1
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Herling TW, Cassaignau AME, Wentink AS, Peter QAE, Kumar PC, Kartanas T, Schneider MM, Cabrita LD, Christodoulou J, Knowles TPJ. Thermodynamic profiles for cotranslational trigger factor substrate recognition. SCIENCE ADVANCES 2024; 10:eadn4824. [PMID: 38985872 PMCID: PMC11235164 DOI: 10.1126/sciadv.adn4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Molecular chaperones are central to the maintenance of proteostasis in living cells. A key member of this protein family is trigger factor (TF), which acts throughout the protein life cycle and has a ubiquitous role as the first chaperone encountered by proteins during synthesis. However, our understanding of how TF achieves favorable interactions with such a diverse substrate base remains limited. Here, we use microfluidics to reveal the thermodynamic determinants of this process. We find that TF binding to empty 70S ribosomes is enthalpy-driven, with micromolar affinity, while nanomolar affinity is achieved through a favorable entropic contribution for both intrinsically disordered and folding-competent nascent chains. These findings suggest a general mechanism for cotranslational TF function, which relies on occupation of the exposed TF-substrate binding groove rather than specific complementarity between chaperone and nascent chain. These insights add to our wider understanding of how proteins can achieve broad substrate specificity.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Anaïs M. E. Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Anne S. Wentink
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Quentin A. E. Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pavan C. Kumar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tadas Kartanas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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2
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Cutri A, Shrout JD, Bohn PW. Metabolic and Oxidative Stress Effects on the Spectroelectrochemical Behavior of Single Pseudomonas aeruginosa Cells. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:659-666. [PMID: 37886305 PMCID: PMC10598847 DOI: 10.1021/cbmi.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen capable of causing a wide range of diseases in immunocompromised patients. In order to better understand P. aeruginosa behavior and virulence and to advance drug therapies to combat infection, it would be beneficial to understand how P. aeruginosa cells survive stressful conditions, especially environmental stressors. Here, we report on a strategy that measures potential-dependent fluorescence of individual P. aeruginosa cells, as a sentinel, for cellular response to starvation, hunger, and oxidative stress. This is accomplished using a micropore electrode array capable of trapping large numbers of isolated, vertically oriented cells at well-defined spatial positions in order to study large arrays of single cells in parallel. We find that conditions promoting either starvation or oxidative stress produce discernible changes in the fluorescence response, demonstrated by an increase in the prevalence of fluorescence transients, one of three canonical spectroelectrochemical behaviors exhibited by single P. aeruginosa cells. In contrast, more modest nutrient limitations have little to no effect on the spectroelectrochemical response when compared to healthy cells in the stationary phase. These findings demonstrate the capabilities of micropore electrode arrays for studying the behavior of single microbial cells under conditions where the intercellular spacing, orientation, and chemical environment of the cells are controlled. Realizing single-cell studies under such well-defined conditions makes it possible to study fundamental stress responses with unprecedented control.
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Affiliation(s)
- Allison
R. Cutri
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Joshua D. Shrout
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department
of Biological Sciences, University of Notre
Dame, Notre Dame, Indiana 46556, United
States
| | - Paul W. Bohn
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
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3
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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4
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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization. Nat Commun 2023; 14:1336. [PMID: 36906676 PMCID: PMC10008558 DOI: 10.1038/s41467-023-36879-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/13/2023] Open
Abstract
Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
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5
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Niwa T, Nakazawa K, Hoshi K, Tadakuma H, Ito K, Taguchi H. Application of fluorescence correlation spectroscopy to investigate the dynamics of a ribosome-associated trigger factor in Escherichia coli. Front Mol Biosci 2022; 9:891128. [PMID: 36090041 PMCID: PMC9452904 DOI: 10.3389/fmolb.2022.891128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/26/2022] [Indexed: 11/15/2022] Open
Abstract
Co-translational protein folding is one of the central topics in molecular biology. In Escherichia coli, trigger factor (TF) is a primary chaperone that facilitates co-translational folding by directly interacting with nascent polypeptide chains on translating ribosomes. In this study, we applied fluorescence correlation spectroscopy (FCS), which can analyze the diffusion properties of fluorescent molecules by measuring the fluctuations of the fluorescent intensity, to investigate the interaction between TF and a nascent chain on translating ribosomes both in vitro and in vivo. The FCS analysis with a reconstituted cell-free translation system revealed that the interaction of fluorescently labeled TF with a nascent chain depended on the emergence of the nascent chain from the ribosome exit tunnel, and this interaction was not inhibited by excess amounts of other chaperones. Furthermore, the translation-dependent interaction between GFP-fused TFs and nascent chains was also observed in living E. coli cells. The FCS-based approach established here could be an effective method to investigate the dynamics of other ribosome-associated chaperones besides TF.
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Affiliation(s)
- Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Koki Nakazawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kensuke Hoshi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hisashi Tadakuma
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, China
| | - Koichi Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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6
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He YU, Wang S, Yin X, Sun F, He B, Liu X. Comparison of Extracellular Proteins from Virulent and Avirulent Vibrio parahaemolyticus Strains To Identify Potential Virulence Factors. J Food Prot 2020; 83:155-162. [PMID: 31860395 DOI: 10.4315/0362-028x.jfp-19-188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vibrio parahaemolyticus is a leading seafood-borne pathogen that causes gastroenteritis, septicemia, and serious wound infections due to the actions of virulence-associated proteins. We compared the extracellular proteins of nonvirulent JHY20 and virulent ATCC 33847 V. parahaemolyticus reference strains. Eighteen extracellular proteins were identified from secretory profiles, and 11 (68.75%) of the 16 proteins in ATCC 33847 are associated with virulence and/or protection against adverse conditions: trigger factor, chaperone SurA, aspartate-semialdehyde dehydrogenase, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, glutamate 5-kinase, alanine dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, outer membrane protein OmpV, ribosome-associated inhibitor A, chaperone protein Skp, and universal stress protein. Two nontoxic-related proteins, amino acid ABC transporter substrate-binding protein and an uncharacterized protein, were identified in JHY20. The results provide a theoretical basis for supporting safety risk assessment of aquatic foods, illuminate the pathogenic mechanisms of V. parahaemolyticus, and assist the identification of novel vaccine candidates for foodborne pathogens.
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Affiliation(s)
- Y U He
- College of Food (Biotechnology) Engineering.,Key Construction Laboratory of Food Resources Development and the Quality Safety, Xuzhou University of Technology, Jiangsu, Xuzhou 221018, People's Republic of China
| | - Shuai Wang
- College of Food (Biotechnology) Engineering.,Key Construction Laboratory of Food Resources Development and the Quality Safety, Xuzhou University of Technology, Jiangsu, Xuzhou 221018, People's Republic of China
| | | | - Fengjiao Sun
- Logistics & Security Department, Shanghai Civil Aviation College, Shanghai 201300, People's Republic of China
| | - Bin He
- Environment Monitoring Station, Zaozhuang Municipal Bureau of Ecology and Environment, Shandong 277100, People's Republic of China
| | - Xiao Liu
- Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450001, People's Republic of China
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7
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Smit JH, Li Y, Warszawik EM, Herrmann A, Cordes T. ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data. PLoS One 2019; 14:e0217524. [PMID: 31216308 PMCID: PMC6583990 DOI: 10.1371/journal.pone.0217524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Single-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique. With the cost of microscopes dropping and the availability of fully automated microscopes, the volume of microscopy data produced has increased tremendously. These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis. Furthermore, requirements for analysis procedures have become more stringent given the demand of various journals to make data and analysis procedures available. To address these issues we have developed a new data analysis package for analysis of fluorescence microscopy data from rod-like cells. Our software ColiCoords structures microscopy data at the single-cell level and implements a coordinate system describing each cell. This allows for the transformation of Cartesian coordinates from transmission light and fluorescence images and single-molecule localization microscopy (SMLM) data to cellular coordinates. Using this transformation, many cells can be combined to increase the statistical power of fluorescence microscopy datasets of any kind. ColiCoords is open source, implemented in the programming language Python, and is extensively documented. This allows for modifications for specific needs or to inspect and publish data analysis procedures. By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research. The source code and documentation can be found via the project's GitHub page.
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Affiliation(s)
- Jochem H. Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yichen Li
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Eliza M. Warszawik
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andreas Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
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8
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Liew ATF, Foo YH, Gao Y, Zangoui P, Singh MK, Gulvady R, Kenney LJ. Single cell, super-resolution imaging reveals an acid pH-dependent conformational switch in SsrB regulates SPI-2. eLife 2019; 8:e45311. [PMID: 31033442 PMCID: PMC6557628 DOI: 10.7554/elife.45311] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022] Open
Abstract
After Salmonella is phagocytosed, it resides in an acidic vacuole. Its cytoplasm acidifies to pH 5.6; acidification activates pathogenicity island 2 (SPI-2). SPI-2 encodes a type three secretion system whose effectors modify the vacuole, driving endosomal tubulation. Using super-resolution imaging in single bacterial cells, we show that low pH induces expression of the SPI-2 SsrA/B signaling system. Single particle tracking, atomic force microscopy, and single molecule unzipping assays identified pH-dependent stimulation of DNA binding by SsrB. A so-called phosphomimetic form (D56E) was unable to bind to DNA in live cells. Acid-dependent DNA binding was not intrinsic to regulators, as PhoP and OmpR binding was not pH-sensitive. The low level of SPI-2 injectisomes observed in single cells is not due to fluctuating SsrB levels. This work highlights the surprising role that acid pH plays in virulence and intracellular lifestyles of Salmonella; modifying acid survival pathways represents a target for inhibiting Salmonella.
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Affiliation(s)
- Andrew Tze Fui Liew
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yunfeng Gao
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Parisa Zangoui
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | | | - Ranjit Gulvady
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Linda J Kenney
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
- Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUnited States
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9
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Cohen A, Troib S, Dotan S, Najmuldeen H, Yesilkaya H, Kushnir T, Shagan M, Portnoi M, Nachmani H, Benisty R, Tal M, Ellis R, Chalifa-Caspi V, Dagan R, Nebenzahl YM. Streptococcus pneumoniae Cell Wall-Localized Trigger Factor Elicits a Protective Immune Response and Contributes to Bacterial Adhesion to the Host. Sci Rep 2019; 9:4295. [PMID: 30862841 PMCID: PMC6414539 DOI: 10.1038/s41598-019-40779-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/24/2018] [Indexed: 12/16/2022] Open
Abstract
Trigger factor (TF) has a known cytoplasmic function as a chaperone. In a previous study we showed that pneumococcal TF is also cell-wall localized and this finding combined with the immunogenic characteristic of TF, has led us to determine the vaccine potential of TF and decipher its involvement in pneumococcal pathogenesis. Bioinformatic analysis revealed that TF is conserved among pneumococci and has no human homologue. Immunization of mice with recombinant (r)TF elicited a protective immune response against a pneumococcal challenge, suggesting that TF contributes to pneumococcal pathogenesis. Indeed, rTF and an anti-rTF antiserum inhibited bacterial adhesion to human lung derived epithelial cells, indicating that TF contributes to the bacterial adhesion to the host. Moreover, bacteria lacking TF demonstrated reduced adhesion, in vitro, to lung-derived epithelial cells, neural cells and glial cells. The reduced adhesion could be restored by chromosomal complementation. Furthermore, bacteria lacking TF demonstrated significantly reduced virulence in a mouse model. Taken together, the ability of rTF to elicit a protective immune response, involvement of TF in bacterial adhesion, conservation of the protein among pneumococcal strains and the lack of human homologue, all suggest that rTF can be considered as a future candidate vaccine with a much broader coverage as compared to the currently available pneumococcal vaccines.
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Affiliation(s)
- Aviad Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shani Troib
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Hastyar Najmuldeen
- Department of Infection, Immunity and Inflammation to Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom.,Department of Biology, College of Science, University of Sulaimani, Sulaimani, Iraq
| | - Hasan Yesilkaya
- Department of Infection, Immunity and Inflammation to Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Tatyana Kushnir
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Marilou Shagan
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maxim Portnoi
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hannie Nachmani
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Rachel Benisty
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Vered Chalifa-Caspi
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yaffa Mizrachi Nebenzahl
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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10
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Rösch TC, Oviedo-Bocanegra LM, Fritz G, Graumann PL. SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome. Sci Rep 2018; 8:15747. [PMID: 30356068 PMCID: PMC6200787 DOI: 10.1038/s41598-018-33842-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/02/2018] [Indexed: 01/08/2023] Open
Abstract
Single-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living cells at high spatial and temporal resolution. Even though SMT is becoming a widely used method in bacterial cell biology, there is no program employing different analytical tools for the quantitative evaluation of tracking data. We developed SMTracker, a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualizing and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by-track basis. Diffusion constants are calculated a) by a Gaussian mixture model (GMM) panel, analyzing the distribution of positional displacements in x- and y-direction using a multi-state diffusion model (e.g. DNA-bound vs. freely diffusing molecules), and inferring the diffusion constants and relative fraction of molecules in each state, or b) by square displacement analysis (SQD), using the cumulative probability distribution of square displacements to estimate the diffusion constants and relative fractions of up to three diffusive states, or c) through mean-squared displacement (MSD) analyses, allowing the discrimination between Brownian, sub- or superdiffusive behavior. A spatial distribution analysis (SDA) panel analyzes the subcellular localization of molecules, summarizing the localization of trajectories in 2D- heat maps. Using SMTracker, we show that the global transcriptional repressor AbrB performs highly dynamic binding throughout the Bacillus subtilis genome, with short dwell times that indicate high on/off rates in vivo. While about a third of AbrB molecules are in a DNA-bound state, 40% diffuse through the chromosome, and the remaining molecules freely diffuse through the cells. AbrB also forms one or two regions of high intensity binding on the nucleoids, similar to the global gene silencer H-NS in Escherichia coli, indicating that AbrB may also confer a structural function in genome organization.
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Affiliation(s)
- Thomas C Rösch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Luis M Oviedo-Bocanegra
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Georg Fritz
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Department of Physics, Philipps Universität Marburg, Marburg, Germany.
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Department of Chemistry, Philipps Universität Marburg, Marburg, Germany.
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11
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Fan D, Cao S, Zhou Q, Zhang Y, Yue L, Han C, Yang B, Wang Y, Ma Z, Zhu L, Liu C. Exploring the roles of substrate-binding surface of the chaperone site in the chaperone activity of trigger factor. FASEB J 2018; 32:fj201701576. [PMID: 29906241 DOI: 10.1096/fj.201701576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Trigger factor (TF) is a key component of the prokaryotic chaperone network, which is involved in many basic cellular processes, such as protein folding, protein trafficking, and ribosome assembly. The major chaperone site of TF has a cradle-like structure in which protein substrate may fold without interference from other proteins. Here, we investigated in vivo and in vitro the roles of hydrophobic and charged patches on the edge and interior of cradle during TF-assisted protein folding. Our results showed that most of the surface of the cradle was involved in TF-assisted protein folding, which was larger than found in early studies. Although the inner surface of cradle was mostly hydrophobic, both hydrophobic and electrostatic patches were indispensable for TF to facilitate correct protein folding. However, hydrophobic patches were more important for the antiaggregation activity of TF. Furthermore, it was found that the patches on the surface of cradle were involved in TF-assisted protein folding in a spatial and temporal order. These results suggest that the folding-favorable interface between the cradle and substrate was dynamic during TF-assisted protein folding, which enabled TF to be involved in the folding of substrate in an aggressive manner rather than acting as a classic holdase.-Fan, D., Cao, S., Zhou, Q., Zhang, Y., Yue, L., Han, C., Yang, B., Wang, Y., Ma, Z., Zhu, L., Liu, C. Exploring the roles of substrate-binding surface of chaperone site in the chaperone activity of trigger factor.
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Affiliation(s)
- Dongjie Fan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shunan Cao
- Key Laboratory for Polar Science, State Ocean Administration, Polar Research Institute of China, Shanghai, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- ChosenMed Technology Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, China
| | - You Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Yue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Bo Yang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhuo Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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