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Gaddy KE, Bensch EM, Cavanagh J, Milton ME. Insights into DNA-binding motifs and mechanisms of Francisella tularensis novicida two-component system response regulator proteins QseB, KdpE, and BfpR. Biochem Biophys Res Commun 2024; 722:150150. [PMID: 38805787 DOI: 10.1016/j.bbrc.2024.150150] [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: 03/06/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Two component system bacterial response regulators are typically DNA-binding proteins which enable the genetic regulation of many adaptive bacterial behaviors. Despite structural similarity across response regulator families, there is a diverse array of DNA-binding mechanisms. Bacteria usually encode several dozen two-component system response regulators, but Francisella tularensis only encodes three. Due to their simplified response regulatory network, Francisella species are a model for studying the role of response regulator proteins in virulence. Here, we show that Francisella response regulators QseB, KdpE, and BfpR all utilize different DNA-binding mechanisms. Our evidence suggests that QseB follows a simple mechanism whereby it binds a single inverted repeat sequence with a higher affinity upon phosphorylation. This behavior is independent of whether QseB is a positive or negative regulator of the gene as demonstrated by qseB and priM promoter sequences, respectively. Similarly, KdpE binds DNA more tightly upon phosphorylation, but also exhibits a cooperative binding isotherm. While we propose a KdpE binding site, it is possible that KdpE has a complex DNA-binding mechanism potentially involving multiple copies of KdpE being recruited to a promoter region. Finally, we show that BfpR appears to bind a region of its own promoter sequence with a lower affinity upon phosphorylation. Further structural and enzymatic work will need to be performed to deconvolute the KdpE and BfpR binding mechanisms.
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Affiliation(s)
- Keegan E Gaddy
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Elody M Bensch
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Morgan E Milton
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA.
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2
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Ghoshal M, Bechtel TD, Gibbons JG, McLandsborough L. Adaptive laboratory evolution of Salmonella enterica in acid stress. Front Microbiol 2023; 14:1285421. [PMID: 38033570 PMCID: PMC10687551 DOI: 10.3389/fmicb.2023.1285421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Adaptive laboratory evolution (ALE) studies play a crucial role in understanding the adaptation and evolution of different bacterial species. In this study, we have investigated the adaptation and evolution of Salmonella enterica serovar Enteritidis to acetic acid using ALE. Materials and methods Acetic acid concentrations below the minimum inhibitory concentration (sub-MIC) were used. Four evolutionary lineages (EL), namely, EL1, EL2, EL3, and EL4, of S. Enteritidis were developed, each demonstrating varying levels of resistance to acetic acid. Results The acetic acid MIC of EL1 remained constant at 27 mM throughout 70 days, while the MIC of EL2, EL3, and EL4 increased throughout the 70 days. EL4 was adapted to the highest concentration of acetic acid (30 mM) and demonstrated the highest increase in its MIC against acetic acid throughout the study, reaching an MIC of 35 mM on day 70. The growth rates of the evolved lineages increased over time and were dependent on the concentration of acetic acid used during the evolutionary process. EL4 had the greatest increase in growth rate, reaching 0.33 (h-1) after 70 days in the presence of 30 mM acetic acid as compared to EL1, which had a growth rate of 0.2 (h-1) after 70 days with no exposure to acetic acid. Long-term exposure to acetic acid led to an increased MIC of human antibiotics such as ciprofloxacin and meropenem against the S. enterica evolutionary lineages. The MIC of ciprofloxacin for EL1 stayed constant at 0.016 throughout the 70 days while that of EL4 increased to 0.047. Bacterial whole genome sequencing revealed single-nucleotide polymorphisms in the ELs in various genes known to be involved in S. enterica virulence, pathogenesis, and stress response including phoP, phoQ, and fhuA. We also observed genome deletions in some of the ELs as compared to the wild-type S. Enteritidis which may have contributed to the bacterial acid adaptation. Discussion This study highlights the potential for bacterial adaptation and evolution under environmental stress and underscores the importance of understanding the development of cross resistance to antibiotics in S. enterica populations. This study serves to enhance our understanding of the pathogenicity and survival strategies of S. enterica under acetic acid stress.
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Affiliation(s)
- Mrinalini Ghoshal
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Tyler D. Bechtel
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Lynne McLandsborough
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
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Zhang R, Luo Y, Gang L, Xu Y, Zhang X, Peng Q, Slamti L, Lereclus D, Wang G, Song F. Key amino acids residues enhance the ability of CpcR to activate cry gene expression in Bacillus thuringiensis. Res Microbiol 2023; 174:104051. [PMID: 36907231 DOI: 10.1016/j.resmic.2023.104051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/11/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
Typical Bacillus thuringiensis (Bt) produces one or more parasporal crystals composed of insecticidal Cry proteins during the sporulation, and the parasporal crystals and spores are produced from the same cell. Strain Bt LM1212 is different from typical Bt strains in that its crystals and spores are produced in different cells. Previous studies have found that the cell differentiation process of Bt LM1212 is related to the transcription factor CpcR which activates the cry-gene promoters. In addition, CpcR could activate the Bt LM1212 cry35-like gene promoter (P35) when introduced in the heterologous HD73- strain. It was shown that P35 was only activated in non-sporulating cells. In this study, the peptidic sequences of CpcR homologous proteins found in other strains of the Bacillus cereus group were used as references to identify two key amino acid sites for CpcR activity. The function of these amino acids was investigated by measuring P35 activation by CpcR in strain HD73-. These results will lay a foundation for the optimization of the insecticidal protein expression system in non-sporulating cells.
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Affiliation(s)
- Ruibin Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yang Luo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Lili Gang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yanrong Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Leyla Slamti
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Didier Lereclus
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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Gebremichael Y, Crandall J, Mukhopadhyay R, Xu F. Salmonella Subpopulations Identified from Human Specimens Express Heterogenous Phenotypes That Are Relevant to Clinical Diagnosis. Microbiol Spectr 2023; 11:e0167922. [PMID: 36507668 PMCID: PMC9927314 DOI: 10.1128/spectrum.01679-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Clonal bacterial cells can give rise to functionally heterogeneous subpopulations. This diversification is considered an adaptation strategy that has been demonstrated for several bacterial species, including Salmonella enterica serovar Typhimurium. In previous studies on mouse models infected orally with pure Salmonella cultures, derived bacterial cells collected from animal tissues were found to express heterogenous phenotypes. Here, we show mixed Salmonella populations, apparently derived from the same progenitor, present in human specimens collected at a single disease time point, and in a long-term-infected patient, these Salmonella were no longer expressing surface-exposed antigen epitopes by isolates collected at earlier days of the disease. The subpopulations express different phenotypes related to cell surface antigen expression, motility, biofilm formation, biochemical metabolism, and antibiotic resistance, which can all contribute to pathogenicity. Some of the phenotypes correlate with single nucleotide polymorphisms or other sequence changes in bacterial genomes. These genetic variations can alter synthesis of cell membrane-associated molecules such as lipopolysaccharides and lipoproteins, leading to changes in bacterial surface structure and function. This study demonstrates the limitation of Salmonella diagnostic methods that are based on a single-cell population which may not represent the heterogenous bacterial community in infected humans. IMPORTANCE In animal model systems, heterogenous Salmonella phenotypes were found previously to regulate bacterial infections. We describe in this communication that different Salmonella phenotypes also exist in infected humans at a single disease time point and that their phenotypic and molecular traits are associated with different aspects of pathogenicity. Notably, variation in genes encoding antibiotic resistance and two-component systems were observed from the subpopulations of a patient suffering from persistent salmonellosis. Therefore, clinical and public health interventions of the disease that are based on diagnosis of a single-cell population may miss other subpopulations that can cause residual human infections.
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Affiliation(s)
- Yismashoa Gebremichael
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - John Crandall
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Rituparna Mukhopadhyay
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Fengfeng Xu
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
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Trebosc V, Lucchini V, Narwal M, Wicki B, Gartenmann S, Schellhorn B, Schill J, Bourotte M, Frey D, Grünberg J, Trauner A, Ferrari L, Felici A, Champion OL, Gitzinger M, Lociuro S, Kammerer RA, Kemmer C, Pieren M. Targeting virulence regulation to disarm Acinetobacter baumannii pathogenesis. Virulence 2022; 13:1868-1883. [PMID: 36261919 PMCID: PMC9586577 DOI: 10.1080/21505594.2022.2135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of anti-virulence drug therapy against Acinetobacter baumannii infections would provide an alternative to traditional antibacterial therapy that are increasingly failing. Here, we demonstrate that the OmpR transcriptional regulator plays a pivotal role in the pathogenesis of diverse A. baumannii clinical strains in multiple murine and G. mellonella invertebrate infection models. We identified OmpR-regulated genes using RNA sequencing and further validated two genes whose expression can be used as robust biomarker to quantify OmpR inhibition in A. baumannii. Moreover, the determination of the structure of the OmpR DNA binding domain of A. baumannii and the development of in vitro protein-DNA binding assays enabled the identification of an OmpR small molecule inhibitor. We conclude that OmpR is a valid and unexplored target to fight A. baumannii infections and we believe that the described platform combining in silico methods, in vitro OmpR inhibitory assays and in vivo G. mellonella surrogate infection model will facilitate future drug discovery programs.
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Affiliation(s)
| | - Valentina Lucchini
- BioVersys AG, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | | | | | | | - Daniel Frey
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Jürgen Grünberg
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Livia Ferrari
- Microbiology Discovery, Aptuit Srl, an Evotec Company, Verona, Italy
| | - Antonio Felici
- Microbiology Discovery, Aptuit Srl, an Evotec Company, Verona, Italy
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Abstract
Duck infectious serositis, also known as Riemerella anatipestifer disease, infects domestic ducks, geese, and turkeys and wild birds. However, the regulatory mechanism of its pathogenicity remains unclear. The PhoPR two-component system (TCS) was first reported in Gram-negative bacteria in our previous research and was demonstrated to be involved in virulence and gene expression. Here, DNA affinity purification sequencing (DAP-seq) was applied to further explore the regulation of PhoPR in relation to pathogenicity in R. anatipestifer. A conserved motif was identified upstream of 583 candidate target genes which were directly regulated by PhoP. To further confirm the genes which are regulated by PhoR and PhoP, single-gene-deletion strains were constructed. The results of transcriptome analysis using next-generation RNA sequencing showed 136 differentially expressed genes (DEGs) between the ΔphoP strain and the wild type (WT) and 183 DEGs between the ΔphoR strain and the WT. The candidate target genes of PhoP were further identified by combining transcriptome analysis and DAP-seq, which revealed that the main direct regulons of PhoP are located on the membrane and PhoP is involved in regulating aerotolerance. Using the in vivo duck model, the pathogenicity of ΔphoP and ΔphoR mutants was found to be significantly lower than that of the WT. Together, our findings provide insight into the direct regulation of PhoP and suggest that phoPR is essential for the pathogenicity of R. anatipestifer. The gene deletion strains are expected to be candidate live vaccine strains of R. anatipestifer which can be used as ideal genetic engineering vector strains for the expression of foreign antigens. IMPORTANCE Riemerella anatipestifer is a significant pathogen with high mortality in the poultry industry that causes acute septicemia and infectious polyserositis in ducks, chickens, geese, and other avian species. Previously, we characterized the two-component system encoded by phoPR and found that R. anatipestifer almost completely lost its pathogenicity for ducklings when phoPR was deleted. However, the mechanism of PhoPR regulation of virulence in R. anatipestifer had not been deeply explored. In this study, we utilized DAP-seq to explore the DNA-binding sites of PhoP as a response regulator in the global genome. Furthermore, phoP and phoR were deleted separately, and transcriptomics analysis of the corresponding gene deletion strains was performed. We identified a series of directly regulated genes of the PhoPR two-component system. The duckling model showed that both PhoP and PhoR are essential virulence-related factors in R. anatipestifer.
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Kong L, Su M, Sang J, Huang S, Wang M, Cai Y, Xie M, Wu J, Wang S, Foster SJ, Zhang J, Han A. The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans. Front Microbiol 2022; 13:820089. [PMID: 35558126 PMCID: PMC9087282 DOI: 10.3389/fmicb.2022.820089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.
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Affiliation(s)
- Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanshan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Min Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingquan Xie
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shida Wang
- State Key Laboratory for Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, The Florey Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Jiaqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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Aspartic Acid Stabilized Iron Oxide Nanoparticles for Biomedical Applications. NANOMATERIALS 2022; 12:nano12071151. [PMID: 35407269 PMCID: PMC9000734 DOI: 10.3390/nano12071151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 01/23/2023]
Abstract
Aspartic acid stabilized iron oxide nanoparticles (A-IONPs) with globular shape and narrow size distribution were prepared by the co-precipitation method in aqueous medium. A quantum-mechanical approach to aspartic acid optimized structure displayed negative charged sites, relatively high dipole moment, and hydrophilicity, which recommended it for interaction with iron cations and surrounding water electrical dipoles. A-IONPs were characterized by TEM, XRD, ATR-FTIR, EDS, DSC, TG, DLS, NTA, and VSM techniques. Theoretical study carried out by applying Hartree-Fock and density functional algorithms suggested that some aspartic acid properties related to the interaction can develop with nanoparticles and water molecules. The results of experimental investigation showed that the mean value of particle physical diameters was 9.17 ± 2.2 nm according to TEM image analysis, the crystallite size was about 8.9 nm according to XRD data, while the magnetic diameter was about 8.8 nm, as was determined from VSM data interpretation with Langevin's theory. The A-IONP suspension was characterized by zeta-potential of about -11.7 mV, while the NTA investigation revealed a hydrodynamic diameter of 153.9 nm. These results recommend the A-IONP suspension for biomedical applications.
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Distinct Interaction Mechanism of RNAP and ResD and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilisψ. J Bacteriol 2021; 204:e0043221. [PMID: 34898263 DOI: 10.1128/jb.00432-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ResD-ResE signal transduction system plays a pivotal role in anaerobic nitrate respiration in Bacillus subtilis. The nasD operon encoding nitrite reductase is essential for nitrate respiration and is tightly controlled by the ResD response regulator. To understand the mechanism of ResD-dependent transcription activation of the nasD operon, we explored ResD-RNA polymerase (RNAP), ResD-DNA, and RNAP-DNA interactions required for nasD transcription. Full transcriptional activation requires the upstream promoter region where five molecules of ResD bind. The distal ResD-binding subsite at -87 to -84 partially overlaps a sequence similar to the consensus distal subsite of the upstream (UP) element with which the Escherichia coli C-terminal domain of the α subunit (αCTD) of RNAP interacts to stimulate transcription. We propose that interaction between αCTD and ResD at the promoter-distal site is essential for stimulating nasD transcription. Although nasD has an extended -10 promoter, it lacks a reasonable -35 element. Genetic analysis and structural simulations predicted that the absence of the -35 element might be compensated by interactions between σA and αCTD, and between αCTD and ResD at the promoter-proximal ResD-binding subsite. Thus, our work suggested that ResD likely participates in nasD transcription activation by binding to two αCTD subunits at the proximal and distal promoter sites, representing a unique configuration for transcription activation. IMPORTANCE A significant number of ResD-controlled genes have been identified and transcription regulatory pathways in which ResD participates have emerged. Nevertheless, the mechanism of how ResD activates transcription of different genes in a nucleotide sequence-specific manner has been less explored. This study suggested that among the five ResD-binding subsites in the promoter of the nasD operon, the promoter-proximal and -distal ResD-binding subsites play important roles in nasD activation by adapting different modes of protein-protein and protein-DNA interactions. The finding of a new-type of protein-promoter architecture provides insight into the understanding of transcription activation mechanisms controlled by transcription factors including the ubiquitous response regulators of two-component regulatory systems particularly in Gram-positive bacteria.
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Maciunas LJ, Porter N, Lee PJ, Gupta K, Loll PJ. Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states. Acta Crystallogr D Struct Biol 2021; 77:1027-1039. [PMID: 34342276 PMCID: PMC8329863 DOI: 10.1107/s2059798321006288] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/17/2021] [Indexed: 11/10/2022] Open
Abstract
Vancomycin has historically been used as a last-resort treatment for serious bacterial infections. However, vancomycin resistance has become widespread in certain pathogens, presenting a serious threat to public health. Resistance to vancomycin is conferred by a suite of resistance genes, the expression of which is controlled by the VanR-VanS two-component system. VanR is the response regulator in this system; in the presence of vancomycin, VanR accepts a phosphoryl group from VanS, thereby activating VanR as a transcription factor and inducing expression of the resistance genes. This paper presents the X-ray crystal structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states at resolutions of 2.3 and 2.0 Å, respectively. Comparison of the two structures illustrates that phosphorylation of VanR is accompanied by a disorder-to-order transition of helix 4, which lies within the receiver domain of the protein. This transition generates an interface that promotes dimerization of the receiver domain; dimerization in solution was verified using analytical ultracentrifugation. The inactive conformation of the protein does not appear intrinsically unable to bind DNA; rather, it is proposed that in the activated form DNA binding is enhanced by an avidity effect contributed by the receiver-domain dimerization.
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Affiliation(s)
- Lina J. Maciunas
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Graduate Program in Biochemistry, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Nadia Porter
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Summer Undergraduate Research Fellowship Program, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Paula J. Lee
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Patrick J. Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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Zannoni A, Pelliciari S, Musiani F, Chiappori F, Roncarati D, Scarlato V. Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori. Int J Mol Sci 2021; 22:ijms22157848. [PMID: 34360614 PMCID: PMC8345958 DOI: 10.3390/ijms22157848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.
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Affiliation(s)
- Annamaria Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Simone Pelliciari
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Federica Chiappori
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR), 20054 Segrate, Italy;
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
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Structural basis for promoter DNA recognition by the response regulator OmpR. J Struct Biol 2020; 213:107638. [PMID: 33152421 DOI: 10.1016/j.jsb.2020.107638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 11/21/2022]
Abstract
OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR-DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc-DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this "druggable" target.
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13
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Lembke M, Höfler T, Walter AN, Tutz S, Fengler V, Schild S, Reidl J. Host stimuli and operator binding sites controlling protein interactions between virulence master regulator ToxR and ToxS in Vibrio cholerae. Mol Microbiol 2020; 114:262-278. [PMID: 32251547 PMCID: PMC7496328 DOI: 10.1111/mmi.14510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) are key mechanisms in the maintenance of biological regulatory networks. Herein, we characterize PPIs within ToxR and its co-activator, ToxS, to understand the mechanisms of ToxR transcription factor activation. ToxR is a key transcription activator that is supported by ToxS for virulence gene regulation in Vibrio cholerae. ToxR comprises a cytoplasmic DNA-binding domain that is linked by a transmembrane domain to a periplasmic signal receiver domain containing two cysteine residues. ToxR-ToxR and ToxR-ToxS PPIs were detected using an adenylate-cyclase-based bacterial two-hybrid system approach in Escherichia coli. We found that the ToxR-ToxR PPIs are significantly increased in response to ToxR operators, the co-activator ToxS and bile salts. We suggest that ToxS and bile salts promote the interaction between ToxR molecules that ultimately results in dimerization. Upon binding of operators, ToxR-ToxR PPIs are found at the highest frequency. Moreover, disulfide-bond-dependent interaction in the periplasm results in homodimer formation that is promoted by DNA binding. The formation of these homodimers and the associated transcriptional activity of ToxR were strongly dependent on the oxidoreductases DsbA/DsbC. These findings show that protein and non-protein partners, that either transiently or stably interact with ToxR, fine-tune ToxR PPIs, and its associated transcriptional activity in changing environments.
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Affiliation(s)
- Mareike Lembke
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Thomas Höfler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Sarah Tutz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Vera Fengler
- Division of Physiological Chemistry, Medical University of Graz, Graz, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,BioHealth, University of Graz, Graz, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,BioHealth, University of Graz, Graz, Austria
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14
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Xi D, Li Y, Yan J, Li Y, Wang X, Cao B. Small RNA coaR contributes to intestinal colonization in Vibrio cholerae via the two-component system EnvZ/OmpR. Environ Microbiol 2020; 22:4231-4243. [PMID: 31868254 DOI: 10.1111/1462-2920.14906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/20/2019] [Indexed: 11/30/2022]
Abstract
Vibrio cholerae is a waterborne bacterium responsible for worldwide outbreaks of acute and fatal cholera. Recently, small regulatory RNAs (sRNAs) have become increasingly recognized as important regulators of virulence gene expression in response to environmental signals. In this study, we determined that two-component system EnvZ/OmpR was required for intestinal colonization in V. cholerae O1 EI Tor strain E12382. Analysis of the characteristics of OmpR revealed a potential binding site in the intergenic region between vc1470 and vc1471, and qRT-PCR showed that expression of the intergenic region increased 5.3-fold in the small intestine compared to LB medium. Race and northern blot assays were performed and demonstrated a new sRNA, coaR (cholerae osmolarity and acidity related regulatory RNA). A ΔcoaR mutant showed a deficient colonization ability in small intestine with CI of 0.15. We identified a target of coaR, tcpI, a negative regulator of the major pilin subunit of TcpA. The ΔtcpI mutant has an increased colonization with CI of 3.16. The expression of coaR increased 2.8-fold and 3.3-fold under relative acidic and hypertonic condition. In summary, coaR was induced under the condition of high osmolarity and acid stress via EnvZ/OmpR and explained that tcpI relieves pH-mediated repression of toxin co-regulated pilus synthesis.
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Affiliation(s)
- Daoyi Xi
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yujia Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Xiaochen Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
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15
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Kenney LJ, Anand GS. EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0001-2019. [PMID: 32003321 PMCID: PMC7192543 DOI: 10.1128/ecosalplus.esp-0001-2019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Indexed: 01/09/2023]
Abstract
Two-component regulatory systems represent the major paradigm for signal transduction in prokaryotes. The simplest systems are composed of a sensor kinase and a response regulator. The sensor is often a membrane protein that senses a change in environmental conditions and is autophosphorylated by ATP on a histidine residue. The phosphoryl group is transferred onto an aspartate of the response regulator, which activates the regulator and alters its output, usually resulting in a change in gene expression. In this review, we present a historical view of the archetype EnvZ/OmpR two-component signaling system, and then we provide a new view of signaling based on our recent experiments. EnvZ responds to cytoplasmic signals that arise from changes in the extracellular milieu, and OmpR acts canonically (requiring phosphorylation) to regulate the porin genes and noncanonically (without phosphorylation) to activate the acid stress response. Herein, we describe how insights gleaned from stimulus recognition and response in EnvZ are relevant to nearly all sensor kinases and response regulators.
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Affiliation(s)
- Linda J Kenney
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Mechanobiology Institute, T-Lab, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
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16
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Morgan SJ, French EL, Plecha SC, Krukonis ES. The wing of the ToxR winged helix-turn-helix domain is required for DNA binding and activation of toxT and ompU. PLoS One 2019; 14:e0221936. [PMID: 31498842 PMCID: PMC6733452 DOI: 10.1371/journal.pone.0221936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 08/19/2019] [Indexed: 02/02/2023] Open
Abstract
ToxR and TcpP, two winged helix-turn-helix (w-HTH) family transcription factors, co-activate expression of the toxT promoter in Vibrio cholerae. ToxT then directly regulates a number of genes required for virulence. In addition to co-activation of toxT, ToxR can directly activate the ompU promoter and repress the ompT promoter. Based on a previous study suggesting that certain wing residues of ToxR are preferentially involved in toxT co-activation compared to direct ompU activation, we employed alanine-scanning mutagenesis to determine which residues in the wing of ToxR are required for activation of each promoter. All of the ToxR wing residues tested that were critical for transcriptional activation of toxT and/or ompU were also critical for DNA binding. While some ToxR wing mutants had reduced interaction with TcpP, that reduced interaction did not correlate with a specific defect in toxT activation. Rather, such mutants also affected ompU activation and DNA binding. Based on these findings we conclude that the primary role of the wing of ToxR is to bind DNA, along with the DNA recognition helix of ToxR, and this function is required both for direct activation of ompU and co-activation of toxT.
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Affiliation(s)
- Sarah J. Morgan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States of America
| | - Emily L. French
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI, United States of America
| | - Sarah C. Plecha
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI, United States of America
| | - Eric S. Krukonis
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States of America
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI, United States of America
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America
- * E-mail:
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17
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Liew ATF, Foo YH, Gao Y, Zangoui P, Singh MK, Gulvady R, Kenney LJ. Single cell, super-resolution imaging reveals an acid pH-dependent conformational switch in SsrB regulates SPI-2. eLife 2019; 8:e45311. [PMID: 31033442 PMCID: PMC6557628 DOI: 10.7554/elife.45311] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022] Open
Abstract
After Salmonella is phagocytosed, it resides in an acidic vacuole. Its cytoplasm acidifies to pH 5.6; acidification activates pathogenicity island 2 (SPI-2). SPI-2 encodes a type three secretion system whose effectors modify the vacuole, driving endosomal tubulation. Using super-resolution imaging in single bacterial cells, we show that low pH induces expression of the SPI-2 SsrA/B signaling system. Single particle tracking, atomic force microscopy, and single molecule unzipping assays identified pH-dependent stimulation of DNA binding by SsrB. A so-called phosphomimetic form (D56E) was unable to bind to DNA in live cells. Acid-dependent DNA binding was not intrinsic to regulators, as PhoP and OmpR binding was not pH-sensitive. The low level of SPI-2 injectisomes observed in single cells is not due to fluctuating SsrB levels. This work highlights the surprising role that acid pH plays in virulence and intracellular lifestyles of Salmonella; modifying acid survival pathways represents a target for inhibiting Salmonella.
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Affiliation(s)
- Andrew Tze Fui Liew
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yunfeng Gao
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Parisa Zangoui
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | | | - Ranjit Gulvady
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Linda J Kenney
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
- Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUnited States
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18
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Li Y, Kong L, Shen J, Wang Q, Liu Q, Yang W, Deng Z, You D. Characterization of the positive SARP family regulator PieR for improving piericidin A1 production in Streptomyces piomogeues var. Hangzhouwanensis. Synth Syst Biotechnol 2018; 4:16-24. [PMID: 30560207 PMCID: PMC6290260 DOI: 10.1016/j.synbio.2018.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 01/06/2023] Open
Abstract
Piericidin A1, a member of ɑ-pyridone antibiotic, exhibits various biological activities such as antimicrobial, antifungal, and antitumor properties and possesses potent respiration-inhibitory activity against insects due to its competitive binding capacity to mitochondrial complex I. The biosynthetic pathway of piericidin A1 has been reported in Streptomyces piomogeues var. Hangzhouwanensis, while the regulatory mechanism remains poorly understood. In this study, a Streptomyces antibiotic regulatory protein (SARP) family transcriptional regulator PieR was characterized. Genetic disruption and complementation manipulations revealed that PieR positively regulated the production of piericidin A1. Moreover, the overexpression of pieR contributed to the improvement of piericidin A1 productivity. The real-time quantitative PCR (RT-qPCR) was carried out and the data showed that pieR stimulated the transcription of all the biosynthesis-related genes for piericidin A1. In order to explore the regulatory mechanism, electrophoresis mobility shift assays (EMSA) and DNase I footprinting experiments have been conducted. A protected region covering 50 nucleotides within the upstream region of pieR was identified and two 5-nt direct repeat sequences (5′-CCGGA-3′) in the protected region were found. These findings, taken together, set stage for transcriptional control engineering in the view of optimizing piericidin A1 production and thus provide a viable potent route for the construction of strains with high productivity.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jufang Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weinan Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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19
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Chakraborty S, Kenney LJ. A New Role of OmpR in Acid and Osmotic Stress in Salmonella and E. coli. Front Microbiol 2018; 9:2656. [PMID: 30524381 PMCID: PMC6262077 DOI: 10.3389/fmicb.2018.02656] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022] Open
Abstract
Bacteria survive and respond to diverse environmental conditions and during infection inside the host by systematic regulation of stress response genes. E. coli and S. Typhimurium can undergo large changes in intracellular osmolality (up to 1.8 Osmol/kg) and can tolerate cytoplasmic acidification to at least pHi 5.6. Recent analyses of single cells challenged a long held view that bacteria respond to extracellular acid stress by rapid acidification followed by a rapid recovery. It is now appreciated that both S. Typhimurium and E. coli maintain an acidic cytoplasm through the actions of the outer membrane protein regulator OmpR via its regulation of distinct signaling pathways. However, a comprehensive comparison of OmpR regulons between S. Typhimurium and E. coli is lacking. In this study, we examined the expression profiles of wild-type and ompR null strains of the intracellular pathogen S. Typhimurium and a commensal E. coli in response to acid and osmotic stress. Herein, we classify distinct OmpR regulons and also identify shared OmpR regulatory pathways between S. Typhimurium and E. coli in response to acid and osmotic stress. Our study establishes OmpR as a key regulator of bacterial virulence, growth and metabolism, in addition to its role in regulating outer membrane proteins.
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Affiliation(s)
- Smarajit Chakraborty
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Linda J. Kenney
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- Departments of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, United States
- Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
- Jesse Brown Veterans Administration Medical Center, Chicago, IL, United States
- *Correspondence: Linda J. Kenney,
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20
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Joyce AP, Havranek JJ. Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors. QUANTITATIVE BIOLOGY 2018; 6:68-84. [PMID: 37990674 PMCID: PMC10662834 DOI: 10.1007/s40484-018-0130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 10/18/2022]
Abstract
Background Sequence-specific binding by transcription factors (TFs) plays a significant role in the selection and regulation of target genes. At the protein:DNA interface, amino acid side-chains construct a diverse physicochemical network of specific and non-specific interactions, and seemingly subtle changes in amino acid identity at certain positions may dramatically impact TF:DNA binding. Variation of these specificity-determining residues (SDRs) is a major mechanism of functional divergence between TFs with strong structural or sequence homology. Methods In this study, we employed a combination of high-throughput specificity profiling by SELEX and Spec-seq, structural modeling, and evolutionary analysis to probe the binding preferences of winged helix-turn-helix TFs belonging to the OmpR sub-family in Escherichia coli. Results We found that E. coli OmpR paralogs recognize tandem, variably spaced repeats composed of "GT-A" or "GCT"-containing half-sites. Some divergent sequence preferences observed within the "GT-A" mode correlate with amino acid similarity; conversely, "GCT"-based motifs were observed for a subset of paralogs with low sequence homology. Direct specificity profiling of a subset of OmpR homologues (CpxR, RstA, and OmpR) as well as predicted "SDR-swap" variants revealed that individual SDRs may impact sequence preferences locally through direct contact with DNA bases or distally via the DNA backbone. Conclusions Overall, our work provides evidence for a common structural code for sequence-specific wHTH:DNA interactions, and demonstrates that surprisingly modest residue changes can enable recognition of highly divergent sequence motifs. Further examination of SDR predictions will likely reveal additional mechanisms controlling the evolutionary divergence of this important class of transcriptional regulators.
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Affiliation(s)
- Adam P. Joyce
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - James J. Havranek
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
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21
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Draughn GL, Milton ME, Feldmann EA, Bobay BG, Roth BM, Olson AL, Thompson RJ, Actis LA, Davies C, Cavanagh J. The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism. J Mol Biol 2018; 430:806-821. [PMID: 29438671 DOI: 10.1016/j.jmb.2018.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 01/19/2023]
Abstract
The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global health care. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling. We also show that BfmR binds the previously proposed bfmRS promoter sequence with moderate affinity. While BfmR shares many traits with other OmpR/PhoB family response regulators, some unusual properties were observed. Most importantly, we observe that when phosphorylated, BfmR binds this promoter sequence with a lower affinity than when not phosphorylated. All other OmpR/PhoB family members studied to date show an increase in DNA-binding affinity upon phosphorylation. Understanding the structural and biochemical mechanisms of BfmR will aid in the development of new antimicrobial therapies.
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Affiliation(s)
- G Logan Draughn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Department of Discovery Sciences, RTI International, 3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA
| | - Morgan E Milton
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA; Department of Discovery Sciences, RTI International, 3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA
| | - Erik A Feldmann
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Benjamin G Bobay
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Braden M Roth
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Andrew L Olson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Richele J Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Luis A Actis
- Department of Microbiology, Miami University, Oxford, OH 45056, USA
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - John Cavanagh
- Department of Discovery Sciences, RTI International, 3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA.
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22
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Colgan AM, Quinn HJ, Kary SC, Mitchenall LA, Maxwell A, Cameron ADS, Dorman CJ. Negative supercoiling of DNA by gyrase is inhibited in Salmonella enterica serovar Typhimurium during adaptation to acid stress. Mol Microbiol 2018; 107:734-746. [PMID: 29352745 DOI: 10.1111/mmi.13911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/26/2022]
Abstract
DNA in intracellular Salmonella enterica serovar Typhimurium relaxes during growth in the acidified (pH 4-5) macrophage vacuole and DNA relaxation correlates with the upregulation of Salmonella genes involved in adaptation to the macrophage environment. Bacterial ATP levels did not increase during adaptation to acid pH unless the bacterium was deficient in MgtC, a cytoplasmic-membrane-located inhibitor of proton-driven F1 F0 ATP synthase activity. Inhibiting ATP binding by DNA gyrase and topo IV with novobiocin enhanced the effect of low pH on DNA relaxation. Bacteria expressing novobiocin-resistant (NovR ) derivatives of gyrase or topo IV also exhibited DNA relaxation at acid pH, although further relaxation with novobiocin was not seen in the strain with NovR gyrase. Thus, inhibition of the negative supercoiling activity of gyrase was the primary cause of enhanced DNA relaxation in drug-treated bacteria. The Salmonella cytosol reaches pH 5-6 in response to an external pH of 4-5: the ATP-dependent DNA supercoiling activity of purified gyrase was progressively inhibited by lowering the pH in this range, as was the ATP-dependent DNA relaxation activity of topo IV. We propose that DNA relaxation in Salmonella within macrophage is due to acid-mediated impairment of the negative supercoiling activity of gyrase.
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Affiliation(s)
- Aoife M Colgan
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Heather J Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Stefani C Kary
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.,Department of Biology, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andrew D S Cameron
- Department of Biology, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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23
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Chakraborty S, Winardhi RS, Morgan LK, Yan J, Kenney LJ. Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells. Nat Commun 2017; 8:1587. [PMID: 29138484 PMCID: PMC5686162 DOI: 10.1038/s41467-017-02030-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Unlike eukaryotes, bacteria undergo large changes in osmolality and cytoplasmic pH. It has been described that during acid stress, bacteria internal pH promptly acidifies, followed by recovery. Here, using pH imaging in single living cells, we show that following acid stress, bacteria maintain an acidic cytoplasm and the osmotic stress transcription factor OmpR is required for acidification. The activation of this response is non-canonical, involving a regulatory mechanism requiring the OmpR cognate kinase EnvZ, but not OmpR phosphorylation. Single cell analysis further identifies an intracellular pH threshold ~6.5. Acid stress reduces the internal pH below this threshold, increasing OmpR dimerization and DNA binding. During osmotic stress, the internal pH is above the threshold, triggering distinct OmpR-related pathways. Preventing intracellular acidification of Salmonella renders it avirulent, suggesting that acid stress pathways represent a potential therapeutic target. These results further emphasize the advantages of single cell analysis over studies of population averages.
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Affiliation(s)
- Smarajit Chakraborty
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Ricksen S Winardhi
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, Singapore, 117551, Singapore
| | - Leslie K Morgan
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA.,Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, 60612, USA
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, Singapore, 117551, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore. .,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA. .,Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, 60612, USA. .,Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
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24
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Dorman CJ, Dorman MJ. Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium. Environ Microbiol 2017. [PMID: 28631437 PMCID: PMC5655915 DOI: 10.1111/1462-2920.13838] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Indirect readout mechanisms of transcription control rely on the recognition of DNA shape by transcription factors (TFs). TFs may also employ a direct readout mechanism that involves the reading of the base sequence in the DNA major groove at the binding site. TFs with winged helix-turn-helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adjacent minor groove. Such wHTH proteins are important regulators of virulence gene transcription in many pathogens; they also control housekeeping genes. This article considers the cases of the non-invasive Gram-negative pathogen Vibrio cholerae and the invasive pathogen Salmonella enterica serovar Typhimurium. Both possess clusters of A + T-rich horizontally acquired virulence genes that are silenced by the nucleoid-associated protein H-NS and regulated positively or negatively by wHTH TFs: for example, ToxR and LeuO in V. cholerae; HilA, LeuO, SlyA and OmpR in S. Typhimurium. Because of their relatively relaxed base sequence requirements for target recognition, indirect readout mechanisms have the potential to engage regulatory proteins with many more targets than might be the case using direct readout, making indirect readout an important, yet often ignored, contributor to the expression of pathogenic phenotypes.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Matthew J Dorman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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25
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Desai SK, Kenney LJ. To ∼P or Not to ∼P? Non-canonical activation by two-component response regulators. Mol Microbiol 2016; 103:203-213. [PMID: 27656860 DOI: 10.1111/mmi.13532] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2016] [Indexed: 12/30/2022]
Abstract
Bacteria sense and respond to their environment through the use of two-component regulatory systems. The ability to adapt to a wide range of environmental stresses is directly related to the number of two-component systems an organism possesses. Recent advances in this area have identified numerous variations on the archetype systems that employ a sensor kinase and a response regulator. It is now evident that many orphan regulators that lack cognate kinases do not rely on phosphorylation for activation and new roles for unphosphorylated response regulators have been identified. The significance of recent findings and suggestions for further research are discussed.
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Affiliation(s)
- Stuti K Desai
- Mechanobiology Institute, 5A Engineering Drive 1, National University of Singapore, Singapore, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, 5A Engineering Drive 1, National University of Singapore, Singapore, Singapore.,Jesse Brown Veteran's Administration Medical Center, Chicago, IL, USA.,Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, USA
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26
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Brosse A, Korobeinikova A, Gottesman S, Guillier M. Unexpected properties of sRNA promoters allow feedback control via regulation of a two-component system. Nucleic Acids Res 2016; 44:9650-9666. [PMID: 27439713 PMCID: PMC5175337 DOI: 10.1093/nar/gkw642] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 06/21/2016] [Accepted: 07/07/2016] [Indexed: 12/22/2022] Open
Abstract
Two-component systems (TCS) and small regulatory RNAs (sRNAs) are both widespread regulators of gene expression in bacteria. TCS are in most cases transcriptional regulators. A large class of sRNAs act as post-transcriptional regulators of gene expression that modulate the translation and/or stability of target-mRNAs. Many connections have been recently unraveled between these two types of regulators, resulting in mixed regulatory circuits with poorly characterized properties. This study focuses on the negative feedback circuit that exists between the EnvZ-OmpR TCS and the OmrA/B sRNAs. We have shown that OmpR directly activates transcription from the omrA and omrB promoters, allowing production of OmrA/B sRNAs that target multiple mRNAs, including the ompR-envZ mRNA. This control of ompR-envZ by the Omr sRNAs does not affect the amount of phosphorylated OmpR, i.e. the presumably active form of the regulator. Accordingly, expression of robust OmpR targets, such as the ompC or ompF porin genes, is not affected by OmrA/B. However, we find that several OmpR targets, including OmrA/B themselves, are sensitive to changing total OmpR levels. As a result, OmrA/B limit their own synthesis. These findings unravel an additional layer of control in the expression of some OmpR targets and suggest the existence of differential regulation within the OmpR regulon.
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Affiliation(s)
- Anaïs Brosse
- CNRS UMR8261, Associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Anna Korobeinikova
- CNRS UMR8261, Associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maude Guillier
- CNRS UMR8261, Associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
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27
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Nieckarz M, Raczkowska A, Dębski J, Kistowski M, Dadlez M, Heesemann J, Rossier O, Brzostek K. Impact of OmpR on the membrane proteome of Yersinia enterocolitica in different environments: repression of major adhesin YadA and heme receptor HemR. Environ Microbiol 2016; 18:997-1021. [PMID: 26627632 DOI: 10.1111/1462-2920.13165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/26/2015] [Accepted: 11/29/2015] [Indexed: 01/22/2023]
Abstract
Enteropathogenic Yersinia enterocolitica is able to grow within or outside the mammalian host. Previous transcriptomic studies have indicated that the regulator OmpR plays a role in the expression of hundreds of genes in enterobacteria. Here, we have examined the impact of OmpR on the production of Y. enterocolitica membrane proteins upon changes in temperature, osmolarity and pH. Proteomic analysis indicated that the loss of OmpR affects the production of 120 proteins, a third of which are involved in uptake/transport, including several that participate in iron or heme acquisition. A set of proteins associated with virulence was also affected. The influence of OmpR on the abundance of adhesin YadA and heme receptor HemR was examined in more detail. OmpR was found to repress YadA production and bind to the yadA promoter, suggesting a direct regulatory effect. In contrast, the repression of hemR expression by OmpR appears to be indirect. These findings provide new insights into the role of OmpR in remodelling the cell surface and the adaptation of Y. enterocolitica to different environmental niches, including the host.
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Affiliation(s)
- Marta Nieckarz
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
| | - Adrianna Raczkowska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
| | - Janusz Dębski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Michał Kistowski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Michał Dadlez
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, Warsaw, 02-106, Poland.,Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Jürgen Heesemann
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Pettenkoferstrasse 9a, Munich, 80336, Germany
| | - Ombeline Rossier
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Pettenkoferstrasse 9a, Munich, 80336, Germany
| | - Katarzyna Brzostek
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, Warsaw, 02-096, Poland
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28
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Nguyen MP, Yoon JM, Cho MH, Lee SW. Prokaryotic 2-component systems and the OmpR/PhoB superfamily. Can J Microbiol 2015; 61:799-810. [DOI: 10.1139/cjm-2015-0345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In bacteria, 2-component regulatory systems (TCSs) are the critical information-processing pathways that link stimuli to specific adaptive responses. Signals perceived by membrane sensors, which are generally histidine kinases, are transmitted by response regulators (RRs) to allow cells to cope rapidly and effectively with environmental challenges. Over the past few decades, genes encoding components of TCSs and their responsive proteins have been identified, crystal structures have been described, and signaling mechanisms have been elucidated. Here, we review recent findings and interesting breakthroughs in bacterial TCS research. Furthermore, we discuss structural features, mechanisms of activation and regulation, and cross-regulation of RRs, with a focus on the largest RR family, OmpR/PhoB, to provide a comprehensive overview of these critically important signaling molecules.
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Affiliation(s)
| | - Joo-Mi Yoon
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Man-Ho Cho
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Sang-Won Lee
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
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29
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Shimada T, Takada H, Yamamoto K, Ishihama A. Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets. Genes Cells 2015; 20:915-31. [PMID: 26332955 DOI: 10.1111/gtc.12282] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/26/2015] [Indexed: 12/22/2022]
Abstract
The two-component system (TCS) is a sophisticated bacterial signal transduction system for regulation of genome transcription in response to environmental conditions. The EnvZ-OmpR system is one of the well-characterized TCS of Escherichia coli, responding to changes in environmental osmolality. Regulation has largely focused on the differential expression of two porins, OmpF and OmpC, which transport small molecules across the outer membrane. Recently, it has become apparent that OmpR serves a more global regulatory role and regulates additional targets. To identify the entire set of regulatory targets of OmpR, we performed the genomic SELEX screening of OmpR-binding sites along the E. coli genome. As a result, more than 30 novel genes have been identified to be under the direct control of OmpR. One abundant group includes the genes encoding a variety of membrane-associated transporters that mediate uptake or efflux of small molecules, while another group encodes a set of transcription regulators, raising a concept that OmpR is poised to control a diverse set of responses by altering downstream transcriptional regulators.
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Affiliation(s)
- Tomohiro Shimada
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, 184-8584, Japan.,Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, 226-8503, Japan
| | - Hiraku Takada
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, 184-8584, Japan
| | - Kaneyoshi Yamamoto
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, 184-8584, Japan.,Department of Frontier Bioscience, Hosei University, Koganai, Tokyo, 184-8584, Japan
| | - Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Koganai, Tokyo, 184-8584, Japan.,Department of Frontier Bioscience, Hosei University, Koganai, Tokyo, 184-8584, Japan
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30
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Katsir G, Jarvis M, Phillips M, Ma Z, Gunsalus RP. The Escherichia coli NarL receiver domain regulates transcription through promoter specific functions. BMC Microbiol 2015; 15:174. [PMID: 26307095 PMCID: PMC4549865 DOI: 10.1186/s12866-015-0502-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022] Open
Abstract
Background The Escherichia coli response regulator NarL controls transcription of genes involved in nitrate respiration during anaerobiosis. NarL consists of two domains joined by a linker that wraps around the interdomain interface. Phosphorylation of the NarL N-terminal receiver domain (RD) releases the, otherwise sequestered, C-terminal output domain (OD) that subsequently binds specific DNA promoter sites to repress or activate gene expression. The aim of this study is to investigate the extent to which the NarL OD and RD function independently to regulate transcription, and the affect of the linker on OD function. Results NarL OD constructs containing different linker segments were examined for their ability to repress frdA-lacZ or activate narG-lacZ reporter fusion genes. These in vivo expression assays revealed that the NarL OD, in the absence or presence of linker helix α6, constitutively repressed frdA-lacZ expression regardless of nitrate availability. However, the presence of the linker loop α5-α6 reversed this repression and also showed impaired DNA binding in vitro. The OD alone could not activate narG-lacZ expression; this activity required the presence of the NarL RD. A footprint assay demonstrated that the NarL OD only partially bound recognition sites at the narG promoter, and the binding affinity was increased by the presence of the phosphorylated RD. Analytical ultracentrifugation used to examine domain oligomerization showed that the NarL RD forms dimers in solution while the OD is monomeric. Conclusions The NarL RD operates as an on-off switch to occlude or release the OD in a nitrate-responsive manner, but has additional roles to directly stimulate transcription at promoters for which the OD lacks independent function. One such role of the RD is to enhance the DNA binding affinity of the OD to target promoter sites. The data also imply that NarL phosphorylation results in RD dimerization and in the separation of the entire linker region from the OD. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0502-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Galit Katsir
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,Molecular Biology Institute, University of California, Los Angeles, USA.,Present address: San Jose City College, San Jose, CA, USA
| | - Michael Jarvis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA.,Present address: Ambry Genetics, Aliso Viejo, CA, USA
| | - Martin Phillips
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Zhongcai Ma
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA.,Present address: NeuroInDx, Inc, Signal Hill, CA, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA. .,Molecular Biology Institute, University of California, Los Angeles, USA.
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31
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Foo YH, Spahn C, Zhang H, Heilemann M, Kenney LJ. Single cell super-resolution imaging of E. coli OmpR during environmental stress. Integr Biol (Camb) 2015; 7:1297-308. [PMID: 26156621 DOI: 10.1039/c5ib00077g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-component signaling systems are a major strategy employed by bacteria, and to some extent, yeast and plants, to respond to environmental stress. The EnvZ/OmpR system in E. coli responds to osmotic and acid stress and is responsible for regulating the protein composition of the outer membrane. EnvZ is a histidine kinase located in the inner membrane. Upon activation, it is autophosphorylated by ATP and subsequently, it activates OmpR. Phosphorylated OmpR binds with high affinity to the regulatory regions of the ompF and ompC porin genes to regulate their transcription. We set out to visualize these two-components in single bacterial cells during different environmental stress conditions and to examine the subsequent modifications to the bacterial nucleoid as a result. We created a chromosomally-encoded, active, fluorescent OmpR-PAmCherry fusion protein and compared its expression levels with RNA polymerase. Quantitative western blotting had indicated that these two proteins were expressed at similar levels. From our images, it is evident that OmpR is significantly less abundant compared to RNA polymerase. In cross-sectional axial images, we observed OmpR molecules closely juxtaposed near the inner membrane during acidic and hyposomotic growth. In acidic conditions, the chromosome was compacted. Surprisingly, under acidic conditions, we also observed evidence of a spatial correlation between the DNA and the inner membrane, suggesting a mechanical link through an active DNA-OmpR-EnvZ complex. This work represents the first direct visualization of a response regulator with respect to the bacterial chromosome.
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Affiliation(s)
- Yong Hwee Foo
- Mechanobiology Institute, T-Lab, 5A Engineering Drive 1, National University of Singapore, Singapore 117411
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32
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The Amino Acid Arginine 210 of the Response Regulator HrpG of Xanthomonas citri subsp. citri Is Required for HrpG Function in Virulence. PLoS One 2015; 10:e0125516. [PMID: 25961560 PMCID: PMC4427454 DOI: 10.1371/journal.pone.0125516] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 03/24/2015] [Indexed: 11/19/2022] Open
Abstract
Xanthomonas citri subsp. citri colonizes its hosts through the trafficking of effector proteins to the plant cell by the type III protein secretion system. In X. citri subsp. citri, as in other plant pathogens, the hrp cluster encodes the type III protein secretion system and is regulated by the transcription factors HrpG and HrpX. HrpG belongs to the OmpR family's response regulator of EnvZ/OmpR two-component signal transduction system. Here, we show that the arginine 210 residue is crucial for the transcriptional activity of HrpG revealed by the absence of disease in host plants and hypersensitive response in non-host plants when a strain carrying this point mutation is used in plant infiltration assays. Also, this strain showed decreased expression levels of hrp genes in bacteria grown in culture or when they were recovered from citrus leaves. Moreover, we show for the first time that HrpG binds to both hrpX and its own promoter, and the change of the arginine 210 by a cysteine does not prevent the binding to both promoters. Nevertheless, in vitro hrpX transcription was observed only with HrpG whereas no transcription was detected with the R210C mutant. HrpG was able to interact with itself as well as with the mutant R210C suggesting that it functions as a dimer. The mutant protein R210C showed altered protease sensitivity, suggesting that Arg210 is essential for protein active conformation and thus for transcriptional activity. Our results indicate that arginine 210 in HrpG, as it may occur with this conserved residue in other members of this family of response regulators, is not required for DNA binding whereas is essential for hrp genes transcription and therefore for pathogenicity and HR induction.
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33
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Chakraborty S, Mizusaki H, Kenney LJ. A FRET-based DNA biosensor tracks OmpR-dependent acidification of Salmonella during macrophage infection. PLoS Biol 2015; 13:e1002116. [PMID: 25875623 PMCID: PMC4397060 DOI: 10.1371/journal.pbio.1002116] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system responds to osmotic stress and regulates expression of outer membrane proteins. In Salmonella, EnvZ/OmpR also controls expression of another two-component system SsrA/B, which is located on Salmonella Pathogenicity Island (SPI) 2. SPI-2 encodes a type III secretion system, which functions as a nanomachine to inject bacterial effector proteins into eukaryotic cells. During the intracellular phase of infection, Salmonella switches from assembling type III secretion system structural components to secreting effectors into the macrophage cytoplasm, enabling Salmonella to replicate in the phagocytic vacuole. Major questions remain regarding how bacteria survive the acidified vacuole and how acidification affects bacterial secretion. We previously reported that EnvZ sensed cytoplasmic signals rather than extracellular ones, as intracellular osmolytes altered the dynamics of a 17-amino-acid region flanking the phosphorylated histidine. We reasoned that the Salmonella cytoplasm might acidify in the macrophage vacuole to activate OmpR-dependent transcription of SPI-2 genes. To address these questions, we employed a DNA-based FRET biosensor ("I-switch") to measure bacterial cytoplasmic pH and immunofluorescence to monitor effector secretion during infection. Surprisingly, we observed a rapid drop in bacterial cytoplasmic pH upon phagocytosis that was not predicted by current models. Cytoplasmic acidification was completely dependent on the OmpR response regulator, but did not require known OmpR-regulated genes such as ompC, ompF, or ssaC (SPI-2). Microarray analysis highlighted the cadC/BA operon, and additional experiments confirmed that it was repressed by OmpR. Acidification was blocked in the ompR null background in a Cad-dependent manner. Acid-dependent activation of OmpR stimulated type III secretion; blocking acidification resulted in a neutralized cytoplasm that was defective for SPI-2 secretion. Based upon these findings, we propose that Salmonella infection involves an acid-dependent secretion process in which the translocon SseB moves away from the bacterial cell surface as it associates with the vacuolar membrane, driving the secretion of SPI-2 effectors such as SseJ. New steps in the SPI-2 secretion process are proposed.
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Affiliation(s)
| | - Hideaki Mizusaki
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Linda J. Kenney
- Mechanobiology Institute, National University of Singapore, Singapore
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, University of Illinois-Chicago, Chicago, Illinois, United States of America
- * E-mail:
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34
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Graves JL, Tajkarimi M, Cunningham Q, Campbell A, Nonga H, Harrison SH, Barrick JE. Rapid evolution of silver nanoparticle resistance in Escherichia coli. Front Genet 2015; 6:42. [PMID: 25741363 PMCID: PMC4330922 DOI: 10.3389/fgene.2015.00042] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 11/16/2022] Open
Abstract
The recent exponential increase in the use of engineered nanoparticles (eNPs) means both greater intentional and unintentional exposure of eNPs to microbes. Intentional use includes the use of eNPs as biocides. Unintentional exposure results from the fact that eNPs are included in a variety of commercial products (paints, sunscreens, cosmetics). Many of these eNPs are composed of heavy metals or metal oxides such as silver, gold, zinc, titanium dioxide, and zinc oxide. It is thought that since metallic/metallic oxide NPs impact so many aspects of bacterial physiology that it will difficult for bacteria to evolve resistance to them. This study utilized laboratory experimental evolution to evolve silver nanoparticle (AgNP) resistance in the bacterium Escherichia coli (K-12 MG1655), a bacterium that does not harbor any known silver resistance elements. After 225 generations of exposure to the AgNP environment, the treatment populations demonstrated greater fitness vs. control strains as measured by optical density (OD) and colony forming units (CFU) in the presence of varying concentrations of 10 nm citrate-coated silver nanoparticles (AgNP) or silver nitrate (AgNO3). Genomic analysis shows that changes associated with AgNP resistance were already accumulating within the treatment populations by generation 100, and by generation 200 three mutations had swept to high frequency in the AgNP resistance stocks. This study indicates that despite previous claims to the contrary bacteria can easily evolve resistance to AgNPs, and this occurs by relatively simple genomic changes. These results indicate that care should be taken with regards to the use of eNPs as biocides as well as with regards to unintentional exposure of microbial communities to eNPs in waste products.
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Affiliation(s)
- Joseph L. Graves
- Department of Nanoengineering, Joint School for Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University/University of North CarolinaGreensboro, NC, USA
| | - Mehrdad Tajkarimi
- Department of Nanoscience, Joint School for Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University/University of North CarolinaGreensboro, NC, USA
| | - Quincy Cunningham
- Department of Biology, North Carolina Agricultural and Technical State UniversityGreensboro, NC, USA
| | - Adero Campbell
- Department of Biology, Bennett CollegeGreensboro, NC, USA
| | - Herve Nonga
- Student Research Opportunity Program, Michigan State UniversityEast Lansing, MI, USA
| | - Scott H. Harrison
- Department of Biology, North Carolina Agricultural and Technical State UniversityGreensboro, NC, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, The University of Texas at AustinAustin, TX, USA
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35
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Juárez-Rodríguez MD, Torres-Escobar A, Demuth DR. Transcriptional regulation of the Aggregatibacter actinomycetemcomitans ygiW-qseBC operon by QseB and integration host factor proteins. MICROBIOLOGY-SGM 2014; 160:2583-2594. [PMID: 25223341 DOI: 10.1099/mic.0.083501-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The QseBC two-component system plays a pivotal role in regulating virulence and biofilm growth of the oral pathogen Aggregatibacter actinomycetemcomitans. We previously showed that QseBC autoregulates the ygiW-qseBC operon. In this study, we characterized the promoter that drives ygiW-qseBC expression. Using lacZ transcriptional fusion constructs and 5'-rapid amplification of cDNA ends, we showed that ygiW-qseBC expression is driven by a promoter that initiates transcription 53 bases upstream of ygiW and identified putative cis-acting promoter elements, whose function was confirmed using site-specific mutagenesis. Using electrophoretic mobility shift assays, two trans-acting proteins were shown to interact with the ygiW-qseBC promoter. The QseB response regulator bound to probes containing the direct repeat sequence CTTAA-N6-CTTAA, where the CTTAA repeats flank the -35 element of the promoter. The ygiW-qseBC expression could not be detected in A. actinomycetemcomitans ΔqseB or ΔqseBC strains, but was restored to WT levels in the ΔqseBC mutant when complemented by single copy chromosomal insertion of qseBC. Interestingly, qseB partially complemented the ΔqseBC strain, suggesting that QseB could be activated in the absence of QseC. QseB activation required its phosphorylation since complementation did not occur using qseB(pho-), encoding a protein with the active site aspartate substituted with alanine. These results suggest that QseB is a strong positive regulator of ygiW-qseBC expression. In addition, integration host factor (IHF) bound to two sites in the promoter region and an additional site near the 5' end of the ygiW ORF. The expression of ygiW-qseBC was increased by twofold in ΔihfA and ΔihfB strains of A. actinomycetemcomitans, suggesting that IHF is a negative regulator of the ygiW-qseBC operon.
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Affiliation(s)
- María Dolores Juárez-Rodríguez
- Research Group in Oral Health and Systemic Disease, University of Louisville School of Dentistry, 501 S. Preston Street, Louisville, KY 40202, USA
| | - Ascención Torres-Escobar
- Research Group in Oral Health and Systemic Disease, University of Louisville School of Dentistry, 501 S. Preston Street, Louisville, KY 40202, USA
| | - Donald R Demuth
- Research Group in Oral Health and Systemic Disease, University of Louisville School of Dentistry, 501 S. Preston Street, Louisville, KY 40202, USA
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Li YC, Chang CK, Chang CF, Cheng YH, Fang PJ, Yu T, Chen SC, Li YC, Hsiao CD, Huang TH. Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element. Nucleic Acids Res 2014; 42:8777-88. [PMID: 24990372 PMCID: PMC4117788 DOI: 10.1093/nar/gku572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.
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Affiliation(s)
- Yi-Chuan Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ya-Hsin Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Pei-Ju Fang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Sheng-Chia Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yi-Ching Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, ROC
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Barta ML, Hickey JM, Anbanandam A, Dyer K, Hammel M, Hefty PS. Atypical response regulator ChxR from Chlamydia trachomatis is structurally poised for DNA binding. PLoS One 2014; 9:e91760. [PMID: 24646934 PMCID: PMC3960148 DOI: 10.1371/journal.pone.0091760] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/14/2014] [Indexed: 01/23/2023] Open
Abstract
ChxR is an atypical two-component signal transduction response regulator (RR) of the OmpR/PhoB subfamily encoded by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Despite structural homology within both receiver and effector domains to prototypical subfamily members, ChxR does not require phosphorylation for dimer formation, DNA binding or transcriptional activation. Thus, we hypothesized that ChxR is in a conformation optimal for DNA binding with limited interdomain interactions. To address this hypothesis, the NMR solution structure of the ChxR effector domain was determined and used in combination with the previously reported ChxR receiver domain structure to generate a full-length dimer model based upon SAXS analysis. Small-angle scattering of ChxR supported a dimer with minimal interdomain interactions and effector domains in a conformation that appears to require only subtle reorientation for optimal major/minor groove DNA interactions. SAXS modeling also supported that the effector domains were in a head-to-tail conformation, consistent with ChxR recognizing tandem DNA repeats. The effector domain structure was leveraged to identify key residues that were critical for maintaining protein - nucleic acid interactions. In combination with prior analysis of the essential location of specific nucleotides for ChxR recognition of DNA, a model of the full-length ChxR dimer bound to its cognate cis-acting element was generated.
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Affiliation(s)
- Michael L. Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - John M. Hickey
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Asokan Anbanandam
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas, United States of America
| | - Kevin Dyer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - P. Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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Quinn HJ, Cameron ADS, Dorman CJ. Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response. PLoS Genet 2014; 10:e1004215. [PMID: 24603618 PMCID: PMC3945435 DOI: 10.1371/journal.pgen.1004215] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/16/2014] [Indexed: 12/26/2022] Open
Abstract
The evolution of new gene networks is a primary source of genetic innovation that allows bacteria to explore and exploit new niches, including pathogenic interactions with host organisms. For example, the archetypal DNA binding protein, OmpR, is identical between Salmonella Typhimurium serovar Typhimurium and Escherichia coli, but regulatory specialization has resulted in different environmental triggers of OmpR expression and largely divergent OmpR regulons. Specifically, ompR mRNA and OmpR protein levels are elevated by acid pH in S. Typhimurium but not in E. coli. This differential expression pattern is due to differences in the promoter regions of the ompR genes and the E. coli ompR orthologue can be made acid-inducible by introduction of the appropriate sequences from S. Typhimurium. The OmpR regulon in S. Typhimurium overlaps that of E. coli at only 15 genes and includes many horizontally acquired genes (including virulence genes) that E. coli does not have. We found that OmpR binds to its genomic targets in higher abundance when the DNA is relaxed, something that occurs in S. Typhimurium as a result of acid stress and which is a requirement for optimal expression of its virulence genes. The genomic targets of OmpR do not share a strong nucleotide sequence consensus: we propose that the ability of OmpR to recruit additional genes to its regulon arises from its modest requirements for specificity in its DNA targets with its preference for relaxed DNA allowing it to cooperate with DNA-topology-based allostery to modulate transcription in response to acid stress.
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Affiliation(s)
- Heather J. Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Andrew D. S. Cameron
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Charles J. Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
- * E-mail:
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Lou YC, Wang I, Rajasekaran M, Kao YF, Ho MR, Hsu STD, Chou SH, Wu SH, Chen C. Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae. Nucleic Acids Res 2013; 42:4080-93. [PMID: 24371275 PMCID: PMC3973317 DOI: 10.1093/nar/gkt1345] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrAC) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrAN). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrAC and characterized the interactions between PmrAC or BeF3(-)-activated full-length PmrA (PmrAF) and two DNA sequences from the pbgP promoter of K. pneumoniae. We showed that PmrAC binds to the PmrA box, which was verified to contain two half-sites, 5'-CTTAAT-3' and 5'-CCTAAG-3', in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrAC-DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrAC, PmrAF recognizes the two sites simultaneously and specifically. In the PmrAF-DNA complex, PmrAN may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrAC molecules aid in bending and binding of the DNA duplex for transcription activation.
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Affiliation(s)
- Yuan-Chao Lou
- Institute of Biomedical Sciences, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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40
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Purssell A, Poole K. Functional characterization of the NfxB repressor of the mexCD–oprJ multidrug efflux operon of Pseudomonas aeruginosa. Microbiology (Reading) 2013; 159:2058-2073. [DOI: 10.1099/mic.0.069286-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Andrew Purssell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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41
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Choudhury HG, Beis K. The dimeric form of the unphosphorylated response regulator BaeR. Protein Sci 2013; 22:1287-93. [PMID: 23868292 DOI: 10.1002/pro.2311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 11/09/2022]
Abstract
Bacterial response regulators (RRs) can regulate the expression of genes that confer antibiotic resistance; they contain a receiver and an effector domain and their ability to bind DNA is based on the dimerization state. This is triggered by phosphorylation of the receiver domain by a kinase. However, even in the absence of phosphorylation RRs can exist in equilibrium between monomers and dimers with phosphorylation shifting the equilibrium toward the dimer form. We have determined the crystal structure of the unphosphorylated dimeric BaeR from Escherichia coli. The dimer interface is formed by a domain swap at the receiver domain. In comparison with the unphosphorylated dimeric PhoP from Mycobacterium tuberculosis, BaeR displays an asymmetry of the effector domains.
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Affiliation(s)
- Hassanul G Choudhury
- Division of Molecular Biosciences, Imperial College London, London, South Kensington, SW7 2AZ, United Kingdom; Membrane Protein Lab, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire, OX11 0DE, United Kingdom; Research Complex at Harwell, Harwell Oxford, Didcot, Oxforsdhire OX11 0FA, United Kingdom
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42
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Krug M, Lee SJ, Boos W, Diederichs K, Welte W. The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose. Protein Sci 2013; 22:800-8. [PMID: 23576322 DOI: 10.1002/pro.2263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 01/02/2023]
Abstract
TrmB is a repressor that binds maltose, maltotriose, and sucrose, as well as other α-glucosides. It recognizes two different operator sequences controlling the TM (Trehalose/Maltose) and the MD (Maltodextrin) operon encoding the respective ABC transporters and sugar-degrading enzymes. Binding of maltose to TrmB abrogates repression of the TM operon but maintains the repression of the MD operon. On the other hand, binding of sucrose abrogates repression of the MD operon but maintains repression of the TM operon. The three-dimensional structure of TrmB in complex with sucrose was solved and refined to a resolution of 3.0 Å. The structure shows the N-terminal DNA binding domain containing a winged-helix-turn-helix (wHTH) domain followed by an amphipathic helix with a coiled-coil motif. The latter promotes dimerization and places the symmetry mates of the putative recognition helix in the wHTH motif about 30 Å apart suggesting a canonical binding to two successive major grooves of duplex palindromic DNA. This suggests that the structure resembles the conformation of TrmB recognizing the pseudopalindromic TM promoter but not the conformation recognizing the nonpalindromic MD promoter.
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Affiliation(s)
- Michael Krug
- Department of Biology, University of Konstanz, Konstanz, Germany
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43
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Chen SC, Chang CF, Fan PJ, Cheng YH, Yu T, Huang TH. (1)H, (13)C and (15)N resonance assignments of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniae. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:85-88. [PMID: 22481468 DOI: 10.1007/s12104-012-9383-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/24/2012] [Indexed: 05/31/2023]
Abstract
Bacterial cells often use two-component signal transduction systems to regulate genes in response to environmental stimuli. The RstA/RstB system is a two-component regulatory system consisting of the membrane sensor, RstB, and its cognate response regulator RstA. The RstA of Klebsiella pneumoniae consists of a N-terminal receiver domain (NRD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of the response regulator induces a conformational change in the regulatory domain of RstA, which results in activation of the effector domain to regulate the downstream genes, including the ferrous iron transport system (Feo), at low-pH condition. Here we report the (1)H, (13)C and (15)N resonance assignments and secondary structure identification of the DBD of RstA from K. pneumoniae as a first step for unraveling the structural and functional relationship of the RstA/RstB two component system.
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Affiliation(s)
- Sheng-Chia Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan, ROC
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44
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Barbieri CM, Wu T, Stock AM. Comprehensive analysis of OmpR phosphorylation, dimerization, and DNA binding supports a canonical model for activation. J Mol Biol 2013; 425:1612-26. [PMID: 23399542 DOI: 10.1016/j.jmb.2013.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 01/22/2013] [Accepted: 02/02/2013] [Indexed: 11/16/2022]
Abstract
The OmpR/PhoB family of response regulators (RRs) is the largest class of two-component system signal transduction proteins. Extensive biochemical and structural characterization of these transcription factors has provided insights into their activation and DNA-binding mechanisms. For the most part, OmpR/PhoB family proteins are thought to become activated through phosphorylation from their cognate histidine kinase partners, which in turn facilitates an allosteric change in the RR, enabling homodimerization and subsequently enhanced DNA binding. Incongruently, it has been suggested that OmpR, the eponymous member of this RR family, becomes activated via different mechanisms, whereby DNA binding plays a central role in facilitating dimerization and phosphorylation. Characterization of the rate and extent of the phosphorylation of OmpR and OmpR DNA-binding mutants following activation of the EnvZ/OmpR two-component system shows that DNA binding is not essential for phosphorylation of OmpR in vivo. In addition, detailed analyses of the energetics of DNA binding and dimerization of OmpR in both its unphosphorylated and phosphorylated state indicate that phosphorylation enhances OmpR dimerization and that this dimerization enhancement is the energetic driving force for phosphorylation-mediated regulation of OmpR-DNA binding. These findings suggest that OmpR phosphorylation-mediated activation follows the same paradigm as the other members of the OmpR/PhoB family of RRs in contrast to previously proposed models of OmpR activation.
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Affiliation(s)
- Christopher M Barbieri
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, USA
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Perkins TT, Davies MR, Klemm EJ, Rowley G, Wileman T, James K, Keane T, Maskell D, Hinton JCD, Dougan G, Kingsley RA. ChIP-seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization. Mol Microbiol 2013; 87:526-38. [PMID: 23190111 PMCID: PMC3586657 DOI: 10.1111/mmi.12111] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2012] [Indexed: 12/25/2022]
Abstract
OmpR is a multifunctional DNA binding regulator with orthologues in many enteric bacteria that exhibits classical regulator activity as well as nucleoid-associated protein-like characteristics. In the enteric pathogen Salmonella enterica, using chromatin immunoprecipitation of OmpR:FLAG and nucleotide sequencing, 43 putative OmpR binding sites were identified in S. enterica serovar Typhi, 22 of which were associated with OmpR-regulated genes. Mutation of a sequence motif (TGTWACAW) that was associated with the putative OmpR binding sites abrogated binding of OmpR:6×His to the tviA upstream region. A core set of 31 orthologous genes were found to exhibit OmpR-dependent expression in both S. Typhi and S. Typhimurium. S. Typhimurium-encoded orthologues of two divergently transcribed OmpR-regulated operons (SL1068-71 and SL1066-67) had a putative OmpR binding site in the inter-operon region in S. Typhi, and were characterized using in vitro and in vivo assays. These operons are widely distributed within S. enterica but absent from the closely related Escherichia coli. SL1066 and SL1067 were required for growth on N-acetylmuramic acid as a sole carbon source. SL1068-71 exhibited sequence similarity to sialic acid uptake systems and contributed to colonization of the ileum and caecum in the streptomycin-pretreated mouse model of colitis.
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Affiliation(s)
- Timothy T Perkins
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Mark R Davies
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Elizabeth J Klemm
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Gary Rowley
- School of Biological Sciences University of East Anglia NorwichNR4 7TJ UK
| | - Thomas Wileman
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Keith James
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Thomas Keane
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Duncan Maskell
- Department of Veterinary Medicine University of Cambridge Madingley Road CambridgeCB3 0ES UK
| | - Jay C D Hinton
- Institute of Integrative Biology University of Liverpool Crown Street LiverpoolL69 7ZB UK
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
| | - Robert A Kingsley
- The Wellcome Trust Sanger Institute The Wellcome Trust Genome Campus, Hinxton CambridgeCB10 1SA UK
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46
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Song W, Lin X, Che S. Identification of Regulatory Sequences and Expression Analysis of OmpR Gene Under Different Stress Conditions in the Antarctic Bacterium Psychrobacter sp. G. Curr Microbiol 2012. [DOI: 10.1007/s00284-012-0266-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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47
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Rentschler AE, Lovrich SD, Fitton R, Enos-Berlage J, Schwan WR. OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment. MICROBIOLOGY-SGM 2012; 159:316-327. [PMID: 23175504 DOI: 10.1099/mic.0.059386-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) causes more than 90 % of all human urinary tract infections through type 1 piliated UPEC cells binding to bladder epithelial cells. The FimB and FimE site-specific recombinases orient the fimS element containing the fimA structural gene promoter. Regulation of fimB and fimE depends on environmental pH and osmolality. The EnvZ/OmpR two-component system affects osmoregulation in E. coli. To ascertain if OmpR directly regulated the fimB gene promoters, gel mobility shift and DNase I footprinting experiments were performed using OmpR or phosphorylated OmpR (OmpR-P) mixed with the fimB promoter regions of UPEC strain NU149. Both OmpR-P and OmpR bound weakly to one fimB promoter. Because there was weak binding to one fimB promoter, strain NU149 was grown in different pH and osmolality environments, and total RNAs were extracted from each population and converted to cDNAs. Quantitative reverse-transcriptase PCR showed no differences in ompR transcription among the different growth conditions. Conversely, Western blots showed a significant increase in OmpR protein in UPEC cells grown in a combined low pH/high osmolality environment versus a neutral pH/high osmolality environment. In a high osmolality environment, the ompR mutant expressed more fimB transcripts and Phase-ON positioning of the fimS element as well as higher type 1 pili levels than wild-type cells. Together these results suggest that OmpR may be post-transcriptionally regulated in UPEC cells growing in a low pH/high osmolality environment, which regulates fimB in UPEC.
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48
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Thanikkal EJ, Mangu JCK, Francis MS. Interactions of the CpxA sensor kinase and cognate CpxR response regulator from Yersinia pseudotuberculosis. BMC Res Notes 2012; 5:536. [PMID: 23013530 PMCID: PMC3517363 DOI: 10.1186/1756-0500-5-536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 09/22/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The CpxA sensor kinase-CpxR response regulator two-component regulatory system is a sentinel of bacterial envelope integrity. Integrating diverse signals, it can alter the expression of a wide array of components that serve to shield the envelope from damage and to promote bacterial survival. In bacterial pathogens such as Yersinia pseudotuberculosis, this also extends to pathogenesis. CpxR is thought to dimerize upon phosphorylation by the sensor kinase CpxA. This phosphorylation enables CpxR binding to specific DNA sequences where it acts on gene transcription. As Cpx pathway activation is dependent on protein-protein interactions, we performed an interaction analysis of CpxR and CpxA from Y. pseudotuberculosis. RESULTS CpxR full-length and truncated versions that either contained or lacked a putative internal linker were all assessed for their ability to homodimerize and interact with CpxA. Using an adenylate cyclase-based bacterial two hybrid approach, full-length CpxR readily engaged with CpxA. The CpxR N-terminus could also homodimerize with itself and with a full-length CpxR. A second homodimerization assay based upon the λcI repressor also demonstrated that the CpxR C-terminus could homodimerize. While the linker was not specifically required, it enhanced CpxR homodimerization. Mutagenesis of cpxR identified the aspartate at residue 51, putative N-terminal coiled-coil and C-terminal winged-helix-turn-helix domains as mediators of CpxR homodimerization. Scrutiny of CpxA full-length and truncated versions revealed that dimerization involved the N-terminus and an internal dimerization and histidine phosphotransfer domain. CONCLUSIONS This interaction analysis mapped regions of CpxR and CpxA that were responsible for interactions with self or with each other. When combined with other physiological and biochemical tests both hybrid-based assays can be useful in dissecting molecular contacts that may underpin Cpx pathway activation and repression.
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Affiliation(s)
- Edvin J Thanikkal
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
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49
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A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. PLoS Genet 2012; 8:e1002615. [PMID: 22457642 PMCID: PMC3310775 DOI: 10.1371/journal.pgen.1002615] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/07/2012] [Indexed: 01/28/2023] Open
Abstract
DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein–DNA and protein–protein interactions is poorly understood. For example, relaxation of DNA supercoiling strongly induces the well-studied pathogenicity gene ssrA (also called spiR) in Salmonella enterica, but neither the mechanism nor the proteins involved are known. We have found that relaxation of DNA supercoiling induces expression of the Salmonella pathogenicity island (SPI)-2 regulator ssrA as well as the SPI-1 regulator hilC through a mechanism that requires the two-component regulator OmpR-EnvZ. Additionally, the ompR promoter is autoregulated in the same fashion. Conversely, the SPI-1 regulator hilD is induced by DNA relaxation but is repressed by OmpR. Relaxation of DNA supercoiling caused an increase in OmpR binding to DNA and a concomitant decrease in binding by the nucleoid-associated protein FIS. The reciprocal occupancy of DNA by OmpR and FIS was not due to antagonism between these transcription factors, but was instead a more intrinsic response to altered DNA topology. Surprisingly, DNA relaxation had no detectable effect on the binding of the global repressor H-NS. These results reveal the underlying molecular mechanism that primes SPI genes for rapid induction at the onset of host invasion. Additionally, our results reveal novel features of the archetypal two-component regulator OmpR. OmpR binding to relaxed DNA appears to generate a locally supercoiled state, which may assist promoter activation by relocating supercoiling stress-induced destabilization of DNA strands. Much has been made of the mechanisms that have evolved to regulate horizontally-acquired genes such as SPIs, but parallels among the ssrA, hilC, and ompR promoters illustrate that a fundamental form of regulation based on DNA topology coordinates the expression of these genes regardless of their origins. DNA is often considered to be a passive carrier of genetic information, but in fact DNA is an active participant in coordinating the expression of the genes it carries. This is because DNA is a dynamic molecule that can assume a wide range of topologies, and this has a direct impact on the formation of the protein–DNA complexes that drive gene expression. In a bacterium, the chromosome is supercoiled to variable levels according to environmental conditions, and supercoiling in turn governs the topology of gene promoters. Thus DNA supercoiling is able to transduce environmental signals to regulate promoter output. A previous study found that the intestinal pathogen Salmonella enterica may use changes in DNA supercoiling to detect when it has entered host immune cells, allowing the bacterium to induce the pathogenicity genes it requires to evade killing by macrophage. In dissecting the underlying molecular mechanisms, we have found that changes in DNA supercoiling also upregulate other key pathogenicity genes, and we have identified the proteins involved in this gene regulatory process. These findings indicate that a fundamental level of gene control arising from the interplay between protein transcription factors and DNA topology regulates Salmonella pathogenicity.
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Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites. PLoS One 2012; 7:e30102. [PMID: 22291906 PMCID: PMC3264566 DOI: 10.1371/journal.pone.0030102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 12/13/2011] [Indexed: 12/04/2022] Open
Abstract
Expression of KdpFABC, a K+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABCBS) via the winged helix-turn-helix type DNA binding domain (KdpEDBD). Exploration of E. coli KdpEDBD and kdpFABCBS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpEDBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpEDBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpEDBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.
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