1
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Lukose B, Maruno T, Faidh M, Uchiyama S, Naganathan A. Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS. Nucleic Acids Res 2024; 52:2157-2173. [PMID: 38340344 PMCID: PMC10954469 DOI: 10.1093/nar/gkae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Environmentally regulated gene expression is critical for bacterial survival under stress conditions, including extremes in temperature, osmolarity and nutrient availability. Here, we dissect the thermo- and osmo-responsory behavior of the transcriptional repressor H-NS, an archetypal nucleoid-condensing sensory protein, ubiquitous in enterobacteria that infect the mammalian gut. Through experiments and thermodynamic modeling, we show that H-NS exhibits osmolarity, temperature and concentration dependent self-association, with a highly polydisperse native ensemble dominated by monomers, dimers, tetramers and octamers. The relative population of these oligomeric states is determined by an interplay between dimerization and higher-order oligomerization, which in turn drives a competition between weak homo- versus hetero-oligomerization of protein-protein and protein-DNA complexes. A phosphomimetic mutation, Y61E, fully eliminates higher-order self-assembly and preserves only dimerization while weakening DNA binding, highlighting that oligomerization is a prerequisite for strong DNA binding. We further demonstrate the presence of long-distance thermodynamic connectivity between dimerization and oligomerization sites on H-NS which influences the binding of the co-repressor Cnu, and switches the DNA binding mode of the hetero-oligomeric H-NS:Cnu complex. Our work thus uncovers important organizational principles in H-NS including a multi-layered thermodynamic control, and provides a molecular framework broadly applicable to other thermo-osmo sensory proteins that employ similar mechanisms to regulate gene expression.
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Affiliation(s)
- Bincy Lukose
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Mohammed A Faidh
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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2
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Joyeux M. Organization of the bacterial nucleoid by DNA-bridging proteins and globular crowders. Front Microbiol 2023; 14:1116776. [PMID: 36925468 PMCID: PMC10011147 DOI: 10.3389/fmicb.2023.1116776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most important contributions to the compaction of the DNA coil are the cross-linking of the DNA by nucleoid proteins (like H-NS and StpA) and the demixing of DNA and other abundant globular macromolecules which do not bind to the DNA (like ribosomes). The present work deals with the interplay of DNA-bridging proteins and globular macromolecular crowders, with the goal of determining the extent to which they collaborate in organizing the nucleoid. In order to answer this question, a coarse-grained model was developed and its properties were investigated through Brownian dynamics simulations. These simulations reveal that the radius of gyration of the DNA coil decreases linearly with the effective volume ratio of globular crowders and the number of DNA bridges formed by nucleoid proteins in the whole range of physiological values. Moreover, simulations highlight the fact that the number of DNA bridges formed by nucleoid proteins depends crucially on their ability to self-associate (oligomerize). An explanation for this result is proposed in terms of the mean distance between DNA segments and the capacity of proteins to maintain DNA-bridging in spite of the thermal fluctuations of the DNA network. Finally, simulations indicate that non-associating proteins preserve a high mobility inside the nucleoid while contributing to its compaction, leading to a DNA/protein complex which looks like a liquid droplet. In contrast, self-associating proteins form a little deformable network which cross-links the DNA chain, with the consequence that the DNA/protein complex looks more like a gel.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, St Martin d'Hères, France
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3
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Jing Kay Lam K, Zhang Z, Saier Jr MH. Histone-like Nucleoid Structuring (H-NS) Protein Silences the beta-glucoside (bgl) Utilization Operon in Escherichia coli by Forming a DNA Loop. Comput Struct Biotechnol J 2022; 20:6287-6301. [DOI: 10.1016/j.csbj.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022] Open
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4
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Tran D, Zhang Z, Lam KJK, Saier MH. Effects of Global and Specific DNA-Binding Proteins on Transcriptional Regulation of the E. coli bgl Operon. Int J Mol Sci 2022; 23:ijms231810343. [PMID: 36142257 PMCID: PMC9499468 DOI: 10.3390/ijms231810343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Using reporter gene (lacZ) transcriptional fusions, we examined the transcriptional dependencies of the bgl promoter (Pbgl) and the entire operon regulatory region (Pbgl-bglG) on eight transcription factors as well as the inducer, salicin, and an IS5 insertion upstream of Pbgl. Crp-cAMP is the primary activator of both Pbgl and the bgl operon, while H-NS is a strong dominant operon repressor but only a weak repressor of Pbgl. H-NS may exert its repressive effect by looping the DNA at two binding sites. StpA is a relatively weak repressor in the absence of H-NS, while Fis also has a weak repressive effect. Salicin has no effect on Pbgl activity but causes a 30-fold induction of bgl operon expression. Induction depends on the activity of the BglF transporter/kinase. IS5 insertion has only a moderate effect on Pbgl but causes a much greater activation of the bgl operon expression by preventing the full repressive effects of H-NS and StpA. While several other transcription factors (BglJ, RcsB, and LeuO) have been reported to influence bgl operon transcription when overexpressed, they had little or no effect when present at wild type levels. These results indicate the important transcriptional regulatory mechanisms operative on the bgl operon in E. coli.
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5
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Son B, Patterson-West J, Arroyo-Mendoza M, Ramachandran R, Iben J, Zhu J, Rao V, Dimitriadis E, Hinton D. A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing. Nucleic Acids Res 2021; 49:9229-9245. [PMID: 34365505 PMCID: PMC8450097 DOI: 10.1093/nar/gkab678] [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: 09/10/2020] [Revised: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleoid Associated Proteins (NAPs) organize the bacterial chromosome within the nucleoid. The interaction of the NAP H-NS with DNA also represses specific host and xenogeneic genes. Previously, we showed that the bacteriophage T4 early protein MotB binds to DNA, co-purifies with H-NS/DNA, and improves phage fitness. Here we demonstrate using atomic force microscopy that MotB compacts the DNA with multiple MotB proteins at the center of the complex. These complexes differ from those observed with H-NS and other NAPs, but resemble those formed by the NAP-like proteins CbpA/Dps and yeast condensin. Fluorescent microscopy indicates that expression of motB in vivo, at levels like that during T4 infection, yields a significantly compacted nucleoid containing MotB and H-NS. motB overexpression dysregulates hundreds of host genes; ∼70% are within the hns regulon. In infected cells overexpressing motB, 33 T4 late genes are expressed early, and the T4 early gene repEB, involved in replication initiation, is up ∼5-fold. We postulate that MotB represents a phage-encoded NAP that aids infection in a previously unrecognized way. We speculate that MotB-induced compaction may generate more room for T4 replication/assembly and/or leads to beneficial global changes in host gene expression, including derepression of much of the hns regulon.
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Affiliation(s)
- Bokyung Son
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Patterson-West
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James R Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jingen Zhu
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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6
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Zhao X, Remington JM, Schneebeli ST, Arold ST, Li J. Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament. J Phys Chem Lett 2021; 12:7878-7884. [PMID: 34382809 PMCID: PMC9346976 DOI: 10.1021/acs.jpclett.1c01710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The histone-like nucleoid structuring (H-NS) protein controls the expression of hundreds of genes in Gram-positive bacteria through its capability to coat and condense DNA. This mechanism requires the formation of superhelical H-NS protein filaments that are sensitive to temperature and salinity, allowing H-NS to act as an environment sensor. We use multiscale modeling and simulations to obtain detailed insights into the mechanism of H-NS filament's sensitivity to environmental changes. Through the simulations of the superhelical H-NS filament, we reveal how different environments induce heterogeneity of H-NS monomers. Further, we observe that transient self-association within the H-NS filament creates temperature-inducible strain and might mildly oppose DNA binding. We also probe different H-NS-DNA complex architectures and show that complexation enhances the stability of both DNA and H-NS superhelices. Overall, our results provide unprecedented molecular insights into the environmental sensing and DNA interactions of a prototypical nucleoid-structuring bacterial protein filament.
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Affiliation(s)
- Xiaochuan Zhao
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Jacob M. Remington
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Severin T. Schneebeli
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
| | - Stefan T. Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Jianing Li
- Departments of Chemistry and Materials Science, University of Vermont, Burlington VT 05405
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7
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Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins. Biophys J 2020; 120:370-378. [PMID: 33340542 DOI: 10.1016/j.bpj.2020.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (∼80%), RNA (∼10%), and a number of different proteins (∼10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrapping the DNA. These so-called architectural properties of nucleoid proteins are still poorly understood. For example, the reason why certain proteins compact the DNA coil in certain environments but make the DNA more rigid instead in other environments is the subject of ongoing debates. Here, we address the question of the impact of the self-association of nucleoid proteins on their architectural properties and try to determine whether differences in self-association are sufficient to induce large changes in the organization of the DNA coil. More specifically, we developed two coarse-grained models of proteins, which interact identically with the DNA but self-associate differently by forming either clusters or filaments in the absence of the DNA. We showed through Brownian dynamics simulations that self-association of the proteins dramatically increases their ability to shape the DNA coil. Moreover, we observed that cluster-forming proteins significantly compact the DNA coil (similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming proteins significantly increase the stiffness of the DNA chain instead (similar to the DNA-stiffening mode of H-NS proteins). This work consequently suggests that the knowledge of the DNA-binding properties of the proteins is in itself not sufficient to understand their architectural properties. Rather, their self-association properties must also be investigated in detail because they might actually drive the formation of different DNA-protein complexes.
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8
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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9
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Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation. Proc Natl Acad Sci U S A 2020; 117:18540-18549. [PMID: 32675239 PMCID: PMC7414142 DOI: 10.1073/pnas.2005019117] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid–liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid–liquid phase separation is a common mechanism for intracellular organization in both eukaryotic and prokaryotic cells. Once described as mere “bags of enzymes,” bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid–liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.
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10
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Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame R. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res 2020; 48:2156-2172. [PMID: 31925429 PMCID: PMC7039000 DOI: 10.1093/nar/gkz1226] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/29/2019] [Accepted: 12/19/2019] [Indexed: 01/07/2023] Open
Abstract
H-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive. Here, we focus on the H-NS family protein MvaT from Pseudomonas aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strength on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins.
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Affiliation(s)
- Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Yann G J Sterckx
- Laboratory of Medical Biochemistry, University of Antwerp, Campus Drie Eiken, University Square 1, 2610 Wilrijk, Belgium
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jocelyne Vreede
- Department of Computational Chemistry, Van’t Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - Peter van Schaik
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
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11
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Yaghini N. Population balance modeling of assembly formation; accounting for the H-NS protein oligomerization and DNA binding mechanisms. Int J Biol Macromol 2019; 142:33-51. [PMID: 31491518 DOI: 10.1016/j.ijbiomac.2019.08.229] [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: 06/18/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
The results obtained in this study demonstrate H-NS oligomerization in solution is not sufficient in forming large structures of H-NS-DNA assemblies indicating oligomerization along bacterial DNA is crucial. We present a comprehensive and novel multi-scale modeling scheme to study protein-protein and protein-DNA interactions, with the focus on population balance modeling of assemblies formed by the H-NS protein and bacterial DNA. The model helps understanding how the concentration of H-NS influences the formation of H-NS-DNA assemblies. The presented model covers the two underlying molecular mechanisms involved in assembly formation, H-NS oligomerization in solution and H-NS-DNA binding. Within protein oligomerization interactions, protein molecules are entitled to dimerize, propagate, recombine and deform (break). In addition, DNA binding and unbinding interactions are included to account for formation of filaments along DNA. All mechanisms have been modeled with their associated forward (formation) and backward (deformation) interactions. The results obtained agree well with former experimental studies.
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Affiliation(s)
- Nazila Yaghini
- Department of Mechanical Engineering, Materials Technology Group, Eindhoven University of Technology, P.O. Box 513, Eindhoven, MB 5600, the Netherlands
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12
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Leng M, Lu Z, Qin Z, Qi Y, Lu G, Tang J. Flp, a Fis-like protein, contributes to the regulation of type III secretion and virulence processes in the phytopathogen Xanthomonas campestris pv. campestris. MOLECULAR PLANT PATHOLOGY 2019; 20:1119-1133. [PMID: 31090173 PMCID: PMC6640185 DOI: 10.1111/mpp.12818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability of the plant pathogen Xanthomonas campestris pv. campestris (Xcc) to cause disease is dependent on its ability to adapt quickly to the host environment during infection. Like most bacterial pathogens, Xcc has evolved complex regulatory networks that ensure expression and regulation of their virulence genes. Here, we describe the identification and characterization of a Fis-like protein (named Flp), which plays an important role in virulence and type III secretion system (T3SS) gene expression in Xcc. Deletion of flp caused reduced virulence and hypersensitive response (HR) induction of Xcc and alterations in stress tolerance. Global transcriptome analyses revealed the Flp had a broad regulatory role and that most T3SS HR and pathogenicity (hrp) genes were down-regulated in the flp mutant. β-glucuronidase activity assays implied that Flp regulates the expression of hrp genes via controlling the expression of hrpX. More assays confirmed that Flp binds to the promoter of hrpX and affected the transcription of hrpX directly. Interestingly, the constitutive expression of hrpX in the flp mutant restored the HR phenotype but not full virulence. Taken together, the findings describe the unrecognized regulatory role of Flp protein that controls hrp gene expression and pathogenesis in Xcc.
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Affiliation(s)
- Ming Leng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
| | - Zhuo‐Jian Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
| | - Zuo‐Shu Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
| | - Yan‐Hua Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
| | - Guang‐Tao Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
| | - Ji‐Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and TechnologyGuangxi University100 Daxue RoadNanningGuangxi530004China
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13
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Gulvady R, Gao Y, Kenney LJ, Yan J. A single molecule analysis of H-NS uncouples DNA binding affinity from DNA specificity. Nucleic Acids Res 2019; 46:10216-10224. [PMID: 30239908 PMCID: PMC6212787 DOI: 10.1093/nar/gky826] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/06/2018] [Indexed: 12/29/2022] Open
Abstract
Heat-stable nucleoid structuring protein (H-NS) plays a crucial role in gene silencing within prokaryotic cells and is important in pathogenesis. It was reported that H-NS silences nearly 5% of the genome, yet the molecular mechanism of silencing is not well understood. Here, we employed a highly-sensitive single-molecule counting approach, and measured the dissociation constant (KD) of H-NS binding to single DNA binding sites. Charged residues in the linker domain of H-NS provided the most significant contribution to DNA binding affinity. Although H-NS was reported to prefer A/T-rich DNA (a feature of pathogenicity islands) over G/C-rich DNA, the dissociation constants obtained from such sites were nearly identical. Using a hairpin unzipping assay, we were able to uncouple non-specific DNA binding steps from nucleation site binding and subsequent polymerization. We propose a model in which H-NS initially engages with non-specific DNA via reasonably high affinity (∼60 nM KD) electrostatic interactions with basic residues in the linker domain. This initial contact enables H-NS to search along the DNA for specific nucleation sites that drive subsequent polymerization and gene silencing.
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Affiliation(s)
- Ranjit Gulvady
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yunfeng Gao
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Jesse Brown Veterans Administration Medical Center, Chicago, IL 6061, USA.,Department of Microbiology and Immunology, University of Illinois-Chicago, Chicago, IL 60612, USA.,Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Department of Physics, National University of Singapore, Singapore 117542, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore
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14
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Kondakova T, Cronan JE. Transcriptional regulation of fatty acid cis-trans isomerization in the solvent-tolerant soil bacterium, Pseudomonas putida F1. Environ Microbiol 2019; 21:1659-1676. [PMID: 30702193 PMCID: PMC7357427 DOI: 10.1111/1462-2920.14546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022]
Abstract
One key to the success of Pseudomonas spp. is their ability to reside in hostile environments. Pseudomonas spp. possess a cis-trans isomerase (Cti) an enzyme that converts the cis-unsaturated fatty acids (FAs) of the membrane lipids to their trans-isomers to rigidify the membrane and thereby resist stresses. Whereas the posttranslational Cti regulation has been previously reported, transcriptional cti regulation remains to be studied in more details. Here, we have studied cti transcriptional regulation in the solvent-tolerant strain Pseudomonas putida F1. Two cti transcriptional start sites (cti-279 and cti-77) were identified with cti-279 transcript being dominant. Expression of cti was found to increase with temperature increase, addition of the organic solvent, octanol and in the stationary growth phase. We found that cti expression was repressed by the cyclic-AMP receptor protein (Crp) and repression required the cyclic-AMP ligand of Crp. Production of trans-unsaturated FAs was found to decrease after 24 h of growth. Although this decrease was accompanied by an increase in cyclopropane FA content, this was not at the expense of trans-unsaturated FAs demonstrating the absence of competition between Cti and Cfa in FA modification.
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Affiliation(s)
- Tatiana Kondakova
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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15
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Moretti C, Trabalza S, Granieri L, Caballo‐Ponce E, Devescovi G, Del Pino AM, Ramos C, Venturi V, van den Burg HA, Buonaurio R, Palmerini CA. A Na + /Ca 2+ exchanger of the olive pathogen Pseudomonas savastanoi pv. savastanoi is critical for its virulence. MOLECULAR PLANT PATHOLOGY 2019; 20:716-730. [PMID: 30912619 PMCID: PMC6637891 DOI: 10.1111/mpp.12787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In a number of compatible plant-bacterium interactions, a rise in apoplastic Ca2+ levels is observed, suggesting that Ca2+ represents an important environmental clue, as reported for bacteria infecting mammalians. We demonstrate that Ca2+ entry in Pseudomonas savastanoi pv. savastanoi (Psav) strain DAPP-PG 722 is mediated by a Na+ /Ca2+ exchanger critical for virulence. Using the fluorescent Ca2+ probe Fura 2-AM, we demonstrate that Ca2+ enters Psav cells foremost when they experience low levels of energy, a situation mimicking the apoplastic fluid. In fact, Ca2+ entry was suppressed in the presence of high concentrations of glucose, fructose, sucrose or adenosine triphosphate (ATP). Since Ca2+ entry was inhibited by nifedipine and LiCl, we conclude that the channel for Ca2+ entry is a Na+ /Ca2+ exchanger. In silico analysis of the Psav DAPP-PG 722 genome revealed the presence of a single gene coding for a Na+ /Ca2+ exchanger (cneA), which is a widely conserved and ancestral gene within the P. syringae complex based on gene phylogeny. Mutation of cneA compromised not only Ca2+ entry, but also compromised the Hypersensitive response (HR) in tobacco leaves and blocked the ability to induce knots in olive stems. The expression of both pathogenicity (hrpL, hrpA and iaaM) and virulence (ptz) genes was reduced in this Psav-cneA mutant. Complementation of the Psav-cneA mutation restored both Ca2+ entry and pathogenicity in olive plants, but failed to restore the HR in tobacco leaves. In conclusion, Ca2+ entry acts as a 'host signal' that allows and promotes Psav pathogenicity on olive plants.
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Affiliation(s)
- Chiaraluce Moretti
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Simone Trabalza
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Letizia Granieri
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Eloy Caballo‐Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea La MayoraUniversidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMACSIC)Área de GenéticaMálagaSpain
| | - Giulia Devescovi
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Alberto Marco Del Pino
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Cayo Ramos
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS)University of AmsterdamAmsterdamNetherlands
| | - Roberto Buonaurio
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Carlo Alberto Palmerini
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
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16
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A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair. Nat Commun 2019; 10:1995. [PMID: 31040281 PMCID: PMC6491433 DOI: 10.1038/s41467-019-10002-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/12/2019] [Indexed: 02/07/2023] Open
Abstract
Uropathogenic E. coli experience a wide range of osmolarity conditions before and after successful infection. Stress-responsive regulatory proteins in bacteria, particularly proteins of the Hha family and H-NS, a transcription repressor, sense such osmolarity changes and regulate transcription through unknown mechanisms. Here we use an array of experimental probes complemented by molecular simulations to show that Cnu, a member of the Hha protein family, acts as an exquisite molecular sensor of solvent ionic strength. The osmosensory behavior of Cnu involves a fine-tuned modulation of disorder in the fourth helix and the three-dimensional structure in a graded manner. Order-disorder transitions in H-NS act synergistically with molecular swelling of Cnu contributing to a salt-driven switch in binding cooperativity. Thus, sensitivity to ambient conditions can be imprinted at the molecular level by tuning not just the degree of order in the protein conformational ensemble but also through population redistributions of higher-order molecular complexes. The bacterial protein Cnu together with the transcription repressor H-NS regulate expression of virulence factors in an osmo-sensitive manner. Here authors show that the structure of Cnu swells with decreasing ionic strength driving the oligomerization of H-NS and regulating osmo-sensory response.
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17
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Yoshitani K, Hizukuri Y, Akiyama Y. An in vivo protease activity assay for investigating the functions of the Escherichia coli membrane protease HtpX. FEBS Lett 2019; 593:842-851. [PMID: 30903618 DOI: 10.1002/1873-3468.13368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 11/06/2022]
Abstract
Escherichia coli HtpX is an M48 family zinc metalloproteinase located in the cytoplasmic membrane. Previous studies suggested that it is involved in the quality control of membrane proteins. However, its in vivo proteolytic function has not been characterized in detail, mainly because the physiological substrates have not been identified and no model substrate that allows sensitive detection of the protease activity is available. We constructed a new model substrate of HtpX and established an in vivo semiquantitative and convenient protease activity assay system for HtpX. This system enables detection of differential protease activities of HtpX mutants carrying mutations in conserved regions. This system would also be useful for investigating the functions of HtpX and its homologs in other bacteria.
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Affiliation(s)
- Kohei Yoshitani
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
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18
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Srinivas S, Cronan JE. Coping with inadvertent lysis of Escherichia coli cultures: Strains resistant to lysogeny and infection by the stealthy lysogenic phage Φ80. Biotechnol Bioeng 2019; 116:1820-1826. [PMID: 30882900 DOI: 10.1002/bit.26971] [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: 12/14/2018] [Revised: 02/10/2019] [Accepted: 03/14/2019] [Indexed: 11/08/2022]
Abstract
Phage Φ80 can infect Escherichia coli in a stealthy manner and persist by forming lysogens. Such Φ80 lysogens are fairly common and often go undetected unless the host is grown at temperatures below 37°C. Since low growth temperatures are required for growing temperature-sensitive mutants and often preferred for large-scale applications such as protein production, Φ80-resistant strains would be useful. We report the construction of E. coli strains that cannot be efficiently lysogenized or infected by bacteriophage Φ80. These strains contain combinations of deletions or mutations in the bacterial attachment site for Φ80 integration and/or deletions in the genes required for phage absorption to the host outer membrane. These strains should help contain and prevent Φ80 infection of E. coli cultures in a laboratory or industrial setting.
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Affiliation(s)
- Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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19
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Predicting the mechanism and rate of H-NS binding to AT-rich DNA. PLoS Comput Biol 2019; 15:e1006845. [PMID: 30845209 PMCID: PMC6424460 DOI: 10.1371/journal.pcbi.1006845] [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: 08/13/2018] [Revised: 03/19/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA duplexes or to adjacent sites on the same duplex, depending on external conditions. Several nucleotide sequences have been identified to which H-NS binds with high affinity, indicating H-NS prefers AT-rich DNA. To date, highly detailed structural information of the H-NS DNA complex remains elusive. Molecular simulation can complement experiments by modelling structures and their time evolution in atomistic detail. In this paper we report an exploration of the different binding modes of H-NS to a high affinity nucleotide sequence and an estimate of the associated rate constant. By means of molecular dynamics simulations, we identified three types of binding for H-NS to AT-rich DNA. To further sample the transitions between these binding modes, we performed Replica Exchange Transition Interface Sampling, providing predictions of the mechanism and rate constant of H-NS binding to DNA. H-NS interacts with the DNA through a conserved QGR motif, aided by a conserved arginine at position 93. The QGR motif interacts first with phosphate groups, followed by the formation of hydrogen bonds between acceptors in the DNA minor groove and the sidechains of either Q112 or R114. After R114 inserts into the minor groove, the rest of the QGR motif follows. Full insertion of the QGR motif in the minor groove is stable over several tens of nanoseconds, and involves hydrogen bonds between the bases and both backbone and sidechains of the QGR motif. The rate constant for the process of H-NS binding to AT-rich DNA resulting in full insertion of the QGR motif is in the order of 106 M−1s−1, which is rate limiting compared to the non-specific association of H-NS to the DNA backbone at a rate of 108 M−1s−1. The Histone-like Nucleoid Structuring protein (H-NS) occurs in enterobacteria, such as Salmonella typhimurium and Escherichia coli, and structures DNA by forming filaments along DNA duplexes. Several nucleotide sequences have been identified to which H-NS binds with high affinity. Yet, obtaining highly detailed structural information of the H-NS DNA complex has proven to be a major challenge, which has not been yet resolved. By employing molecular dynamics simulations we were able to provide high resolution insights into the mechanism of DNA binding by H-NS. We identified various ways in which H-NS can bind to DNA. In all binding events, a conserved region in the protein initiates the association of H-NS to DNA. Our results show that H-NS binds in the minor groove of AT-rich DNA via a series of intermediate steps. Using advanced molecular simulation methods we predicted that the process of H-NS binding to the DNA backbone to full insertion into the minor groove occurs in the order of a million times per second, which is slower than the non-specific association of H-NS to the DNA backbone.
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20
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Suzuki H, Nishida K, Tamaki H. Shochu slop is an excellent medium for Escherichia coli K-12. Lett Appl Microbiol 2019; 68:505-508. [PMID: 30835838 DOI: 10.1111/lam.13148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
We found that shochu slop, the residue generated during the production of distilled shochu liquor, which must be treated as industrial waste, can be used as an excellent medium for Escherichia coli culture. LB medium is generally used in laboratories for culturing E. coli. However, it is not the optimal medium for E. coli culture because the bacterial cells cannot grow to very high densities in LB medium. On the other hand, E. coli can grow to higher densities in Terrific broth and this medium is used when researchers want to grow E. coli to high density or to obtain a protein with high yield. In this study, we removed solid matter from shochu slop, adjusted the pH of the mixture to 7 and subsequently used the slop for E. coli culture. The ability of shochu slop to support E. coli growth was compared with those of LB Miller medium and Terrific broth. The results indicate that sweet potato shochu slop as culture medium for E. coli is comparable to Terrific broth and much better than LB Miller medium in terms of supporting cell proliferation, and plasmid and enzyme production. SIGNIFICANCE AND IMPACT OF THE STUDY: Shochu manufacturers incur a cost to dispose shochu slop, which is recognized as food manufactural residues. Escherichia coli has been used in laboratories and in industry. However, culture media used in the laboratories are expensive and those used in industry are expensive because of their large scale. We found that sweet potato shochu slop is an excellent culture medium for E. coli. This finding is not only useful for laboratories and industry, but also beneficial to the effective utilization of this renewable resource to create a sustainable society.
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Affiliation(s)
- H Suzuki
- Division of Applied Biology, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto, Japan
| | - K Nishida
- Division of Applied Biology, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto, Japan
| | - H Tamaki
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
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21
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Qian S, Clomburg JM, Gonzalez R. Engineering Escherichia coli as a platform for the in vivo synthesis of prenylated aromatics. Biotechnol Bioeng 2019; 116:1116-1127. [PMID: 30659582 DOI: 10.1002/bit.26932] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/07/2019] [Accepted: 01/16/2019] [Indexed: 01/13/2023]
Abstract
Prenylated aromatics (PAs) are an important class of natural products with valuable pharmaceutical applications. To address current limitations of their sourcing from plants, here, we present a microbial platform for the in vivo synthesis of PAs based on the aromatic prenyltransferase NphB from Streptomyces sp. strain CL190. As proof of concept, we targeted the prenylation of phenolic/phenolcarboxylic acids, including orsellinic (OSA), divarinolic (DVA), and olivetolic (OLA) acids, whose prenylated products have important biopharmaceutical applications. Although the ability of wild-type NphB to catalyze the prenylation reaction with each acid was validated by in vitro characterization, improvement of product titers in vivo required protein modeling and rational design to engineer NphB variants with increased activity and product selectivity. When a designed NphB variant with eightfold improved catalytic efficiency toward OSA was expressed in an Escherichia coli host engineered to generate geranyl pyrophosphate at high flux through the mevalonate pathway, we observed up to 300 mg/L prenylated products by exogenously supplying OSA. The improved properties of engineered NphB were also utilized to demonstrate the diversification of this in vivo platform by using both different aromatic acceptors and different prenyl donors to generate various PA compounds, including medicinally important compounds such as cannabigerovarinic, cannabigerolic, and grifolic acids.
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Affiliation(s)
- Shuai Qian
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas.,Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas.,Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida
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22
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Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
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23
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Cardoso‐Rurr JS, Paiva JP, Paulino‐Lima IG, Alencar TA, Lage CA, Leitão AC. Microbiological Decontamination of Water: Improving the Solar Disinfection Technique (SODIS) with the Use of Nontoxic Vital Dye Methylene Blue. Photochem Photobiol 2018; 95:618-626. [DOI: 10.1111/php.12999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/02/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Janine S. Cardoso‐Rurr
- Laboratório de Radiobiologia Molecular Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
- Laboratório de Radiações em Biologia Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Juliana Patrão Paiva
- Laboratório de Radiobiologia Molecular Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
- Laboratório de Microbiologia e Avaliação Genotóxica College of Pharmacy Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Ivan G. Paulino‐Lima
- Laboratório de Radiobiologia Molecular Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
- Universities Space Research Association NASA Ames Research Center Moffett Field CA
| | - Tatiana A.M. Alencar
- Laboratório de Radiobiologia Molecular Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Claudia A.S. Lage
- Laboratório de Radiações em Biologia Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Alvaro C. Leitão
- Laboratório de Radiobiologia Molecular Institute of Biophysics Carlos Chagas Filho Federal University of Rio de Janeiro Rio de Janeiro Brazil
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24
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Zeidler S, Hubloher J, König P, Ngu ND, Scholz A, Averhoff B, Müller V. Salt induction and activation of MtlD, the key enzyme in the synthesis of the compatible solute mannitol in Acinetobacter baumannii. Microbiologyopen 2018; 7:e00614. [PMID: 29575790 PMCID: PMC6291793 DOI: 10.1002/mbo3.614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 01/05/2023] Open
Abstract
Mannitol is the major compatible solute, next to glutamate, synthesized by the opportunistic human pathogen Acinetobacter baumannii under low water activities. The key enzyme for mannitol biosynthesis, MtlD, was identified. MtlD is highly similar to the bifunctional mannitol‐1‐phosphate dehydrogenase/phosphatase from Acinetobacter baylyi. After deletion of the mtlD gene from A. baumannii ATCC 19606T cells no longer accumulated mannitol and growth was completely impaired at high salt. Addition of glycine betaine restored growth, demonstrating that mannitol is an important compatible solute in the human pathogen. MtlD was heterologously produced and purified. Enzyme activity was strictly salt dependent. Highest stimulation was reached at 600 mmol/L NaCl. Addition of different sodium as well as potassium salts restored activity, with highest stimulations up to 41 U/mg protein by sodium glutamate. In contrast, an increase in osmolarity by addition of sugars did not restore activity. Regulation of mannitol synthesis was also assayed at the transcriptional level. Reporter gene assays revealed that expression of mtlD is strongly dependent on high osmolarity, not discriminating between different salts or sugars. The presence of glycine betaine or its precursor choline repressed promoter activation. These data indicate a dual regulation of mannitol production in A. baumannii, at the transcriptional and the enzymatic level, depending on high osmolarity.
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Affiliation(s)
- Sabine Zeidler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Josephine Hubloher
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Patricia König
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Ngoc Dinh Ngu
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Anica Scholz
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt, Germany
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25
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Joyeux M. Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes. Biophys J 2018; 114:2317-2325. [PMID: 29576193 DOI: 10.1016/j.bpj.2018.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/05/2018] [Accepted: 02/28/2018] [Indexed: 11/17/2022] Open
Abstract
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer but is still not understood. Unraveling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties. The simulations reported here support a mechanism, according to which the primary role of multivalent cations consists in decreasing the strength of H-NS/DNA interactions compared to H-NS/H-NS interactions, with the latter ones becoming energetically favored with respect to the former ones above a certain threshold of the effective valency of the cations of the buffer. Below the threshold, H-NS dimers form filaments, which stretch along the DNA molecule but are quite inefficient in bridging genomically distant DNA sites (DNA-stiffening mode). In contrast, just above the threshold, H-NS dimers form three-dimensional clusters, which are able to connect DNA sites that are distant from the genomic point of view (DNA-bridging mode). The model provides clear rationales for the experimental observations that the switch between the two modes is a threshold effect and that the ability of H-NS dimers to form higher order oligomers is crucial for their bridging capabilities.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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26
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Vázquez-Ibarra A, Subirana L, Ongay-Larios L, Kawasaki L, Rojas-Ortega E, Rodríguez-González M, de Nadal E, Posas F, Coria R. Activation of the Hog1 MAPK by the Ssk2/Ssk22 MAP3Ks, in the absence of the osmosensors, is not sufficient to trigger osmostress adaptation in Saccharomyces cerevisiae. FEBS J 2018; 285:1079-1096. [PMID: 29341399 DOI: 10.1111/febs.14385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023]
Abstract
Yeast cells respond to hyperosmotic stress by activating the high-osmolarity glycerol (HOG) pathway, which consists of two branches, Hkr1/Msb2-Sho1 and Sln1, which trigger phosphorylation and nuclear internalization of the Hog1 mitogen-activated protein kinase. In the nucleus, Hog1 regulates gene transcription and cell cycle progression, which allows the cell to respond and adapt to hyperosmotic conditions. This study demonstrates that the uncoupling of the known sensors of both branches of the pathway at the level of Ssk1 and Ste11 impairs cell growth in hyperosmotic medium. However, under these conditions, Hog1 was still phosphorylated and internalized into the nucleus, suggesting the existence of an alternative Hog1 activation mechanism. In the ssk1ste11 mutant, phosphorylated Hog1 failed to associate with chromatin and to activate transcription of canonical hyperosmolarity-responsive genes. Accordingly, Hog1 also failed to induce glycerol production at the levels of a wild-type strain. Inactivation of the Ptp2 phosphatase moderately rescued growth impairment of the ssk1ste11 mutant under hyperosmotic conditions, indicating that downregulation of the HOG pathway only partially explains the phenotypes displayed by the ssk1ste11 mutant. Cell cycle defects were also observed in response to stress when Hog1 was phosphorylated in the ssk1ste11 mutant. Taken together, these observations indicate that Hog1 phosphorylation by noncanonical upstream mechanisms is not sufficient to trigger a protective response to hyperosmotic stress.
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Affiliation(s)
- Araceli Vázquez-Ibarra
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Laia Subirana
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Laura Kawasaki
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Eréndira Rojas-Ortega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Miriam Rodríguez-González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Cd de México, México
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27
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Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T. Crystal structure of theDNA‐binding domain of the LysR‐type transcriptional regulator CbnR in complex with aDNAfragment of the recognition‐binding site in the promoter region. FEBS J 2018; 285:977-989. [DOI: 10.1111/febs.14380] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/17/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022]
Affiliation(s)
| | - Naruhiko Adachi
- Structural Biology Research Center Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization (KEK) Tsukuba Japan
- Department of Materials Structure Science Accelerator Science The Graduate University of Advanced Studies (Soken‐dai) Tsukuba Japan
- Precursory Research for Embryonic Science and Technology Japan Science and Technology Agency Tsukuba Japan
| | - Miki Senda
- Structural Biology Research Center Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization (KEK) Tsukuba Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science Gifu University Japan
- Department of Applied Life Sciences Faculty of Agriculture Shizuoka University Japan
| | - Toshiya Senda
- Structural Biology Research Center Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization (KEK) Tsukuba Japan
- Department of Materials Structure Science Accelerator Science The Graduate University of Advanced Studies (Soken‐dai) Tsukuba Japan
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28
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Liang Y, van der Valk RA, Dame RT, Roos WH, Wuite GJL. Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling. Sci Rep 2017; 7:15275. [PMID: 29127381 PMCID: PMC5681504 DOI: 10.1038/s41598-017-15477-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022] Open
Abstract
Atomic force microscopy (AFM) has proven to be a powerful tool for the study of DNA-protein interactions due to its ability to image single molecules at the nanoscale. However, the use of AFM in force spectroscopy to study DNA-protein interactions has been limited. Here we developed a high throughput, AFM based, pulling assay to measure the strength and kinetics of protein bridging of DNA molecules. As a model system, we investigated the interactions between DNA and the Histone-like Nucleoid-Structuring protein (H-NS). We confirmed that H-NS both changes DNA rigidity and forms bridges between DNA molecules. This straightforward methodology provides a high-throughput approach with single-molecule resolution which is widely applicable to study cross-substrate interactions such as DNA-bridging proteins.
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Affiliation(s)
- Yan Liang
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry and Cell Observatory, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. .,Leiden Institute of Chemistry and Cell Observatory, Leiden University, Leiden, The Netherlands.
| | - Wouter H Roos
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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29
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Tramonti A, Milano T, Nardella C, di Salvo ML, Pascarella S, Contestabile R. Salmonella typhimurium PtsJ is a novel MocR-like transcriptional repressor involved in regulating the vitamin B 6 salvage pathway. FEBS J 2017; 284:466-484. [PMID: 27987384 DOI: 10.1111/febs.13994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022]
Abstract
The vitamin B6 salvage pathway, involving pyridoxine 5'-phosphate oxidase (PNPOx) and pyridoxal kinase (PLK), recycles B6 vitamers from nutrients and protein turnover to produce pyridoxal 5'-phosphate (PLP), the catalytically active form of the vitamin. Regulation of this pathway, widespread in living organisms including humans and many bacteria, is very important to vitamin B6 homeostasis but poorly understood. Although some information is available on the enzymatic regulation of PNPOx and PLK, little is known on their regulation at the transcriptional level. In the present work, we identified a new MocR-like regulator, PtsJ from Salmonella typhimurium, which controls the expression of the pdxK gene encoding one of the two PLKs expressed in this organism (PLK1). Analysis of pdxK expression in a ptsJ knockout strain demonstrated that PtsJ acts as a transcriptional repressor. This is the first case of a MocR-like regulator acting as repressor of its target gene. Expression and purification of PtsJ allowed a detailed characterisation of its effector and DNA-binding properties. PLP is the only B6 vitamer acting as effector molecule for PtsJ. A DNA-binding region composed of four repeated nucleotide sequences is responsible for binding of PtsJ to its target promoter. Analysis of binding stoichiometry revealed that protein subunits/DNA molar ratio varies from 4 : 1 to 2 : 1, depending on the presence or absence of PLP. Structural characteristics of DNA transcriptional factor-binding sites suggest that PtsJ binds DNA according to a different model with respect to other characterised members of the MocR subgroup.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.,Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
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30
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Narayan A, Campos LA, Bhatia S, Fushman D, Naganathan AN. Graded Structural Polymorphism in a Bacterial Thermosensor Protein. J Am Chem Soc 2017; 139:792-802. [DOI: 10.1021/jacs.6b10608] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
| | - Luis A. Campos
- National Biotechnology Center, Consejo Superior
de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sandhya Bhatia
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bangalore 560065, India
| | - David Fushman
- Department
of Chemistry and Biochemistry, Center for Biomolecular Structure and
Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
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31
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Winardhi RS, Yan J, Kenney LJ. H-NS Regulates Gene Expression and Compacts the Nucleoid: Insights from Single-Molecule Experiments. Biophys J 2016; 109:1321-9. [PMID: 26445432 DOI: 10.1016/j.bpj.2015.08.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022] Open
Abstract
A set of abundant nucleoid-associated proteins (NAPs) play key functions in organizing the bacterial chromosome and regulating gene transcription globally. Histone-like nucleoid structuring protein (H-NS) is representative of a family of NAPs that are widespread across bacterial species. They have drawn extensive attention due to their crucial function in gene silencing in bacterial pathogens. Recent rapid progress in single-molecule manipulation and imaging technologies has made it possible to directly probe DNA binding by H-NS, its impact on DNA conformation and topology, and its competition with other DNA-binding proteins at the single-DNA-molecule level. Here, we review recent findings from such studies, and provide our views on how these findings yield new insights into the understanding of the roles of H-NS family members in DNA organization and gene silencing.
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Affiliation(s)
- Ricksen S Winardhi
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore.
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois.
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32
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Winardhi RS, Castang S, Dove SL, Yan J. Single-molecule study on histone-like nucleoid-structuring protein (H-NS) paralogue in Pseudomonas aeruginosa: MvaU bears DNA organization mode similarities to MvaT. PLoS One 2014; 9:e112246. [PMID: 25372370 PMCID: PMC4221281 DOI: 10.1371/journal.pone.0112246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/13/2014] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa contains two distinct members of H-NS family of nucleoid-structuring proteins: MvaT and MvaU. Together, these proteins bind to the same regions of the chromosome and function coordinately in the regulation of hundreds of genes. Due to their structural similarity, they can associate to form heteromeric complexes. These findings left us wondering whether they bear similar DNA binding properties that underlie their gene-silencing functions. Using single-molecule stretching and imaging experiments, we found striking similarities in the DNA organization modes of MvaU compared to the previously studied MvaT. MvaU can form protective nucleoprotein filaments that are insensitive to environmental factors, consistent with its role as a repressor of gene expression. Similar to MvaT, MvaU filament can mediate DNA bridging while excessive MvaU can cause DNA aggregation. The almost identical DNA organization modes of MvaU and MvaT explain their functional redundancy, and raise an interesting question regarding the evolutionary benefits of having multiple H-NS paralogues in the Pseudomonas genus.
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Affiliation(s)
- Ricksen S. Winardhi
- NUS Graduate school for Integrative Sciences and Engineering, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Sandra Castang
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore, Singapore
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33
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Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging. Proc Natl Acad Sci U S A 2014; 111:8452-7. [PMID: 24912163 DOI: 10.1073/pnas.1406593111] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactivatable fluorescent proteins (PAFPs) have been widely used for superresolution imaging based on the switching and localization of single molecules. Several properties of PAFPs strongly influence the quality of the superresolution images. These properties include (i) the number of photons emitted per switching cycle, which affects the localization precision of individual molecules; (ii) the ratio of the on- and off-switching rate constants, which limits the achievable localization density; (iii) the dimerization tendency, which could cause undesired aggregation of target proteins; and (iv) the signaling efficiency, which determines the fraction of target-PAFP fusion proteins that is detectable in a cell. Here, we evaluated these properties for 12 commonly used PAFPs fused to both bacterial target proteins, H-NS, HU, and Tar, and mammalian target proteins, Zyxin and Vimentin. Notably, none of the existing PAFPs provided optimal performance in all four criteria, particularly in the signaling efficiency and dimerization tendency. The PAFPs with low dimerization tendencies exhibited low signaling efficiencies, whereas mMaple showed the highest signaling efficiency but also a high dimerization tendency. To address this limitation, we engineered two new PAFPs based on mMaple, which we termed mMaple2 and mMaple3. These proteins exhibited substantially reduced or undetectable dimerization tendencies compared with mMaple but maintained the high signaling efficiency of mMaple. In the meantime, these proteins provided photon numbers and on-off switching rate ratios that are comparable to the best achieved values among PAFPs.
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34
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Winardhi RS, Gulvady R, Mellies JL, Yan J. Locus of enterocyte effacement-encoded regulator (Ler) of pathogenic Escherichia coli competes off histone-like nucleoid-structuring protein (H-NS) through noncooperative DNA binding. J Biol Chem 2014; 289:13739-50. [PMID: 24668810 DOI: 10.1074/jbc.m113.545954] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The locus of enterocyte effacement-encoded regulator (Ler) of enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC) functions to activate transcription of virulence genes silenced by the histone-like nucleoid-structuring protein (H-NS). Despite its important role in the bacterial gene regulation, the binding mode of Ler to DNA and its mechanism in alleviating genes repressed by H-NS are largely unknown. In this study, we use magnetic tweezers to demonstrate that Ler binds extended DNA through a largely noncooperative process, which results in DNA stiffening and DNA folding depending on protein concentration. We also show that Ler can replace prebound H-NS on DNA over a range of potassium and magnesium concentrations. Our findings reveal the DNA binding properties of Ler and shed light to further understand the anti-silencing activity of Ler.
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Affiliation(s)
- Ricksen S Winardhi
- From the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore, the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ranjit Gulvady
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jay L Mellies
- the Biology Department, Reed College, Portland, Oregon 97202, and
| | - Jie Yan
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore, the Department of Physics, National University of Singapore, Singapore 117542, Singapore
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35
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Giangrossi M, Wintraecken K, Spurio R, de Vries R. Probing the relation between protein-protein interactions and DNA binding for a linker mutant of the bacterial nucleoid protein H-NS. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:339-45. [PMID: 24275506 DOI: 10.1016/j.bbapap.2013.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/29/2013] [Accepted: 11/15/2013] [Indexed: 10/26/2022]
Abstract
We have investigated the relationship between oligomerization in solution and DNA binding for the bacterial nucleoid protein H-NS. This was done by comparing oligomerization and DNA binding of H-NS with that of a H-NS D68V-D71V linker mutant. The double linker mutation D68V-D71V, that makes the linker significantly more hydrophobic, leads to a dramatically enhanced and strongly temperature-dependent H-NS oligomerization in solution, as detected by dynamic light scattering. The DNA binding affinity of H-NS D68V-D71V for the hns promoter region is lower and has stronger temperature dependence than that of H-NS. DNase I footprinting experiments show that at high concentrations, regions protected by H-NS D68V-D71V are larger and less defined than for H-NS. In vitro transcription assays show that the enhanced protection also leads to enhanced transcriptional repression. Whereas the lower affinity of the H-NS D68V-D71V for DNA could be caused by competition between oligomerization in solution and oligomerization on DNA, the larger size of protected regions clearly confirms the notion that cooperative binding of H-NS to DNA is related to protein-protein interactions. These results emphasize the relative contributions of protein-protein interactions and substrate-dependent oligomerization in the control of gene repression operated by H-NS.
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Affiliation(s)
- Mara Giangrossi
- University of Camerino, School of Biosciences and Biotechnologies, 62032 Camerino, MC, Italy
| | - Kathelijne Wintraecken
- Lab. Phys. Chem. Colloid Sci., Wageningen University, Dreijenplein 4, 6703 HB Wageningen, The Netherlands
| | - Roberto Spurio
- University of Camerino, School of Biosciences and Biotechnologies, 62032 Camerino, MC, Italy
| | - Renko de Vries
- Lab. Phys. Chem. Colloid Sci., Wageningen University, Dreijenplein 4, 6703 HB Wageningen, The Netherlands.
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36
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Joyeux M, Vreede J. A model of H-NS mediated compaction of bacterial DNA. Biophys J 2013; 104:1615-22. [PMID: 23561538 DOI: 10.1016/j.bpj.2013.02.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/24/2013] [Accepted: 02/12/2013] [Indexed: 12/26/2022] Open
Abstract
The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same duplex. Based on scanning force microscopy imaging and optical trap-driven unzipping assays, it has recently been suggested that DNA compaction may result from the antagonistic effects of H-NS binding to DNA in trans and cis configurations. To get more insight into the compaction mechanism, we constructed a coarse-grained model description of the compaction of bacterial DNA by H-NS. These simulations highlight the fact that DNA compaction indeed results from the subtle equilibrium between several competing factors, which include the deformation dynamics of the plasmid and the several binding modes of protein dimers to DNA, i.e., dangling configurations, cis- and trans-binding. In particular, the degree of compaction is extremely sensitive to the difference in binding energies of the cis and trans configurations. Our simulations also point out that the conformations of the DNA-protein complexes are significantly different in bulk and in planar conditions, suggesting that conformations observed on mica surfaces may differ significantly from those that prevail in living cells.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique UMR5588, Université Joseph Fourier Grenoble 1, St. Martin d'Hères, France.
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37
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McKethan BL, Spiro S. Cooperative and allosterically controlled nucleotide binding regulates the DNA binding activity of NrdR. Mol Microbiol 2013; 90:278-89. [PMID: 23941567 DOI: 10.1111/mmi.12364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2013] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) are required for the synthesis of deoxyribonucleoside triphosphates (dNTPs) from ribonucleotides. In Escherichia coli, regulation of RNR expression is co-ordinated with the cell cycle, and involves several regulatory proteins. One of these, NrdR, has recently been shown to regulate all three nrd operons that encode RNR isoenzymes. Repression by NrdR is believed to be stimulated by elevated dNTPs, although there is no direct evidence for this model. Here, we sought to elucidate the mechanism by which NrdR regulates nrd expression according to the abundance of (d)NTPs. We determined that ATP and dATP bind to NrdR in a negatively cooperative fashion, such that neither can fully occupy the protein. Both nucleotides also appear to act as positive heterotropic effectors, since the binding of one stimulates binding of the other. Nucleotide binding stimulates self-association of NrdR, with tri- and diphosphates stimulating oligomerization more effectively than monophosphates. As-prepared NrdR contains (deoxy)nucleoside monophosphates, diphosphates and triphosphates, and its DNA binding activity is inhibited by triphosphates and diphosphates but not by monophosphates. We propose a model in which NrdR selectively binds (deoxy)nucleoside triphosphates, which are hydrolysed to their monophosphate counterparts in order to regulate DNA binding.
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Affiliation(s)
- Brandon L McKethan
- Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Road, Richardson, TX, 75080, USA
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38
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On the Origin of the Selectivity of Plasmidic H-NS towards Horizontally Acquired DNA: Linking H-NS Oligomerization and Cooperative DNA Binding. J Mol Biol 2013; 425:2347-58. [DOI: 10.1016/j.jmb.2013.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/21/2013] [Accepted: 03/05/2013] [Indexed: 11/24/2022]
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39
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Renault M, García J, Cordeiro TN, Baldus M, Pons M. Protein oligomers studied by solid-state NMR--the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein. FEBS J 2013; 280:2916-28. [PMID: 23601147 DOI: 10.1111/febs.12297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 04/03/2013] [Accepted: 04/16/2013] [Indexed: 11/28/2022]
Abstract
Members of the histone-like nucleoid structuring protein (H-NS) family play roles both as architectural proteins and as modulators of gene expression in Gram-negative bacteria. The H-NS protein participates in modulatory processes that respond to environmental changes in osmolarity, pH, or temperature. H-NS oligomerization is essential for its activity. Structural models of different truncated forms are available. However, high-resolution structural details of full-length H-NS and its DNA-bound state have largely remained elusive. We report on progress in characterizing the biologically active H-NS oligomers with solid-state NMR. We compared uniformly ((13)C,(15)N)-labeled ssNMR preparations of the isolated N-terminal region (H-NS 1-47) and full-length H-NS (H-NS 1-137). In both cases, we obtained ssNMR spectra of good quality and characteristic of well-folded proteins. Analysis of the results of 2D and 3D (13)C-(13)C and (15)N-(13)C correlation experiments conducted at high magnetic field led to assignments of residues located in different topological regions of the free full-length H-NS. These findings confirm that the structure of the N-terminal dimerization domain is conserved in the oligomeric full-length protein. Small changes in the dimerization interface suggested by localized chemical shift variations between solution and solid-state spectra may be relevant for DNA recoginition.
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Affiliation(s)
- Marie Renault
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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40
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Ali SS, Whitney JC, Stevenson J, Robinson H, Howell PL, Navarre WW. Structural insights into the regulation of foreign genes in Salmonella by the Hha/H-NS complex. J Biol Chem 2013; 288:13356-69. [PMID: 23515315 DOI: 10.1074/jbc.m113.455378] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hha facilitates H-NS-mediated silencing of foreign genes in bacteria. RESULTS Two Hha monomers bind opposing faces of the H-NS N-terminal dimerization domain. CONCLUSION Hha binds the dimerization domain of H-NS and may contact DNA via positively charged surface residues. SIGNIFICANCE The structure of Hha and H-NS in complex provides a mechanistic model of how Hha may affect gene regulation. The bacterial nucleoid-associated proteins Hha and H-NS jointly repress horizontally acquired genes in Salmonella, including essential virulence loci encoded within Salmonella pathogenicity islands. Hha is known to interact with the N-terminal dimerization domain of H-NS; however, the manner in which this interaction enhances transcriptional silencing is not understood. To further understand this process, we solved the x-ray crystal structure of Hha in complex with the N-terminal dimerization domain of H-NS (H-NS(1-46)) to 3.2 Å resolution. Two monomers of Hha bind to symmetrical sites on either side of the H-NS(1-46) dimer. Disruption of the Hha/H-NS interaction by the H-NS site-specific mutation I11A results in increased expression of the Hha/H-NS co-regulated gene hilA without affecting the expression levels of proV, a target gene repressed by H-NS in an Hha-independent fashion. Examination of the structure revealed a cluster of conserved basic amino acids that protrude from the surface of Hha on the opposite side of the Hha/H-NS(1-46) interface. Hha mutants with a diminished positively charged surface maintain the ability to interact with H-NS but can no longer regulate hilA. Increased expression of the hilA locus did not correspond to significant depletion of H-NS at the promoter region in chromatin immunoprecipitation assays. However, in vitro, we find Hha improves H-NS binding to target DNA fragments. Taken together, our results show for the first time how Hha and H-NS interact to direct transcriptional repression and reveal that a positively charged surface of Hha enhances the silencing activity of H-NS nucleoprotein filaments.
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Affiliation(s)
- Sabrina S Ali
- Departments of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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41
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Predicting the effect of ions on the conformation of the H-NS dimerization domain. Biophys J 2012; 103:89-98. [PMID: 22828335 DOI: 10.1016/j.bpj.2012.05.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/11/2012] [Accepted: 05/15/2012] [Indexed: 11/23/2022] Open
Abstract
The histone-like nucleoid structuring protein (H-NS) is a DNA-organizing protein in bacteria. It contains a DNA-binding domain and a dimerization domain, connected by a flexible linker region. Dimerization occurs through the formation of a helical bundle, including a coiled-coil interaction motif. Two conformations have been resolved, for different sequences of Escherichia coli H-NS, resulting in an antiparallel coiled-coil for the shorter wild-type sequence, and a parallel coiled-coil for the longer C21S mutant. Because H-NS functions as a thermo- and osmosensor, these conformations may both be functionally relevant. Molecular simulation can complement experiments by modeling the dynamical time evolution of biomolecular systems in atomistic detail. We performed a molecular-dynamics study of the H-NS dimerization domain, showing that the parallel complex is sensitive to changes in salt conditions: it is unstable in absence of NaCl, but stable at physiological salt concentrations. In contrast, the stability of the antiparallel complex is not salt-dependent. The stability of the parallel complex also appears to be affected by mutation of the critical but nonconserved cysteine residue at position 21, whereas the antiparallel complex is not. Together, our simulations suggest that osmoregulation could be mediated by changes in the ratio of parallel- and antiparallel-oriented H-NS dimers.
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Winardhi RS, Fu W, Castang S, Li Y, Dove SL, Yan J. Higher order oligomerization is required for H-NS family member MvaT to form gene-silencing nucleoprotein filament. Nucleic Acids Res 2012; 40:8942-52. [PMID: 22798496 PMCID: PMC3467065 DOI: 10.1093/nar/gks669] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MvaT from Pseudomonas aeruginosa is a member of the histone-like nucleoid structuring protein (H-NS) family of nucleoid-associated proteins widely spread among Gram-negative bacteria that functions to repress the expression of many genes. Recently, it was reported that H-NS from Escherichia coli can form rigid nucleoproteins filaments on DNA, which are important for their gene-silencing function. This raises a question whether the gene-silencing function of MvaT, which has only ∼18% sequence similarity to H-NS, is also based on the formation of nucleoprotein filaments. Here, using magnetic tweezers and atomic force microscopy imaging, we demonstrate that MvaT binds to DNA through cooperative polymerization to form a nucleoprotein filament that can further organize DNA into hairpins or higher-order compact structures. Furthermore, we studied DNA binding by MvaT mutants that fail to repress gene expression in P. aeruginosa because they are specifically defective for higher-order oligomer formation. We found that, although the mutants can organize DNA into compact structures, they fail to form rigid nucleoprotein filaments. Our findings suggest that higher-order oligomerization of MvaT is required for the formation of rigid nucleoprotein filaments that silence at least some target genes in P. aeruginosa. Further, our findings suggest that formation of nucleoprotein filaments provide a general structural basis for the gene-silencing H-NS family members.
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Affiliation(s)
- Ricksen S Winardhi
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456
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Rosselli-Murai LK, Sforça ML, Sassonia RC, Azzoni AR, Murai MJ, de Souza AP, Zeri AC. Structural characterization of the H-NS protein from Xylella fastidiosa and its interaction with DNA. Arch Biochem Biophys 2012; 526:22-8. [PMID: 22772065 DOI: 10.1016/j.abb.2012.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023]
Abstract
The nucleoid-associated protein H-NS is a major component of the bacterial nucleoid involved in DNA compaction and transcription regulation. The NMR solution structure of the Xylella fastidiosa H-NS C-terminal domain (residues 56-134) is presented here and consists of two beta-strands and two alpha helices, with one loop connecting the two beta-strands and a second loop connecting the second beta strand and the first helix. The amide (1)H and (15)N chemical shift signals for a sample of XfH-NS(56-134) were monitored in the course of a titration series with a 14-bp DNA duplex. Most of the residues involved in contacts to DNA are located around the first and second loops and in the first helix at a positively charged side of the protein surface. The overall structure of the Xylella H-NS C-terminal domain differ significantly from Escherichia coli and Salmonella enterica H-NS proteins, even though the DNA binding motif in loop 2 adopt similar conformation, as well as β-strand 2 and loop 1. Interestingly, we have also found that the DNA binding site is expanded to include helix 1, which is not seen in the other structures.
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Ali SS, Xia B, Liu J, Navarre WW. Silencing of foreign DNA in bacteria. Curr Opin Microbiol 2012; 15:175-81. [DOI: 10.1016/j.mib.2011.12.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/20/2011] [Accepted: 12/23/2011] [Indexed: 10/14/2022]
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45
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de Vries R. Influence of mobile DNA-protein-DNA bridges on DNA configurations: coarse-grained Monte-Carlo simulations. J Chem Phys 2012; 135:125104. [PMID: 21974563 DOI: 10.1063/1.3636383] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.
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Affiliation(s)
- Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, P.O. Box 8038, 6700 EK Wageningen, The Netherlands.
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Wang W, Li GW, Chen C, Xie XS, Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011; 333:1445-9. [PMID: 21903814 DOI: 10.1126/science.1204697] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.
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Affiliation(s)
- Wenqin Wang
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. J Bacteriol 2011; 193:4881-92. [PMID: 21764926 DOI: 10.1128/jb.05198-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The 5.5 protein (T7p32) of coliphage T7 (5.5(T7)) was shown to bind and inhibit gene silencing by the nucleoid-associated protein H-NS, but the mechanism by which it acts was not understood. The 5.5(T7) protein is insoluble when expressed in Escherichia coli, but we find that 5.5(T7) can be isolated in a soluble form when coexpressed with a truncated version of H-NS followed by subsequent disruption of the complex during anion-exchange chromatography. Association studies reveal that 5.5(T7) binds a region of H-NS (residues 60 to 80) recently found to contain a distinct domain necessary for higher-order H-NS oligomerization. Accordingly, we find that purified 5.5(T7) can disrupt higher-order H-NS-DNA complexes in vitro but does not abolish DNA binding by H-NS per se. Homologues of the 5.5(T7) protein are found exclusively among members of the Autographivirinae that infect enteric bacteria, and despite fairly low sequence conservation, the H-NS binding properties of these proteins are largely conserved. Unexpectedly, we find that the 5.5(T7) protein copurifies with heterogeneous low-molecular-weight RNA, likely tRNA, through several chromatography steps and that this interaction does not require the DNA binding domain of H-NS. The 5.5 proteins utilize a previously undescribed mechanism of H-NS antagonism that further highlights the critical importance that higher-order oligomerization plays in H-NS-mediated gene repression.
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Refining the binding of the Escherichia coli flagellar master regulator, FlhD4C2, on a base-specific level. J Bacteriol 2011; 193:4057-68. [PMID: 21685294 DOI: 10.1128/jb.00442-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli flagellar master regulator, FlhD(4)C(2), binds to the promoter regions of flagellar class II genes, yet, despite extensive analysis of the FlhD(4)C(2)-regulated promoter region, a detailed consensus sequence has not emerged. We used in vitro and in vivo experimental approaches to determine the nucleotides in the class II promoter, fliAp, required for the binding and function of FlhD(4)C(2). FlhD(4)C(2) protects 48 bp (positions -76 to -29 relative to the σ(70)-dependent transcriptional start site) in the fliA promoter. We divided the 48-bp footprint region into 5 sections to determine the requirement of each DNA segment for the binding and function of FlhD(4)C(2). Results from an in vitro binding competition assay between the wild-type FlhD(4)C(2)-protected fragment and DNA fragments possessing mutations in one section of the 48-bp protected region showed that only one-third of the 48 bp protected by FlhD(4)C(2) is required for FlhD(4)C(2) binding and fliA promoter activity. This in vitro binding result was also seen in vivo with fliA promoter-lacZ fusions carrying the same mutations. Only seven bases (A(12), A(15), T(34), A(36), T(37), A(44), and T(45)) are absolutely required for the promoter activity. Moreover, A(12), A(15), T(34), T(37), and T(45) within the 7 bases are highly specific to fliA promoter activity, and those bases form an asymmetric recognition site for FlhD(4)C(2). The implications of the asymmetry of the FlhD(4)C(2) binding site and its potential impact on FlhD(4)C(2) are discussed.
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Castang S, Dove SL. High-order oligomerization is required for the function of the H-NS family member MvaT in Pseudomonas aeruginosa. Mol Microbiol 2010; 78:916-31. [PMID: 20815825 DOI: 10.1111/j.1365-2958.2010.07378.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
H-NS is an abundant DNA-binding protein that has been implicated in the silencing of foreign DNA in several different bacteria. The ability of H-NS dimers to form higher-order oligomers is thought to aid the polymerization of the protein across AT-rich stretches of DNA and facilitate gene silencing. Although the oligomerization of H-NS from enteric bacteria has been the subject of intense investigation, little is known regarding the oligomerization of H-NS family members from bacteria outside of the enterobacteriaceae, many of which share little sequence similarity with their enteric counterparts. Here we show that MvaT, a member of the H-NS family of proteins from Pseudomonas aeruginosa, can form both dimers and higher-order oligomers, and we identify a region within MvaT that mediates higher-order oligomer formation. Using genetic assays we identify mutants of MvaT that are defective for higher-order oligomer formation. We present evidence that these mutants are functionally impaired and exhibit DNA-binding defects because of their inability to form higher-order oligomers. Our findings support a model in which the ability of MvaT to bind efficiently to the DNA depends upon protein-protein interactions between MvaT dimers and suggest that the ability to form higher-order oligomers is a conserved and essential feature of H-NS family members.
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Affiliation(s)
- Sandra Castang
- Division of Infectious Diseases, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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50
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Arold ST, Leonard PG, Parkinson GN, Ladbury JE. H-NS forms a superhelical protein scaffold for DNA condensation. Proc Natl Acad Sci U S A 2010; 107:15728-32. [PMID: 20798056 PMCID: PMC2936596 DOI: 10.1073/pnas.1006966107] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The histone-like nucleoid structuring (H-NS) protein plays a fundamental role in DNA condensation and is a key regulator of enterobacterial gene expression in response to changes in osmolarity, pH, and temperature. The protein is capable of high-order self-association via interactions of its oligomerization domain. Using crystallography, we have solved the structure of this complete domain in an oligomerized state. The observed superhelical structure establishes a mechanism for the self-association of H-NS via both an N-terminal antiparallel coiled-coil and a second, hitherto unidentified, helix-turn-helix dimerization interface at the C-terminal end of the oligomerization domain. The helical scaffold suggests the formation of a H-NS:plectonemic DNA nucleoprotein complex that is capable of explaining published biophysical and functional data, and establishes a unifying structural basis for coordinating the DNA packaging and transcription repression functions of H-NS.
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Affiliation(s)
- Stefan T. Arold
- Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Unit 1000, 1515 Holcombe Boulevard, Houston, TX 77030
| | - Paul G. Leonard
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom; and
| | - Gary N. Parkinson
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - John E. Ladbury
- Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Unit 1000, 1515 Holcombe Boulevard, Houston, TX 77030
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom; and
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