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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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Baglivo I, Pirone L, Malgieri G, Fattorusso R, Roop II RM, Pedone EM, Pedone PV. MucR binds multiple target sites in the promoter of its own gene and is a heat-stable protein: Is MucR a H-NS-like protein? FEBS Open Bio 2018; 8:711-718. [PMID: 29632823 PMCID: PMC5881533 DOI: 10.1002/2211-5463.12411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/17/2018] [Accepted: 02/21/2018] [Indexed: 01/08/2023] Open
Abstract
The protein MucR from Brucella spp. is involved in the expression regulation of genes necessary for host interaction and infection. MucR is a member of the Ros/MucR family, which comprises prokaryotic zinc-finger proteins and includes Ros from Agrobacterium tumefaciens and the Ml proteins from Mesorhizobium loti. MucR from Brucella spp. can regulate the expression of virulence genes and repress its own gene expression. Despite the well-known role played by MucR in the repression of its own gene, no target sequence has yet been identified in the mucR promoter gene. In this study, we provide the first evidence that MucR from Brucella abortus binds more than one target site in the promoter region of its own gene, suggesting a molecular mechanism by which this protein represses its own expression. Furthermore, a circular dichroism analysis reveals that MucR is a heat-stable protein. Overall, the results of this study suggest that MucR might resemble a H-NS protein.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Luciano Pirone
- Institute of Biostructures and BioimagingC.N.R.NaplesItaly
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
| | - Roy Martin Roop II
- Department of Microbiology and ImmunologyBrody School of MedicineEast Carolina UniversityGreenvilleNCUSA
| | | | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and TechnologiesUniversity of Campania ‘Luigi Vanvitelli’CasertaItaly
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A newly isolated thermostable lipase from Bacillus sp. Int J Mol Sci 2011; 12:2917-34. [PMID: 21686158 PMCID: PMC3116164 DOI: 10.3390/ijms12052917] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/25/2011] [Accepted: 04/12/2011] [Indexed: 11/17/2022] Open
Abstract
A thermophilic lipolytic bacterium identified as Bacillus sp. L2 via 16S rDNA was previously isolated from a hot spring in Perak, Malaysia. Bacillus sp. L2 was confirmed to be in Group 5 of bacterial classification, a phylogenically and phenotypically coherent group of thermophilic bacilli displaying very high similarity among their 16S rRNA sequences (98.5–99.2%). Polymerase chain reaction (PCR) cloning of L2 lipase gene was conducted by using five different primers. Sequence analysis of the L2 lipase gene revealed an open reading frame (ORF) of 1251 bp that codes for 417 amino acids. The signal peptides consist of 28 amino acids. The mature protein is made of 388 amino acid residues. Recombinant lipase was successfully overexpressed with a 178-fold increase in activity compared to crude native L2 lipase. The recombinant L2 lipase (43.2 kDa) was purified to homogeneity in a single chromatography step. The purified lipase was found to be reactive at a temperature range of 55–80 °C and at a pH of 6–10. The L2 lipase had a melting temperature (Tm) of 59.04 °C when analyzed by circular dichroism (CD) spectroscopy studies. The optimum activity was found to be at 70 °C and pH 9. Lipase L2 was strongly inhibited by ethylenediaminetetraacetic acid (EDTA) (100%), whereas phenylmethylsulfonyl fluoride (PMSF), pepstatin-A, 2-mercaptoethanol and dithiothreitol (DTT) inhibited the enzyme by over 40%. The CD spectra of secondary structure analysis showed that the L2 lipase structure contained 38.6% α-helices, 2.2% ß-strands, 23.6% turns and 35.6% random conformations.
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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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Hillebrand A, Wurm R, Menzel A, Wagner R. The seven E. coli ribosomal RNA operon upstream regulatory regions differ in structure and transcription factor binding efficiencies. Biol Chem 2005; 386:523-34. [PMID: 16006239 DOI: 10.1515/bc.2005.062] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Ribosomal RNAs in E. coli are transcribed from seven operons, which are highly conserved in their organization and sequence. However, the upstream regulatory DNA regions differ considerably, suggesting differences in regulation. We have therefore analyzed the conformation of all seven DNA elements located upstream of the major E. coli rRNA P1 promoters. As judged by temperature-dependent gel electrophoresis with isolated DNA fragments comprising the individual P1 promoters and the complete upstream regulatory regions, all seven rRNA upstream sequences are intrinsically curved. The degree of intrinsic curvature was highest for the rrnB and rrnD fragments and less pronounced for the rrnA and rrnE operons. Comparison of the experimentally determined differences in curvature with programs for the prediction of DNA conformation revealed a generally high degree of conformity. Moreover, the analysis showed that the center of curvature is located at about the same position in all fragments. The different upstream regions were analyzed for their capacity to bind the transcription factors FIS and H-NS, which are known as antagonists in the regulation of rRNA synthesis. Gel retardation experiments revealed that both proteins interact with the upstream promoter regions of all seven rDNA fragments, with the affinities of the different DNA fragments for FIS and H-NS and the structure of the resulting complexes deviating considerably. FIS binding was non-cooperative, and at comparable protein concentrations the occupancy of the different DNA fragments varied between two and four binding sites. In contrast, H-NS was shown to bind cooperatively and intermediate states of occupancy could not be resolved for each fragment. The different gel electrophoretic mobilities of the individual DNA/protein complexes indicate variable structures and topologies of the upstream activating sequence regulatory complexes. Our results are highly suggestive of differential regulation of the individual rRNA operons.
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Affiliation(s)
- Annette Hillebrand
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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Rimsky S. Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol 2004; 7:109-14. [PMID: 15063845 DOI: 10.1016/j.mib.2004.02.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
H-NS belongs to the group of histone-like proteins in Gram-negative bacteria and is also a pleiotropic regulator of genes implicated in many responses to environmental changes. It plays a dual role in structuring DNA and in regulating transcription. Recent advances have been made in elucidating the structure and oligomerisation properties of this protein, thus aiding in the understanding of the molecular relationship between its two major functions.
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Affiliation(s)
- Sylvie Rimsky
- Enzymologie et Cinétique Structurale, LBPA, UMR 8113, Ecole Normale Supérieure de Cachan/CNRS/ Université Paris XI, 61 Avenue du Président Wilsons, 94235 Cachan cedex, France.
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Bloch V, Yang Y, Margeat E, Chavanieu A, Augé MT, Robert B, Arold S, Rimsky S, Kochoyan M. The H-NS dimerization domain defines a new fold contributing to DNA recognition. Nat Struct Mol Biol 2003; 10:212-8. [PMID: 12592399 DOI: 10.1038/nsb904] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2002] [Accepted: 01/13/2003] [Indexed: 11/09/2022]
Abstract
H-NS, a protein found in Gram-negative bacteria, is involved in structuring the bacterial chromosome and acts as a global regulator for the expression of a wide variety of genes. These functions are correlated with both its DNA-binding and oligomerization properties. We have identified the minimal dimerization domain of H-NS, a 46 amino acid-long N-terminal fragment, and determined its structure using heteronuclear NMR spectroscopy. The highly intertwined structure of the dimer, reminiscent of a handshake, defines a new structural fold, which may offer a possibility for discriminating prokaryotic from eukaryotic proteins in drug design. Using mutational analysis, we also show that this N-terminal domain actively contributes to DNA binding, conversely to the current paradigm. Together, our data allows us to propose a model for the action of full length H-NS.
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Affiliation(s)
- Vanessa Bloch
- Centre de Biochimie Structurale, CNRS-UMR 5048, INSERM-U554, Université de Montpellier I, 29 rue de Navacelles, 34090 Montpellier, France
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Esposito D, Petrovic A, Harris R, Ono S, Eccleston JF, Mbabaali A, Haq I, Higgins CF, Hinton JCD, Driscoll PC, Ladbury JE. H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. J Mol Biol 2002; 324:841-50. [PMID: 12460581 DOI: 10.1016/s0022-2836(02)01141-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
H-NS plays a role in condensing DNA in the bacterial nucleoid. This 136 amino acid protein comprises two functional domains separated by a flexible linker. High order structures formed by the N-terminal oligomerization domain (residues 1-89) constitute the basis of a protein scaffold that binds DNA via the C-terminal domain. Deletion of residues 57-89 or 64-89 of the oligomerization domain precludes high order structure formation, yielding a discrete dimer. This dimerization event represents the initial event in the formation of high order structure. The dimers thus constitute the basic building block of the protein scaffold. The three-dimensional solution structure of one of these units (residues 1-57) has been determined. Activity of these structural units is demonstrated by a dominant negative effect on high order structure formation on addition to the full length protein. Truncated and site-directed mutant forms of the N-terminal domain of H-NS reveal how the dimeric unit self-associates in a head-to-tail manner and demonstrate the importance of secondary structure in this interaction to form high order structures. A model is presented for the structural basis for DNA packaging in bacterial cells.
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Affiliation(s)
- Diego Esposito
- Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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Reusch RN, Shabalin O, Crumbaugh A, Wagner R, Schröder O, Wurm R. Posttranslational modification of E. coli histone-like protein H-NS and bovine histones by short-chain poly-(R)-3-hydroxybutyrate (cPHB). FEBS Lett 2002; 527:319-22. [PMID: 12220682 DOI: 10.1016/s0014-5793(02)03236-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Short-chain poly-(R)-3-hydroxybutyrate (cPHB), a highly flexible, amphiphilic molecule with salt-solvating properties, is a ubiquitous constituent of prokaryotic and eukaryotic cells, wherein it is mainly conjugated to proteins. The solvating properties and cellular distribution of cPHB suggest it may be associated with proteins that bind and/or transfer DNA. Here we examine Escherichia coli protein H-NS and calf thymus histones, H1, H2A, H2B, H3, and H4, for the presence of cPHB. The proteins are related in that all bind to DNA and are implicated in the compact organization of the chromosome. The presence of cPHB in E. coli H-NS was first detected in Western blots of two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of total cell proteins, probed with anti-cPHB IgG, and then by Western blot analysis of the purified protein. Western blot analysis of the calf thymus histones indicated that each contained cPHB. The presence of cPHB in H-NS and histones was confirmed by chemical assay. The in vivo size of conjugated cPHB could not be established due to the lack of standards and degradation of cPHB during protein purification and storage. The molecular characteristics of cPHB and its presence in histone-like and histone proteins of diverse organisms suggest it may play a role in DNA binding and/or DNA organization.
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Affiliation(s)
- Rosetta N Reusch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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Schröder O, Wagner R. The bacterial regulatory protein H-NS--a versatile modulator of nucleic acid structures. Biol Chem 2002; 383:945-60. [PMID: 12222684 DOI: 10.1515/bc.2002.101] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The small DNA binding protein H-NS is attracting broad interest for its profound involvement in the regulation of bacterial physiology. It is involved in the regulation of many genes in response to a changing environment and functions in the adaptation to many different kinds of stress. Many H-NS-controlled genes, including the hns gene itself, are further linked to global regulatory networks. H-NS thus plays a key role in maintaining bacterial homeostasis under conditions of a rapidly changing environment. In this review we summarize recent results from combined biochemical and biophysical efforts which have yielded new insights into the three-dimensional structure and function of H-NS. The protein consists of two distinct domains separated by an unstructured linker region, and the structural details available today have helped to understand how these domains may interact with each other or with ligand molecules. Functional studies have, in addition, revealed mechanistic clues for the various H-NS activities, like temperature- or growth phase-dependent regulation. Important elements for the specific regulatory activities of H-NS comprise different modes of DNA binding, protein oligomerization, the competition with other regulators and the fact that the topology of the target DNA is modulated during complex formation. The distinctive ability to recognize nucleic acid structures in combination with other proteins also explains H-NS-dependent post-transcriptional activities where the interaction with defined RNA structures and the interference with RNA/protein complexes during mRNA translation are crucial for regulation. Thus, protein/protein interactions, in combination with the recognition and modulation of nucleic acid structures, are key elements of the different mechanisms which make H-NS such a versatile regulator.
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Affiliation(s)
- Oliver Schröder
- Division of Biology and Center for Molecular Genetics, University of California at San Diego, La Jolla 92093-0634, USA
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