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Andreyanov M, Heinrich R, Berlin S. Design of Ultrapotent Genetically Encoded Inhibitors of Kv4.2 for Gating Neural Plasticity. J Neurosci 2024; 44:e2295222023. [PMID: 38154956 PMCID: PMC10869153 DOI: 10.1523/jneurosci.2295-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 11/05/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
The Kv4.2 potassium channel plays established roles in neuronal excitability, while also being implicated in plasticity. Current means to study the roles of Kv4.2 are limited, motivating us to design a genetically encoded membrane tethered Heteropodatoxin-2 (MetaPoda). We find that MetaPoda is an ultrapotent and selective gating-modifier of Kv4.2. We narrow its site of contact with the channel to two adjacent residues within the voltage sensitive domain (VSD) and, with docking simulations, suggest that the toxin binds the VSD from within the membrane. We also show that MetaPoda does not require an external linker of the channel for its activity. In neurons (obtained from female and male rat neonates), MetaPoda specifically, and potently, inhibits all Kv4 currents, leaving all other A-type currents unaffected. Inhibition of Kv4 in hippocampal neurons does not promote excessive excitability, as is expected from a simple potassium channel blocker. We do find that MetaPoda's prolonged expression (1 week) increases expression levels of the immediate early gene cFos and prevents potentiation. These findings argue for a major role of Kv4.2 in facilitating plasticity of hippocampal neurons. Lastly, we show that our engineering strategy is suitable for the swift engineering of another potent Kv4.2-selective membrane-tethered toxin, Phrixotoxin-1, denoted MetaPhix. Together, we provide two uniquely potent genetic tools to study Kv4.2 in neuronal excitability and plasticity.
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Affiliation(s)
- Michael Andreyanov
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa 3525433, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa 3525433, Israel
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa 3525433, Israel
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2
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Lee SW, Phillips KS, Gu H, Kazemzadeh-Narbat M, Ren D. How microbes read the map: Effects of implant topography on bacterial adhesion and biofilm formation. Biomaterials 2020; 268:120595. [PMID: 33360301 DOI: 10.1016/j.biomaterials.2020.120595] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/24/2020] [Accepted: 12/06/2020] [Indexed: 12/19/2022]
Abstract
Microbes have remarkable capabilities to attach to the surface of implanted medical devices and form biofilms that adversely impact device function and increase the risk of multidrug-resistant infections. The physicochemical properties of biomaterials have long been known to play an important role in biofilm formation. More recently, a series of discoveries in the natural world have stimulated great interest in the use of 3D surface topography to engineer antifouling materials that resist bacterial colonization. There is also increasing evidence that some medical device surface topographies, such as those designed for tissue integration, may unintentionally promote microbial attachment. Despite a number of reviews on surface topography and biofilm control, there is a missing link between how bacteria sense and respond to 3D surface topographies and the rational design of antifouling materials. Motivated by this gap, we present a review of how bacteria interact with surface topographies, and what can be learned from current laboratory studies of microbial adhesion and biofilm formation on specific topographic features and medical devices. We also address specific biocompatibility considerations and discuss how to improve the assessment of the anti-biofilm performance of topographic surfaces. We conclude that 3D surface topography, whether intended or unintended, is an important consideration in the rational design of safe medical devices. Future research on next-generation smart antifouling materials could benefit from a greater focus on translation to real-world applications.
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Affiliation(s)
- Sang Won Lee
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, 13244, United States
| | - K Scott Phillips
- United States Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, Silver Spring, MD, 20993, United States.
| | - Huan Gu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, 13244, United States
| | - Mehdi Kazemzadeh-Narbat
- United States Food and Drug Administration, Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Product Evaluation and Quality, Office of Health Technology 6, Silver Spring, MD, 20993, United States; Musculoskeletal Clinical Regulatory Advisers (MCRA), Washington DC, 20001, United States
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, 13244, United States; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, 13244, United States; Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY, 13244, United States; Department of Biology, Syracuse University, Syracuse, NY, 13244, United States.
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3
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Zheng Y, Meng F, Zhu Z, Wei W, Sun Z, Chen J, Yu B, Lou C, Chen GQ. A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts. Nucleic Acids Res 2020; 47:e137. [PMID: 31750522 PMCID: PMC6868347 DOI: 10.1093/nar/gkz785] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/30/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
Natural organisms have evolved intricate regulatory mechanisms that sense and respond to fluctuating environmental temperatures in a heat- or cold-inducible fashion. Unlike dominant heat-inducible switches, very few cold-inducible genetic switches are available in either natural or engineered systems. Moreover, the available cold-inducible switches still have many shortcomings, including high leaky gene expression, small dynamic range (<10-fold) or broad transition temperature (>10°C). To address these problems, a high-performance cold-inducible switch that can tightly control target gene expression is highly desired. Here, we introduce a tight and fast cold-inducible switch that couples two evolved thermosensitive variants, TFts and TEVts, as well as an additional Mycoplasma florum Lon protease (mf-Lon) to effectively turn-off target gene expression via transcriptional and proteolytic mechanisms. We validated the function of the switch in different culture media and various Escherichia coli strains and demonstrated its tightness by regulating two morphogenetic bacterial genes and expressing three heat-unstable recombinant proteins, respectively. Moreover, the additional protease module enabled the cold-inducible switch to actively remove the pre-existing proteins in slow-growing cells. This work establishes a high-performance cold-inducible system for tight and fast control of gene expression which has great potential for basic research, as well as industrial and biomedical applications.
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Affiliation(s)
- Yang Zheng
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fankang Meng
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zihui Zhu
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weijia Wei
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zhi Sun
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Jinchun Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China.,College of Life Science, University of Science and Technology of China, Hefei 230027, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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4
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Poudel C, Mela I, Kaminski CF. High-throughput, multi-parametric, and correlative fluorescence lifetime imaging. Methods Appl Fluoresc 2020; 8:024005. [PMID: 32028271 PMCID: PMC8208541 DOI: 10.1088/2050-6120/ab7364] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss methods and advancements in fluorescence lifetime imaging microscopy that permit measurements to be performed at faster speed and higher resolution than previously possible. We review fast single-photon timing technologies and the use of parallelized detection schemes to enable high-throughput and high content imaging applications. We appraise different technological implementations of fluorescence lifetime imaging, primarily in the time-domain. We also review combinations of fluorescence lifetime with other imaging modalities to capture multi-dimensional and correlative information from a single sample. Throughout the review, we focus on applications in biomedical research. We conclude with a critical outlook on current challenges and future opportunities in this rapidly developing field.
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Affiliation(s)
- Chetan Poudel
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
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5
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Cao H, Villatoro-Hernandez J, Weme RDO, Frenzel E, Kuipers OP. Boosting heterologous protein production yield by adjusting global nitrogen and carbon metabolic regulatory networks in Bacillus subtilis. Metab Eng 2018; 49:143-152. [DOI: 10.1016/j.ymben.2018.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 01/19/2023]
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6
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Sauer C, Ver Loren van Themaat E, Boender LGM, Groothuis D, Cruz R, Hamoen LW, Harwood CR, van Rij T. Exploring the Nonconserved Sequence Space of Synthetic Expression Modules in Bacillus subtilis. ACS Synth Biol 2018; 7:1773-1784. [PMID: 29939720 DOI: 10.1021/acssynbio.8b00110] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing protein expression levels is a key step in the commercial production of enzymes. Predicting promoter activity and translation initiation efficiency based solely on consensus sequences have so far met with mixed results. Here, we addressed this challenge using a "brute-force" approach by designing and synthesizing a large combinatorial library comprising ∼12 000 unique synthetic expression modules (SEMs) for Bacillus subtilis. Using GFP fluorescence as a reporter of gene expression, we obtained a dynamic expression range that spanned 5 orders of magnitude, as well as a maximal 13-fold increase in expression compared with that of the already strong veg expression module. Analyses of the synthetic modules indicated that sequences at the 5'-end of the mRNA were the most important contributing factor to the differences in expression levels, presumably by preventing formation of strong secondary mRNA structures that affect translation initiation. When the gfp coding region was replaced by the coding region of the xynA gene, encoding the industrially relevant B. subtilis xylanase enzyme, only a 3-fold improvement in xylanase production was observed. Moreover, the correlation between GFP and xylanase expression levels was weak. This suggests that the differences in expression levels between the gfp and xynA constructs were due to differences in 5'-end mRNA folding and consequential differences in the rates of translation initiation. Our data show that the use of large libraries of SEMs, in combination with high-throughput technologies, is a powerful approach to improve the production of a specific protein, but that the outcome cannot necessarily be extrapolated to other proteins.
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Affiliation(s)
- Christopher Sauer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | | | | | - Daphne Groothuis
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Rita Cruz
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Leendert W. Hamoen
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Colin R. Harwood
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Tjeerd van Rij
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
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7
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Meiresonne NY, Alexeeva S, van der Ploeg R, den Blaauwen T. Detection of Protein Interactions in the Cytoplasm and Periplasm of Escherichia coli by Förster Resonance Energy Transfer. Bio Protoc 2018; 8:e2697. [PMID: 34179246 PMCID: PMC8203949 DOI: 10.21769/bioprotoc.2697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 11/02/2022] Open
Abstract
This protocol was developed to qualitatively and quantitatively detect protein-protein interactions in Escherichia coli by Förster Resonance Energy Transfer (FRET). The described assay allows for the previously impossible in vivo screening of periplasmic protein-protein interactions. In FRET, excitation of a donor fluorescent molecule results in the transfer of energy to an acceptor fluorescent molecule, which will then emit light if the distance between them is within the 1-10 nm range. Fluorescent proteins can be genetically encoded as fusions to proteins of interest and expressed in the cell and therefore FRET protein-protein interaction experiments can be performed in vivo. Donor and acceptor fluorescent protein fusions are constructed for bacterial proteins that are suspected to interact. These fusions are co-expressed in bacterial cells and the fluorescence emission spectra are measured by subsequently exciting the donor and the acceptor channel. A partial overlap between the emission spectrum of the donor and the excitation spectrum of the acceptor is a prerequisite for FRET. Donor excitation can cross-excite the acceptor for a known percentage even in the absence of FRET. By measuring reference spectra for the background, donor-only and acceptor-only samples, expected emission spectra can be calculated. Sensitized emission for the acceptor on top of the expected spectrum can be attributed to FRET and can be quantified by spectral unmixing.
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Affiliation(s)
- Nils Y. Meiresonne
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Svetlana Alexeeva
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - René van der Ploeg
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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8
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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9
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Hölscher T, Dragoš A, Gallegos-Monterrosa R, Martin M, Mhatre E, Richter A, Kovács ÁT. Monitoring Spatial Segregation in Surface Colonizing Microbial Populations. J Vis Exp 2016. [PMID: 27842347 PMCID: PMC5226080 DOI: 10.3791/54752] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Microbes provide an intriguing system to study social interaction among individuals within a population. The short generation times and relatively simple genetic modification procedures of microbes facilitate the development of the sociomicrobiology field. To assess the fitness of certain microbial species, selected strains or their genetically modified derivatives within one population, can be fluorescently labelled and tracked using microscopy adapted with appropriate fluorescence filters. Expanding colonies of diverse microbial species on agar media can be used to monitor the spatial distribution of cells producing distinctive fluorescent proteins. Here, we present a detailed protocol for the use of green- and red-fluorescent protein producing bacterial strains to follow spatial arrangement during surface colonization, including flagellum-driven community movement (swarming), exopolysaccharide- and hydrophobin-dependent growth mediated spreading (sliding), and complex colony biofilm formation. Non-domesticated isolates of the Gram-positive bacterium, Bacillus subtilis can be utilized to scrutinize certain surface spreading traits and their effect on two-dimensional distribution on the agar-solidified medium. By altering the number of cells used to initiate colony biofilms, the assortment levels can be varied on a continuous scale. Time-lapse fluorescent microscopy can be used to witness the interaction between different phenotypes and genotypes at a certain assortment level and to determine the relative success of either.
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Affiliation(s)
- Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | | | - Marivic Martin
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Anne Richter
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University, Jena;
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10
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Protein-protein interactions: a supra-structural phenomenon demanding trans-disciplinary biophysical approaches. Curr Opin Struct Biol 2015; 35:76-86. [PMID: 26496626 DOI: 10.1016/j.sbi.2015.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/01/2015] [Accepted: 09/28/2015] [Indexed: 01/14/2023]
Abstract
Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can be obtained at increasing resolution, at relevant time-scales and under increasingly relevant experimental conditions, intricate data are interpreted reliably, and the questions posed and answered grow in complexity. With this review, highlights from the study of PPIs using a multitude of biophysical methods, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods.
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11
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Detert Oude Weme R, Seidel G, Kuipers OP. Probing the regulatory effects of specific mutations in three major binding domains of the pleiotropic regulator CcpA of Bacillus subtilis. Front Microbiol 2015; 6:1051. [PMID: 26483775 PMCID: PMC4591507 DOI: 10.3389/fmicb.2015.01051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/14/2015] [Indexed: 11/30/2022] Open
Abstract
Carbon catabolite control is required for efficient use of available carbon sources to ensure rapid growth of bacteria. CcpA is a global regulator of carbon metabolism in Gram-positive bacteria like Bacillus subtilis. In this study the genome-wide gene regulation of a CcpA knockout and three specific CcpA mutants were studied by transcriptome analysis, to further elucidate the function of specific binding sites in CcpA. The following three amino acids were mutated to characterize their function: M17(R) which is involved in DNA binding, T62(H) which is important for the allosteric switch in CcpA upon HPr-Ser46-P binding, and R304(W) which is important for binding of the coeffectors HPr-Ser46-P and fructose-1,6-bisphosphate. The results confirm that CcpA was also involved in gene regulation in the absence of glucose. CcpA-M17R showed a small relief of Carbon Catabolite Control; the CcpA-M17R mutant regulates fewer genes than the CcpA-wt and the palindromicity of the cre site is less important for CcpA-M17R. CcpA-T62H was a stronger repressor than CcpA-wt and also acted as a strong repressor in the absence of glucose. CcpA-R304W was shown here to be less dependent on HPr-Ser46-P for its carbon catabolite control activities. The results presented here provide detailed information on alterations in gene regulation for each CcpA-mutant.
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Affiliation(s)
- Ruud Detert Oude Weme
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Gerald Seidel
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
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