalised in terms of a time-dependent bending rigidity by structural rearrangement of bound HU protein followed by compaction through bridging interaction. Results are discussed in regard to previous results obtained for nucleoid associated proteins H-NS and Hfq, with important implications for protein binding related gene regulation.
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Affiliation(s)
- Durgarao Guttula
- Department of Physics, National University of Singapore, Singapore 117542, Singapore.
| | - Fan Liu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore.
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore.
| | - Véronique Arluison
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France and Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
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25
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Kamagata K, Mano E, Ouchi K, Kanbayashi S, Johnson RC. High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins. J Mol Biol 2018; 430:655-667. [PMID: 29307468 DOI: 10.1016/j.jmb.2018.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 01/25/2023]
Abstract
Architectural DNA-binding proteins function to regulate diverse DNA reactions and have the defining property of significantly changing DNA conformation. Although the 1D movement along DNA by other types of DNA-binding proteins has been visualized, the mobility of architectural DNA-binding proteins on DNA remains unknown. Here, we applied single-molecule fluorescence imaging on arrays of extended DNA molecules to probe the binding dynamics of three structurally distinct architectural DNA-binding proteins: Nhp6A, HU, and Fis. Each of these proteins was observed to move along DNA, and the salt concentration independence of the 1D diffusion implies sliding with continuous contact to DNA. Nhp6A and HU exhibit a single sliding mode, whereas Fis exhibits two sliding modes. Based on comparison of the diffusion coefficients and sizes of many DNA binding proteins, the architectural proteins are categorized into a new group distinguished by an unusually high free-energy barrier for 1D diffusion. The higher free-energy barrier for 1D diffusion by architectural proteins can be attributed to the large DNA conformational changes that accompany binding and impede rotation-coupled movement along the DNA grooves.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan.
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Kana Ouchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Aoba-ku, Sendai980-8577, Japan
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA90095-1737, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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26
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Wang Y, Jia P, Sharif R, Li Z, Li Y, Chen P. High-Level Production of DNA-Specific Endonuclease AsEndI with Synonymous Codon and its Potential Utilization for Removing DNA Contamination. Appl Biochem Biotechnol 2017; 185:641-654. [PMID: 29250754 DOI: 10.1007/s12010-017-2672-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
Abstract
Endonuclease I is a widely distributed periplasmic or extracellular enzyme. A method for the high-level production of recombinant AsEndI (endonuclease I from Aliivibrio salmonicida) in Escherichia coli with secretion expression is investigated. The coding sequence of AsEndI gene was assembled according to the E. coli codon usage bias, and AsEndI was expressed in the periplasm of E. coli TOP10 with a C-terminal 6× His-tagged fusion. The recombinant AsEndI (His-AsEndI) was purified by Ni-NTA resin with a yield of 1.29 × 107 U from 1-L LB medium. His-AsEndI could be classified into Ca2+/Mg2+-dependent nucleases and showed highest nuclease activity to dsDNA at pH 8.0 and 37 °C. His-AsEndI is highly active in a broad range of salt concentration range up to 1.0 M with optimal NaCl concentration at 0.4 M. His-AsEndI can effectively remove DNA contamination in RNA sample or in PCR reagents to the level that cannot be detected by highly sensitive nested PCR and without adverse effects on the subsequent PCR reaction. His-AsEndI can remove DNA contamination at high salt conditions, especially for the DNA that may be shielded by DNA-binding protein at low salt conditions.
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Affiliation(s)
- Yuan Wang
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Peng Jia
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Rahat Sharif
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Zhengchen Li
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Yuhong Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
| | - Peng Chen
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
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27
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Liao JH, Tsai CH, Patel SG, Yang JT, Tu IF, Lo Cicero M, Lipka-Lloyd M, Wu WL, Shen WJ, Ho MR, Chou CC, Sharma GR, Okanishi H, Luk LYP, Tsai YH, Wu SH. Acetylome of Acinetobacter baumannii SK17 Reveals a Highly-Conserved Modification of Histone-Like Protein HU. Front Mol Biosci 2017; 4:77. [PMID: 29230394 PMCID: PMC5711770 DOI: 10.3389/fmolb.2017.00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/06/2017] [Indexed: 12/27/2022] Open
Abstract
Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. This work indicates that acetyllysine plays an important role in bacterial epigenetics.
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Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Tsai
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Sanjay G Patel
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Jhih-Tian Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University, Academia Sinica, Taipei, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Matteo Lo Cicero
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | | | - Wan-Ling Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Jie Shen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Garima R Sharma
- School of Chemistry, Cardiff University, Cardiff, United Kingdom.,Republic Polytechnic, Singapore, Singapore
| | - Hiroki Okanishi
- Department of Tumor Genetics and Biology, Kumamoto University, Kumamoto, Japan
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, Taiwan
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28
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Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells. Proc Natl Acad Sci U S A 2017; 114:12560-12565. [PMID: 29109287 DOI: 10.1073/pnas.1716721114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) facilitate chromosome organization in bacteria, but the precise mechanism remains elusive. H-NS is a NAP that also plays a major role in silencing pathogen genes. We used genetics, single-particle tracking in live cells, superresolution microscopy, atomic force microscopy, and molecular dynamics simulations to examine H-NS/DNA interactions in single cells. We discovered a role for the unstructured linker region connecting the N-terminal oligomerization and C-terminal DNA binding domains. In the present work we demonstrate that linker amino acids promote engagement with DNA. In the absence of linker contacts, H-NS binding is significantly reduced, although no change in chromosome compaction is observed. H-NS is not localized to two distinct foci; rather, it is scattered all around the nucleoid. The linker makes DNA contacts that are required for gene silencing, while chromosome compaction does not appear to be an important H-NS function.
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29
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Bao L, Zhang X, Shi YZ, Wu YY, Tan ZJ. Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling. Biophys J 2017; 112:1094-1104. [PMID: 28355538 DOI: 10.1016/j.bpj.2017.02.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 01/16/2023] Open
Abstract
The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be distinctively different in the aspects of stretching and twist-stretch coupling. Although various studies have been performed to understand the flexibility of dsRNA and dsDNA, there is still a lack of deep understanding of the distinctive differences in the flexibility of dsRNA and dsDNA helices as pertains to their stretching and twist-stretch coupling. In this work, we have explored the relative flexibility in stretching and twist-stretch coupling between dsRNA and dsDNA by all-atom molecular dynamics simulations. The calculated stretch modulus and twist-stretch coupling are in good accordance with the existing experiments. Our analyses show that the differences in stretching and twist-stretch coupling between dsRNA and dsDNA helices are mainly attributed to their different (A- and B-form) helical structures. Stronger basepair inclination and slide in dsRNA is responsible for the apparently weaker stretching rigidity versus that of dsDNA, and the opposite twist-stretch coupling for dsRNA and dsDNA is also attributed to the stronger basepair inclination in dsRNA than in dsDNA. Our calculated macroscopic elastic parameters and microscopic analyses are tested and validated by different force fields for both dsRNA and dsDNA.
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Affiliation(s)
- Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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30
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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31
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Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HYH, Larabell CA, Tainer JA, Adhya S. HU multimerization shift controls nucleoid compaction. SCIENCE ADVANCES 2016; 2:e1600650. [PMID: 27482541 PMCID: PMC4966879 DOI: 10.1126/sciadv.1600650] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/14/2016] [Indexed: 05/05/2023]
Abstract
Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasive Escherichia coli into an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. (M.H.); (J.A.T.)
| | - Dhar Amlanjyoti
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Francis E. Reyes
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Rochelle Parpana
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henry Y. H. Tang
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - John A. Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
- Corresponding author. (M.H.); (J.A.T.)
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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32
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Xiao B, McLean MM, Lei X, Marko JF, Johnson RC. Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase. Sci Rep 2016; 6:23697. [PMID: 27032966 PMCID: PMC4817059 DOI: 10.1038/srep23697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/14/2016] [Indexed: 11/30/2022] Open
Abstract
DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA “braiding” experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements.
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Affiliation(s)
- Botao Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Department of Physics and Astronomy, Northwestern University, Evanston IL 60208.,Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Meghan M McLean
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles CA 90095-1737
| | - Xianbin Lei
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston IL 60208.,Department of Molecular Biosciences, Northwestern University, Evanston IL 60208
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles CA 90095-1737
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33
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Song D, Graham TGW, Loparo JJ. A general approach to visualize protein binding and DNA conformation without protein labelling. Nat Commun 2016; 7:10976. [PMID: 26952553 PMCID: PMC4786781 DOI: 10.1038/ncomms10976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/08/2016] [Indexed: 01/29/2023] Open
Abstract
Single-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein–DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein–DNA interactions. Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation.
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Affiliation(s)
- Dan Song
- Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
| | - Thomas G W Graham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
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34
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Eeftens JM, van der Torre J, Burnham DR, Dekker C. Copper-free click chemistry for attachment of biomolecules in magnetic tweezers. BMC BIOPHYSICS 2015; 8:9. [PMID: 26413268 PMCID: PMC4582843 DOI: 10.1186/s13628-015-0023-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/16/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer that is anchored between a glass surface and a magnetic bead. Whereas the relevant force regime for many biological processes is above 20pN, problems arise at these higher forces, since the molecule of interest can detach from the attachment points at the surface or the bead. Whereas many recipes for attachment of biopolymers have been developed, most methods do not suffice, as the molecules break at high force, or the attachment chemistry leads to nonspecific cross reactions with proteins. RESULTS Here, we demonstrate a novel attachment method using copper-free click chemistry, where a DBCO-tagged DNA molecule is bound to an azide-functionalized surface. We use this new technique to covalently attach DNA to a flow cell surface. We show that this technique results in covalently linked tethers that are torsionally constrained and withstand very high forces (>100pN) in magnetic tweezers. CONCLUSIONS This novel anchoring strategy using copper-free click chemistry allows to specifically and covalently link biomolecules, and conduct high-force single-molecule experiments. Excitingly, this advance opens up the possibility for single-molecule experiments on DNA-protein complexes and molecules that are taken directly from cell lysate.
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Affiliation(s)
- Jorine M Eeftens
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft, Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft, Delft, The Netherlands
| | - Daniel R Burnham
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft, Delft, The Netherlands
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35
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DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response. J Mol Biol 2015. [PMID: 26220077 DOI: 10.1016/j.jmb.2015.07.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rate of dissociation of a DNA-protein complex is often considered to be a property of that complex, without dependence on other nearby molecules in solution. We study the kinetics of dissociation of the abundant Escherichia coli nucleoid protein Fis from DNA, using a single-molecule mechanics assay. The rate of Fis dissociation from DNA is strongly dependent on the solution concentration of DNA. The off-rate (k(off)) of Fis from DNA shows an initially linear dependence on solution DNA concentration, characterized by an exchange rate of k(ex)≈9×10(-4) (ng/μl)(-1) s(-1) for 100 mM univalent salt buffer, with a very small off-rate at zero DNA concentration. The off-rate saturates at approximately k(off,max)≈8×10(-3) s(-1) for DNA concentrations above ≈20 ng/μl. This exchange reaction depends mainly on DNA concentration with little dependence on the length of the DNA molecules in solution or on binding affinity, but this does increase with increasing salt concentration. We also show data for the yeast HMGB protein NHP6A showing a similar DNA-concentration-dependent dissociation effect, with faster rates suggesting generally weaker DNA binding by NHP6A relative to Fis. Our results are well described by a model with an intermediate partially dissociated state where the protein is susceptible to being captured by a second DNA segment, in the manner of "direct transfer" reactions studied for other DNA-binding proteins. This type of dissociation pathway may be important to protein-DNA binding kinetics in vivo where DNA concentrations are large.
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36
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Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells. Nat Commun 2015; 6:7445. [PMID: 26145755 PMCID: PMC4507017 DOI: 10.1038/ncomms8445] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 05/11/2015] [Indexed: 02/04/2023] Open
Abstract
Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle. Binding and unbinding of transcription regulators at operator sites regulates gene expression. By single-molecule tracking of metal-sensing regulators, here the authors show that the unbinding kinetics depends on regulator concentration and chromosome condensation, and varies with their metal-binding states.
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37
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Feldmann EA, Galletto R. The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes. Biochemistry 2014; 53:7471-83. [PMID: 25382181 PMCID: PMC4263426 DOI: 10.1021/bi501049b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Saccharomyces cerevisiae repressor-activator protein
1 (Rap1) is an essential protein involved in multiple steps of DNA
regulation, as an activator in transcription, as a repressor at silencer
elements, and as a major component of the shelterin-like complex at
telomeres. All the known functions of Rap1 require the known high-affinity
and specific interaction of the DNA-binding domain with its recognition
sequences. In this work, we focus on the interaction of the DNA-binding
domain of Rap1 (Rap1DBD) with double-stranded DNA substrates.
Unexpectedly, we found that while Rap1DBD forms a high-affinity
1:1 complex with its DNA recognition site, it can also form lower-affinity
complexes with higher stoichiometries on DNA. These lower-affinity
interactions are independent of the presence of the recognition sequence,
and we propose they originate from the ability of Rap1DBD to bind to DNA in two different binding modes. In one high-affinity
binding mode, Rap1DBD likely binds in the conformation
observed in the available crystal structures. In the other alternative
lower-affinity binding mode, we propose that a single Myb-like domain
of the Rap1DBD makes interactions with DNA, allowing for
more than one protein molecule to bind to the DNA substrates. Our
findings suggest that the Rap1DBD does not simply target
the protein to its recognition sequence but rather it might be a possible
point of regulation.
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Affiliation(s)
- Erik A Feldmann
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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38
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Lim CJ, Kenney LJ, Yan J. Single-molecule studies on the mechanical interplay between DNA supercoiling and H-NS DNA architectural properties. Nucleic Acids Res 2014; 42:8369-78. [PMID: 24990375 PMCID: PMC4117784 DOI: 10.1093/nar/gku566] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Escherichia coli H-NS protein is a major nucleoid-associated protein that is involved in chromosomal DNA packaging and gene regulatory functions. These biological processes are intimately related to the DNA supercoiling state and thus suggest a direct relationship between H-NS binding and DNA supercoiling. Here, we show that H-NS, which has two distinct DNA-binding modes, is able to differentially regulate DNA supercoiling. H-NS DNA-stiffening mode caused by nucleoprotein filament formation is able to suppress DNA plectoneme formation during DNA supercoiling. In contrast, when H-NS is in its DNA-bridging mode, it is able to promote DNA plectoneme formation during DNA supercoiling. In addition, the DNA-bridging mode is able to block twists diffusion thus trapping DNA in supercoiled domains. Overall, this work reveals the mechanical interplay between H-NS and DNA supercoiling which provides insights to H-NS organization of chromosomal DNA based on its two distinct DNA architectural properties.
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Affiliation(s)
- Ci Ji Lim
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, Singapore Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, USA Department of Biological Sciences, National University of Singapore, Singapore
| | - Jie Yan
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
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39
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Graham TGW, Wang X, Song D, Etson CM, van Oijen AM, Rudner DZ, Loparo JJ. ParB spreading requires DNA bridging. Genes Dev 2014; 28:1228-38. [PMID: 24829297 PMCID: PMC4052768 DOI: 10.1101/gad.242206.114] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The bacterial parABS system is employed for plasmid partitioning and chromosome segregation. ParB binds to parS sites and associates with broad regions of adjacent DNA, a phenomenon known as spreading. However, the molecular basis for spreading is unknown. Using single-molecule approaches, Graham et al. demonstrate DNA bridging by B. subtilis ParB (Spo0J). Spo0J mutations that disrupt DNA bridging lead to defective spreading and SMC condensin complex recruitment. This study suggests a novel, conserved mechanism by which ParB proteins function in chromosome organization and segregation. The parABS system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. ParB binds to parS sites on plasmids and chromosomes and associates with broad regions of adjacent DNA, a phenomenon known as spreading. Although essential for ParB function, the mechanism of spreading remains poorly understood. Using single-molecule approaches, we discovered that Bacillus subtilis ParB (Spo0J) is able to trap DNA loops. Point mutants in Spo0J that disrupt DNA bridging are defective in spreading and recruitment of structural maintenance of chromosomes (SMC) condensin complexes in vivo. DNA bridging helps to explain how a limited number of Spo0J molecules per parS site (∼20) can spread over many kilobases and suggests a mechanism by which ParB proteins could facilitate the loading of SMC complexes. We show that DNA bridging is a property of diverse ParB homologs, suggesting broad evolutionary conservation.
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Affiliation(s)
- Thomas G W Graham
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dan Song
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Candice M Etson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Antoine M van Oijen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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40
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Sing CE, Olvera de la Cruz M, Marko JF. Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. Nucleic Acids Res 2014; 42:3783-91. [PMID: 24393773 PMCID: PMC3973338 DOI: 10.1093/nar/gkt1327] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent work has demonstrated concentration-dependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (2011) (Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res., 39:2249)]. The physical origin of this concentration-dependence is unexplained. We use a combination of coarse-grained simulation and theory to demonstrate that this behavior can be explained by taking into account the dimeric nature of the protein, which permits partial dissociation and exchange with other proteins in solution. Concentration-dependent unbinding is generated by this simple model, quantitatively explaining experimental data. This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules.
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Affiliation(s)
- Charles E Sing
- Department of Materials Science, Northwestern University, 2220 Cook Dr. Evanston, IL 60208, USA, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA and Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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41
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Landy J, Lee Y, Jho Y. Limiting law excess sum rule for polyelectrolytes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052315. [PMID: 24329272 DOI: 10.1103/physreve.88.052315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 09/10/2013] [Indexed: 06/03/2023]
Abstract
We revisit the mean-field limiting law screening excess sum rule that holds for rodlike polyelectrolytes. We present an efficient derivation of this law that clarifies its region of applicability: The law holds in the limit of small polymer radius, measured relative to the Debye screening length. From the limiting law, we determine the individual ion excess values for single-salt electrolytes. We also consider the mean-field excess sum away from the limiting region, and we relate this quantity to the osmotic pressure of a dilute polyelectrolyte solution. Finally, we consider numerical simulations of many-body polymer-electrolyte solutions. We conclude that the limiting law often accurately describes the screening of physical charged polymers of interest, such as extended DNA.
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Affiliation(s)
- Jonathan Landy
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - YongJin Lee
- Department of Physics, POSTECH, Pohang 790-784, South Korea and Asia-Pacific Center for Theoretical Physics, Pohang 790-784, South Korea
| | - YongSeok Jho
- Department of Physics, POSTECH, Pohang 790-784, South Korea and Asia-Pacific Center for Theoretical Physics, Pohang 790-784, South Korea
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42
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Parsaeian A, de la Cruz MO, Marko JF. Binding-rebinding dynamics of proteins interacting nonspecifically with a long DNA molecule. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:040703. [PMID: 24229102 PMCID: PMC3894571 DOI: 10.1103/physreve.88.040703] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Indexed: 06/01/2023]
Abstract
We investigate how nonspecific interactions and unbinding-rebinding events give rise to a length- and conformation-dependent enhancement of the "macroscopic" dissociation time of proteins from a DNA, or in general for the release of ligands initially bound to a long polymer. By numerically simulating the release of ligands from polymers of different conformations, we show that the total dissociation time increases logarithmically with polymer length for an extended conformation, and as a power law for self-avoiding and compact conformations. For the latter two cases, the presence of self-avoidance acting between the diffusing ligands affects the power-law exponents. Our results are important in relating kinetic measurements of protein on- and off-rates for large DNAs to equilibrium affinities for a single binding site.
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Affiliation(s)
- Azita Parsaeian
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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43
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Kundukad B, Cong P, van der Maarel JRC, Doyle PS. Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein. Nucleic Acids Res 2013; 41:8280-8. [PMID: 23828037 PMCID: PMC3783175 DOI: 10.1093/nar/gkt593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA-HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ∼2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.
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Affiliation(s)
- Binu Kundukad
- BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore-Massachusetts Institute of Technology Alliance, National University of Singapore, Singapore 117576, Department of Physics, National University of Singapore, Singapore 117542 and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Driessen RPC, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar UD, White MF, Schiessel H, van Noort J, Dame RT. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Res 2012; 41:196-205. [PMID: 23155062 PMCID: PMC3592393 DOI: 10.1093/nar/gks1053] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
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45
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Lin J, Chen H, Dröge P, Yan J. Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF). PLoS One 2012; 7:e49885. [PMID: 23166787 PMCID: PMC3498176 DOI: 10.1371/journal.pone.0049885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.
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Affiliation(s)
- Jie Lin
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Peter Dröge
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PD); (JY)
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (PD); (JY)
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46
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McCauley MJ, Rueter EM, Rouzina I, Maher LJ, Williams MC. Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. Nucleic Acids Res 2012; 41:167-81. [PMID: 23143110 PMCID: PMC3592474 DOI: 10.1093/nar/gks1031] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (∼10 s−1) are higher than those observed for wild-type proteins (∼0.1–1.0 s−1), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB–DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility.
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Affiliation(s)
- Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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47
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Xiao B, Freedman BS, Miller KE, Heald R, Marko JF. Histone H1 compacts DNA under force and during chromatin assembly. Mol Biol Cell 2012; 23:4864-71. [PMID: 23097493 PMCID: PMC3521692 DOI: 10.1091/mbc.e12-07-0518] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Histone H1 binds to linker DNA between nucleosomes, but the dynamics and biological ramifications of this interaction remain poorly understood. We performed single-molecule experiments using magnetic tweezers to determine the effects of H1 on naked DNA in buffer or during chromatin assembly in Xenopus egg extracts. In buffer, nanomolar concentrations of H1 induce bending and looping of naked DNA at stretching forces below 0.6 pN, effects that can be reversed with 2.7-pN force or in 200 mM monovalent salt concentrations. Consecutive tens-of-nanometer bending events suggest that H1 binds to naked DNA in buffer at high stoichiometries. In egg extracts, single DNA molecules assemble into nucleosomes and undergo rapid compaction. Histone H1 at endogenous physiological concentrations increases the DNA compaction rate during chromatin assembly under 2-pN force and decreases it during disassembly under 5-pN force. In egg cytoplasm, histone H1 protects sperm nuclei undergoing genome-wide decondensation and chromatin assembly from becoming abnormally stretched or fragmented due to astral microtubule pulling forces. These results reveal functional ramifications of H1 binding to DNA at the single-molecule level and suggest an important physiological role for H1 in compacting DNA under force and during chromatin assembly.
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Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
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48
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Physical manipulation of the Escherichia coli chromosome reveals its soft nature. Proc Natl Acad Sci U S A 2012; 109:E2649-56. [PMID: 22984156 DOI: 10.1073/pnas.1208689109] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique "micropiston" and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 10(5) k(B)T are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction-decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.
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49
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De Vlaminck I, Henighan T, van Loenhout MTJ, Burnham DR, Dekker C. Magnetic forces and DNA mechanics in multiplexed magnetic tweezers. PLoS One 2012; 7:e41432. [PMID: 22870220 PMCID: PMC3411724 DOI: 10.1371/journal.pone.0041432] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/26/2012] [Indexed: 12/02/2022] Open
Abstract
Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization where large numbers of molecules (say 103) are addressed in the same amount of time required by a single-molecule measurement. We apply offline analysis of recorded images and show that this approach provides a scalable solution for parallel tracking of the xyz-positions of many beads simultaneously. We employ a large field-of-view imaging system to address many DNA-bead tethers in parallel. We model the 3D magnetic field generated by the magnets and derive the magnetic force experienced by DNA-bead tethers across the large field of view from first principles. We furthermore experimentally demonstrate that a DNA-bead tether subject to a rotating magnetic field describes a bicircular, Limaçon rotation pattern and that an analysis of this pattern simultaneously yields information about the force angle and the position of attachment of the DNA on the bead. Finally, we apply MMT in the high-throughput investigation of the distribution of the induced magnetic moment, the position of attachment of DNA on the beads, and DNA flexibility. The methods described herein pave the way to kilo-molecule level magnetic tweezers experiments.
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Affiliation(s)
- Iwijn De Vlaminck
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Thomas Henighan
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Daniel R. Burnham
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- * E-mail:
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50
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Landy J, McIntosh DB, Saleh OA. Quantifying screening ion excesses in single-molecule force-extension experiments. PHYSICAL REVIEW LETTERS 2012; 109:048301. [PMID: 23006113 DOI: 10.1103/physrevlett.109.048301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Indexed: 06/01/2023]
Abstract
We derive a thermodynamic identity that allows one to infer the change in the number of screening ions that are associated with a charged macromolecule as the macromolecule is continuously stretched. Applying this identity to force-extension data on both single-stranded and double-stranded DNA, we find that the number of polymer-associated ions depends nontrivially on both the bulk salt concentration and the bare rigidity of the polymer, with single-stranded DNA exhibiting a relatively large decrease in ion excess upon stretching. We rationalize these observations using simple models for polyelectrolyte extension.
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Affiliation(s)
- Jonathan Landy
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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