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Majdi C, Meffre P, Benfodda Z. Recent advances in the development of bacterial response regulators inhibitors as antibacterial and/or antibiotic adjuvant agent: A new approach to combat bacterial resistance. Bioorg Chem 2024; 150:107606. [PMID: 38968903 DOI: 10.1016/j.bioorg.2024.107606] [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: 03/25/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
The number of new antibacterial agents currently being discovered is insufficient to combat bacterial resistance. It is extremely challenging to find new antibiotics and to introduce them to the pharmaceutical market. Therefore, special attention must be given to find new strategies to combat bacterial resistance and prevent bacteria from developing resistance. Two-component system is a transduction system and the most prevalent mechanism employed by bacteria to respond to environmental changes. This signaling system consists of a membrane sensor histidine kinase that perceives environmental stimuli and a response regulator which acts as a transcription factor. The approach consisting of developing response regulators inhibitors with antibacterial activity or antibiotic adjuvant activity is a novel approach that has never been previously reviewed. In this review we report for the first time, the importance of targeting response regulators and summarizing all existing studies carried out from 2008 until now on response regulators inhibitors as antibacterial agents or / and antibiotic adjuvants. Moreover, we describe the antibacterial activity and/or antibiotic adjuvants activity against the studied bacterial strains and the mechanism of different response regulator inhibitors when it's possible.
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2
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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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3
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Yan Z, Wang J. Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system. Commun Chem 2024; 7:13. [PMID: 38233668 PMCID: PMC10794238 DOI: 10.1038/s42004-024-01098-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The elegant design of protein sequence/structure/function relationships arises from the interaction patterns between amino acid positions. A central question is how evolutionary forces shape the interaction patterns that encode long-range epistasis and binding specificity. Here, we combined family-wide evolutionary analysis of natural homologous sequences and structure-oriented evolution simulation for two-component signaling (TCS) system. The magnitude-frequency relationship of coupling conservation between positions manifests a power-law-like distribution and the positions with highly coupling conservation are sparse but distributed intensely on the binding surfaces and hydrophobic core. The structure-specific interaction pattern involves further optimization of local frustrations at or near the binding surface to adapt the binding partner. The construction of family-wide conserved interaction patterns and structure-specific ones demonstrates that binding specificity is modulated by both direct intermolecular interactions and long-range epistasis across the binding complex. Evolution sculpts the interaction patterns via sequence variations at both family-wide and structure-specific levels for TCS system.
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Affiliation(s)
- Zhiqiang Yan
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, PR China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY, 11790, USA.
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Chen X, Alakavuklar MA, Fiebig A, Crosson S. Cross-regulation in a three-component cell envelope stress signaling system of Brucella. mBio 2023; 14:e0238723. [PMID: 38032291 PMCID: PMC10746171 DOI: 10.1128/mbio.02387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE As intracellular pathogens, Brucella must contend with a variety of host-derived stressors when infecting a host cell. The inner membrane, cell wall, and outer membrane, i.e. the cell envelope, of Brucella provide a critical barrier to host assault. A conserved regulatory mechanism known as two-component signaling (TCS) commonly controls transcription of genes that determine the structure and biochemical composition of the cell envelope during stress. We report the identification of previously uncharacterized TCS genes that determine Brucella ovis fitness in the presence of cell envelope disruptors and within infected mammalian host cells. Our study reveals a new molecular mechanism of TCS-dependent gene regulation, and thereby advances fundamental understanding of transcriptional regulatory processes in bacteria.
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Affiliation(s)
- Xingru Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Melene A. Alakavuklar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Chen X, Alakavuklar MA, Fiebig A, Crosson S. Cross regulation in a three-component cell envelope stress signaling system of Brucella. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536747. [PMID: 37873345 PMCID: PMC10592609 DOI: 10.1101/2023.04.15.536747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A multi-layered structure known as the cell envelope separates the controlled interior of bacterial cells from a fluctuating physical and chemical environment. The transcription of genes that determine cell envelope structure and function is commonly regulated by two-component signaling systems (TCS), comprising a sensor histidine kinase and a cognate response regulator. To identify TCS genes that contribute to cell envelope function in the intracellular mammalian pathogen, Brucella ovis, we subjected a collection of non-essential TCS deletion mutants to compounds that disrupt cell membranes and the peptidoglycan cell wall. Our screen led to the discovery of three TCS proteins that coordinately function to confer resistance to cell envelope stressors and to support B. ovis replication in the intracellular niche. This tripartite regulatory system includes the known cell envelope regulator, CenR, and a previously uncharacterized TCS, EssR-EssS, which is widely conserved in Alphaproteobacteria. The CenR and EssR response regulators bind a shared set of sites on the B. ovis chromosomes to control transcription of an overlapping set of genes with cell envelope functions. CenR directly interacts with EssR and functions to stimulate phosphoryl transfer from the EssS kinase to EssR, while CenR and EssR control the cellular levels of each other via a post-transcriptional mechanism. Our data provide evidence for a new mode of TCS cross-regulation in which a non-cognate response regulator affects both the activity and protein levels of a cognate TCS protein pair.
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Affiliation(s)
- Xingru Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Melene A Alakavuklar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
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6
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Memon AA, Fu X, Fan XY, Xu L, Xiao J, Rahman MU, Yang X, Yao YF, Deng Z, Ma W. Substrate DNA Promoting Binding of Mycobacterium tuberculosis MtrA by Facilitating Dimerization and Interpretation of Affinity by Minor Groove Width. Microorganisms 2023; 11:2505. [PMID: 37894163 PMCID: PMC10609481 DOI: 10.3390/microorganisms11102505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
In order to deepen the understanding of the role and regulation mechanisms of prokaryotic global transcription regulators in complex processes, including virulence, the associations between the affinity and binding sequences of Mycobacterium tuberculosis MtrA have been explored extensively. Analysis of MtrA 294 diversified 26 bp binding sequences revealed that the sequence similarity of fragments was not simply associated with affinity. The unique variation patterns of GC content and periodical and sequential fluctuation of affinity contribution curves were observed along the sequence in this study. Furthermore, docking analysis demonstrated that the structure of the dimer MtrA-DNA (high affinity) was generally consistent with other OmpR family members, while Arg 219 and Gly 220 of the wing domain interacted with the minor groove. The results of the binding box replacement experiment proved that box 2 was essential for binding, which implied the differential roles of the two boxes in the binding process. Furthermore, the results of the substitution of the nucleotide at the 20th and/or 21st positions indicated that the affinity was negatively associated with the value of minor groove width precisely at the 21st position. The dimerization of the unphosphorylated MtrA facilitated by a low-affinity DNA fragment was observed for the first time. However, the proportion of the dimer was associated with the affinity of substrate DNA, which further suggested that the affinity was actually one characteristic of the stability of dimers. Based on the finding of 17 inter-molecule hydrogen bonds identified in the interface of the MtrA dimer, including 8 symmetric complementary ones in the conserved α4-β5-α5 face, we propose that hydrogen bonds should be considered just as important as salt bridges and the hydrophobic patch in the dimerization. Our comprehensive study on a large number of binding fragments with quantitative affinity values provided new insight into the molecular mechanism of dimerization, binding specificity and affinity determination of MtrA and clues for solving the puzzle of how global transcription factors regulate a large quantity of target genes.
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Affiliation(s)
- Aadil Ahmed Memon
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiao-Yong Fan
- Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Lingyun Xu
- Shanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, China
| | - Jihua Xiao
- Shanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, China
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaoqi Yang
- Shanghai Huaxin Biotechnology Co., Ltd., Room 604, Building 1, Tongji Chuangyuan, No. 99 South Changjiang Road, Baoshan District, Shanghai 200441, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Institutes of Medical Sciences, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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7
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Nieves M, Buschiazzo A, Trajtenberg F. Structural features of sensory two component systems: a synthetic biology perspective. Biochem J 2023; 480:127-140. [PMID: 36688908 DOI: 10.1042/bcj20210798] [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: 10/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/24/2023]
Abstract
All living organisms include a set of signaling devices that confer the ability to dynamically perceive and adapt to the fluctuating environment. Two-component systems are part of this sensory machinery that regulates the execution of different genetic and/or biochemical programs in response to specific physical or chemical signals. In the last two decades, there has been tremendous progress in our molecular understanding on how signals are detected, the allosteric mechanisms that control intramolecular information transmission and the specificity determinants that guarantee correct wiring. All this information is starting to be exploited in the development of new synthetic networks. Connecting multiple molecular players, analogous to programming lines of code, can provide the resources to build new sophisticated biocomputing systems. The Synthetic Biology field is starting to revolutionize several scientific fields, such as biomedicine and agriculture, propelling the development of new solutions. Expanding the spectrum of available nanodevices in the toolbox is key to unleash its full potential. This review aims to discuss, from a structural perspective, how to take advantage of the vast array of sensor and effector protein modules involved in two-component systems for the construction of new synthetic circuits.
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Affiliation(s)
- Marcos Nieves
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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9
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Real-time detection of response regulator phosphorylation dynamics in live bacteria. Proc Natl Acad Sci U S A 2022; 119:e2201204119. [PMID: 35994658 PMCID: PMC9436347 DOI: 10.1073/pnas.2201204119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria utilize two-component system (TCS) signal transduction pathways to sense and adapt to changing environments. In a typical TCS, a stimulus induces a sensor histidine kinase (SHK) to phosphorylate a response regulator (RR), which then dimerizes and activates a transcriptional response. Here, we demonstrate that oligomerization-dependent depolarization of excitation light by fused mNeonGreen fluorescent protein probes enables real-time monitoring of RR dimerization dynamics in live bacteria. Using inducible promoters to independently express SHKs and RRs, we detect RR dimerization within seconds of stimulus addition in several model pathways. We go on to combine experiments with mathematical modeling to reveal that TCS phosphosignaling accelerates with SHK expression but decelerates with RR expression and SHK phosphatase activity. We further observe pulsatile activation of the SHK NarX in response to addition and depletion of the extracellular electron acceptor nitrate when the corresponding TCS is expressed from both inducible systems and the native chromosomal operon. Finally, we combine our method with polarized light microscopy to enable single-cell measurements of RR dimerization under changing stimulus conditions. Direct in vivo characterization of RR oligomerization dynamics should enable insights into the regulation of bacterial physiology.
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10
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Abstract
The two-component system PhoP/PhoQ is essential for Salmonella enterica serovar Typhimurium virulence. Here, we report that PhoP is methylated extensively. Two consecutive glutamate (E) and aspartate (D)/E residues, i.e., E8/D9 and E107/E108, and arginine (R) 112 can be methylated. Individual mutation of these above-mentioned residues caused impaired phosphorylation and dimerization or DNA-binding ability of PhoP to a different extent and led to attenuated bacterial virulence. With the help of specific antibodies recognizing methylated E8 and monomethylated R112, we found that the methylation levels of E8 or R112 decreased dramatically when bacteria encountered low magnesium, acidic pH, or phagocytosis by macrophages, under which PhoP can be activated. Furthermore, CheR, a bacterial chemotaxis methyltransferase, was identified to methylate R112. Overexpression of cheR decreased PhoP activity but increased PhoP stability. Together, the current study reveals that methylation plays an important role in regulating PhoP activities in response to environmental cues and, consequently, modulates Salmonella virulence.
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11
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Palethorpe S, Milton ME, Pesci EC, Cavanagh J. Structure of the Acinetobacter baumannii PmrA receiver domain and insights into clinical mutants affecting DNA-binding and promoting colistin resistance. J Biochem 2021; 170:787-800. [PMID: 34585233 DOI: 10.1093/jb/mvab102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Acinetobacter baumannii is an insidious emerging nosocomial pathogen that has developed resistance to all available antimicrobials, including the last resort antibiotic, colistin. Colistin resistance often occurs due to mutations in the PmrAB two component regulatory system. To better understand the regulatory mechanisms contributing to colistin resistance, we have biochemically characterized the A. baumannii PmrA response regulator. Initial DNA-binding analysis shows that A. baumannii PmrA bound to the Klebsiella pneumoniae PmrA box motif. This prompted analysis of the putative A. baumannii PmrAB regulon which indicated that the A. baumannii PmrA consensus box is 5'- HTTAAD N5 HTTAAD. Additionally, we provide the first structural information for the A. baumannii PmrA N-terminal domain through X-ray crystallography, and we present a full-length model using molecular modeling. From these studies, we were able to infer the effects of two critical PmrA mutations, PmrA::I13M and PmrA::P102R, both of which confer increased colistin resistance. Based on these data, we suggest structural and dynamic reasons for how these mutations can affect PmrA function and hence encourage resistive traits. Understanding these mechanisms will aid in the development of new targeted antimicrobial therapies.
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Affiliation(s)
- Samantha Palethorpe
- Department of Microbiology and Immunology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - Morgan E Milton
- Department of Biochemistry and Molecular Biology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - Everett C Pesci
- Department of Microbiology and Immunology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
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12
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Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms 2021; 9:microorganisms9102026. [PMID: 34683347 PMCID: PMC8541618 DOI: 10.3390/microorganisms9102026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/20/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field’s most pressing questions: How does VanS sense vancomycin?
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13
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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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14
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Cho SY, Yoon SI. Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus. Biochem Biophys Res Commun 2021; 555:102-108. [PMID: 33813268 DOI: 10.1016/j.bbrc.2021.03.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 01/24/2023]
Abstract
VbrK and VbrR from the gastroenteritis-causing Vibrio parahaemolyticus are a histidine kinase and response regulator, respectively, that constitute a two-component regulatory system. VbrK responds to β-lactam antibiotics or nitrate and activates VbrR via phosphorylation. Consequently, VbrR transcriptionally regulates the expression of β-lactamase and ExsC and contributes to the survival or virulence of V. parahaemolyticus. Due to the unavailability of the VbrR structure, it remains unclear how VbrR is activated via its N-terminal receiver domain (RD) and recognizes dsDNA via its C-terminal DNA-binding domain (DBD). To reveal the mechanism underlying VbrR-mediated activation, we generated the phosphomimetic protein (VbrRRD-D51E) of the VbrR RD by replacing the D51 residue at the phosphorylation site with glutamate. VbrRRD-D51E exhibits a β7α5 structure rather than the typical β5α5 structure because it contains a unique two-stranded β-sheet. The VbrRRD-D51E structure represents an active state in which the D51E residue interacts with the T78 residue. As a result, the Y97 residue adopts an inward conformation, allowing VbrRRD-D51E to dimerize using the α4-β5-α5 face. These activation events are facilitated by a VbrR-specific residue, R52. Further structural study demonstrated that the VbrR DBD adopts a β-strand-decorated three-helix structure. Based on a comparative structural study, we propose that VbrR recognizes dsDNA by inserting the α8 helix into the major groove of dsDNA and interacting with the minor groove of dsDNA via the β11-β12 region. Our findings will provide a new avenue for development of new antibacterial drugs for treating V. parahaemolyticus infections.
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Affiliation(s)
- So Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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15
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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16
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Acetylation of PhoP K88 Is Involved in Regulating Salmonella Virulence. Infect Immun 2021; 89:IAI.00588-20. [PMID: 33318137 DOI: 10.1128/iai.00588-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
The PhoP-PhoQ two-component regulation system of Salmonella enterica serovar Typhimurium is involved in the response to various environmental stresses and is essential for bacterial virulence. Our previous studies showed that acetylation plays an important role in regulating the activity of PhoP, which consequently mediates the change in virulence of S Typhimurium. Here, we demonstrate that a conserved lysine residue, K88, is crucial for the function of PhoP and its acetylation-downregulated PhoP activities. K88 could be specifically acetylated by acetyl phosphate (AcP), and the acetylation level of K88 decreased significantly after phagocytosis of S Typhimurium by macrophages. Acetylation of K88 inhibited PhoP dimerization and DNA-binding abilities. In addition, mutation of K88 to glutamine, mimicking the acetylated form, dramatically attenuated intestinal inflammation and systemic infection of S Typhimurium in the mouse model. These findings indicate that nonenzymatic acetylation of PhoP by AcP is a fine-tuned mechanism for the virulence of S Typhimurium and highlights that virulence and metabolism in the host are closely linked.
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17
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Ouyang Z, Zheng F, Chew JY, Pei Y, Zhou J, Wen K, Han M, Lemieux MJ, Hwang PM, Wen Y. Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR. Nucleic Acids Res 2020; 47:11418-11429. [PMID: 31598698 PMCID: PMC6868441 DOI: 10.1093/nar/gkz891] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 09/21/2019] [Accepted: 10/01/2019] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus ArlRS is a key two-component regulatory system necessary for adhesion, biofilm formation, and virulence. The response regulator ArlR consists of a C-terminal DNA-binding effector domain and an N-terminal receiver domain that is phosphorylated by ArlS, the cognate transmembrane sensor histidine kinase. We demonstrate that the receiver domain of ArlR adopts the canonical α5β5 response regulator assembly, which dimerizes upon activation, using beryllium trifluoride as an aspartate phosphorylation mimic. Activated ArlR recognizes a 20-bp imperfect inverted repeat sequence in the ica operon, which is involved in intercellular adhesion polysaccharide production. Crystal structures of the inactive and activated forms reveal that activation induces a significant conformational change in the β4-α4 and β5-α5-connecting loops, in which the α4 and α5 helices constitute the homodimerization interface. Crystal structures of the DNA-binding ArlR effector domain indicate that it is able to dimerize via a non-canonical β1–β2 hairpin domain swapping, raising the possibility of a new mechanism for signal transduction from the receiver domain to effector domain. Taken together, the current study provides structural insights into the activation of ArlR and its recognition, adding to the diversity of response regulation mechanisms that may inspire novel antimicrobial strategies specifically targeting Staphylococcus.
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Affiliation(s)
- Zhenlin Ouyang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Fang Zheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jared Y Chew
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Yingmei Pei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jinhong Zhou
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Keqing Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Miao Han
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Peter M Hwang
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Yurong Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China.,Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
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18
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New Insights into Multistep-Phosphorelay (MSP)/ Two-Component System (TCS) Regulation: Are Plants and Bacteria that Different? PLANTS 2019; 8:plants8120590. [PMID: 31835810 PMCID: PMC6963811 DOI: 10.3390/plants8120590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022]
Abstract
The Arabidopsis multistep-phosphorelay (MSP) is a signaling mechanism based on a phosphorelay that involves three different types of proteins: Histidine kinases, phosphotransfer proteins, and response regulators. Its bacterial equivalent, the two-component system (TCS), is the most predominant device for signal transduction in prokaryotes. The TCS has been extensively studied and is thus generally well-understood. In contrast, the MSP in plants was first described in 1993. Although great advances have been made, MSP is far from being completely comprehended. Focusing on the model organism Arabidopsis thaliana, this review summarized recent studies that have revealed many similarities with bacterial TCSs regarding how TCS/MSP signaling is regulated by protein phosphorylation and dephosphorylation, protein degradation, and dimerization. Thus, comparison with better-understood bacterial systems might be relevant for an improved study of the Arabidopsis MSP.
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Abstract
Response regulators function as the output components of two-component systems, which couple the sensing of environmental stimuli to adaptive responses. Response regulators typically contain conserved receiver (REC) domains that function as phosphorylation-regulated switches to control the activities of effector domains that elicit output responses. This modular design is extremely versatile, enabling different regulatory strategies tuned to the needs of individual signaling systems. This review summarizes structural features that underlie response regulator function. An abundance of atomic resolution structures and complementary biochemical data have defined the mechanisms for response regulator enzymatic activities, revealed trends in regulatory strategies utilized by response regulators of different subfamilies, and provided insights into interactions of response regulators with their cognate histidine kinases. Among the hundreds of thousands of response regulators identified, variations abound. This article provides a framework for understanding structural features that enable function of canonical response regulators and a basis for distinguishing noncanonical configurations.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
| | - Sophie Bouillet
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
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20
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Mechaly AE, Haouz A, Sassoon N, Buschiazzo A, Betton JM, Alzari PM. Conformational plasticity of the response regulator CpxR, a key player in Gammaproteobacteria virulence and drug-resistance. J Struct Biol 2018; 204:165-171. [DOI: 10.1016/j.jsb.2018.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 01/27/2023]
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21
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Kou X, Liu Y, Li C, Liu M, Jiang L. Dimerization and Conformational Exchanges of the Receiver Domain of Response Regulator PhoB from Escherichia coli. J Phys Chem B 2018; 122:5749-5757. [DOI: 10.1021/acs.jpcb.8b01034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinhui Kou
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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22
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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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23
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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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24
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Miguel-Romero L, Casino P, Landete JM, Monedero V, Zúñiga M, Marina A. The malate sensing two-component system MaeKR is a non-canonical class of sensory complex for C4-dicarboxylates. Sci Rep 2017; 7:2708. [PMID: 28577341 PMCID: PMC5457438 DOI: 10.1038/s41598-017-02900-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
Microbial colonization of different environments is enabled to a great extent by the plasticity of their sensory mechanisms, among them, the two-component signal transduction systems (TCS). Here, an example of TCS plasticity is presented: the regulation of L-malate catabolism via malic enzyme by MaeRK in Lactobacillales. MaeKR belongs to the citrate family of TCS as the Escherichia coli DcuSR system. We show that the Lactobacillus casei histidine-kinase MaeK is defective in autophosphorylation activity as it lacks a functional catalytic and ATP binding domain. The cognate response regulator MaeR was poorly phosphorylated at its phosphoacceptor Asp in vitro. This phosphorylation, however, enhanced MaeR binding in vitro to its target sites and it was required for induction of regulated genes in vivo. Elucidation of the MaeR structure revealed that response regulator dimerization is accomplished by the swapping of α4-β5-α5 elements between two monomers, generating a phosphoacceptor competent conformation. Sequence and phylogenetic analyses showed that the MaeKR peculiarities are not exclusive to L. casei as they are shared by the rest of orthologous systems of Lactobacillales. Our results reveal MaeKR as a non-canonical TCS displaying distinctive features: a swapped response regulator and a sensor histidine kinase lacking ATP-dependent kinase activity.
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Affiliation(s)
- L Miguel-Romero
- Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain
| | - P Casino
- Departamento de Bioquímica, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - J M Landete
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.,Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - V Monedero
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - M Zúñiga
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - A Marina
- Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain. .,Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, -, Spain.
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25
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The Two-Component System ChtRS Contributes to Chlorhexidine Tolerance in Enterococcus faecium. Antimicrob Agents Chemother 2017; 61:AAC.02122-16. [PMID: 28242664 DOI: 10.1128/aac.02122-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/20/2017] [Indexed: 02/06/2023] Open
Abstract
Enterococcus faecium is one of the primary causes of nosocomial infections. Disinfectants are commonly used to prevent infections with multidrug-resistant E. faecium in hospitals. Worryingly, E. faecium strains that exhibit tolerance to disinfectants have already been described. We aimed to identify and characterize E. faecium genes that contribute to tolerance to the disinfectant chlorhexidine (CHX). We used a transposon mutant library, constructed in a multidrug-resistant E. faecium bloodstream isolate, to perform a genome-wide screen to identify genetic determinants involved in tolerance to CHX. We identified a putative two-component system (2CS), composed of a putative sensor histidine kinase (ChtS) and a cognate DNA-binding response regulator (ChtR), which contributed to CHX tolerance in E. faecium Targeted chtR and chtS deletion mutants exhibited compromised growth in the presence of CHX. Growth of the chtR and chtS mutants was also affected in the presence of the antibiotic bacitracin. The CHX- and bacitracin-tolerant phenotype of E. faecium E1162 was linked to a unique, nonsynonymous single nucleotide polymorphism in chtR Transmission electron microscopy showed that upon challenge with CHX, the ΔchtR and ΔchtS mutants failed to divide properly and formed long chains. Normal growth and cell morphology were restored when the mutations were complemented in trans Morphological abnormalities were also observed upon exposure of the ΔchtR and ΔchtS mutants to bacitracin. The tolerance to both chlorhexidine and bacitracin provided by ChtRS in E. faecium highlights the overlap between responses to disinfectants and antibiotics and the potential for the development of cross-tolerance for these classes of antimicrobials.
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26
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Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier. J Microbiol 2017; 55:464-474. [PMID: 28281198 DOI: 10.1007/s12275-017-6599-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/13/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
The two-component phosphorelay system is the most prevalent mechanism for sensing and transducing environmental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the long-term survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key response regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regulatory N-terminal phospho-receiver domain and a DNA-binding C-terminal activator domain. We solved the three-dimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearothermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the mechanism of phosphorylation-dependent activation unique to Spo0A.
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Foster CA, West AH. Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins 2016; 85:155-176. [PMID: 27802580 PMCID: PMC5242315 DOI: 10.1002/prot.25207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
Abstract
Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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The Response Regulator BfmR Is a Potential Drug Target for Acinetobacter baumannii. mSphere 2016; 1:mSphere00082-16. [PMID: 27303741 PMCID: PMC4888885 DOI: 10.1128/msphere.00082-16] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/12/2016] [Indexed: 11/24/2022] Open
Abstract
Increasing antibiotic resistance in bacteria, particularly Gram-negative bacilli, has significantly affected the ability of physicians to treat infections, with resultant increased morbidity, mortality, and health care costs. In fact, some strains of bacteria are resistant to all available antibiotics, such as Acinetobacter baumannii, which is the focus of this report. Therefore, the development of new antibiotics active against these resistant strains is urgently needed. In this study, BfmR is further validated as an intriguing target for a novel class of antibiotics. Successful inactivation of BfmR would confer the multiple benefits of a decreased ability of A. baumannii to survive in human body fluids, increased sensitivity to complement-mediated bactericidal activity and, importantly, increased sensitivity to other antibiotics. Structural studies support the potential for this “druggable” target, as they identify the potential for small-molecule binding at functionally relevant sites. Next-phase high-throughput screening studies utilizing BfmR are warranted. Identification and validation is the first phase of target-based antimicrobial development. BfmR (RstA), a response regulator in a two-component signal transduction system (TCS) in Acinetobacter baumannii, is an intriguing potential antimicrobial target. A unique characteristic of BfmR is that its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Studies on the clinically relevant strain AB307-0294 have shown BfmR to be essential in vivo. Here, we demonstrate that this phenotype in strains AB307-0294 and AB908 is mediated, in part, by enabling growth in human ascites fluid and serum. Further, BfmR conferred resistance to complement-mediated bactericidal activity that was independent of capsular polysaccharide. Importantly, BfmR also increased resistance to the clinically important antimicrobials meropenem and colistin. BfmR was highly conserved among A. baumannii strains. The crystal structure of the receiver domain of BfmR was determined, lending insight into putative ligand binding sites. This enabled an in silico ligand binding analysis and a blind docking strategy to assess use as a potential druggable target. Predicted binding hot spots exist at the homodimer interface and the phosphorylation site. These data support pursuing the next step in the development process, which includes determining the degree of inhibition needed to impact growth/survival and the development a BfmR activity assay amenable to high-throughput screening for the identification of inhibitors. Such agents would represent a new class of antimicrobials active against A. baumannii which could be active against other Gram-negative bacilli that possess a TCS with shared homology. IMPORTANCE Increasing antibiotic resistance in bacteria, particularly Gram-negative bacilli, has significantly affected the ability of physicians to treat infections, with resultant increased morbidity, mortality, and health care costs. In fact, some strains of bacteria are resistant to all available antibiotics, such as Acinetobacter baumannii, which is the focus of this report. Therefore, the development of new antibiotics active against these resistant strains is urgently needed. In this study, BfmR is further validated as an intriguing target for a novel class of antibiotics. Successful inactivation of BfmR would confer the multiple benefits of a decreased ability of A. baumannii to survive in human body fluids, increased sensitivity to complement-mediated bactericidal activity and, importantly, increased sensitivity to other antibiotics. Structural studies support the potential for this “druggable” target, as they identify the potential for small-molecule binding at functionally relevant sites. Next-phase high-throughput screening studies utilizing BfmR are warranted.
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He X, Wang L, Wang S. Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis. Sci Rep 2016; 6:24442. [PMID: 27079268 PMCID: PMC4832192 DOI: 10.1038/srep24442] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/30/2016] [Indexed: 01/20/2023] Open
Abstract
The transcriptional regulator PhoP is an essential virulence factor in Mycobacterium tuberculosis, and it presents a target for the development of new anti-tuberculosis drugs and attenuated tuberculosis vaccine strains. PhoP binds to DNA as a highly cooperative dimer by recognizing direct repeats of 7-bp motifs with a 4-bp spacer. To elucidate the PhoP-DNA binding mechanism, we determined the crystal structure of the PhoP-DNA complex. The structure revealed a tandem PhoP dimer that bound to the direct repeat. The surprising tandem arrangement of the receiver domains allowed the four domains of the PhoP dimer to form a compact structure, accounting for the strict requirement of a 4-bp spacer and the highly cooperative binding of the dimer. The PhoP-DNA interactions exclusively involved the effector domain. The sequence-recognition helix made contact with the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent minor groove. The structure provides a starting point for the elucidation of the mechanism by which PhoP regulates the virulence of M. tuberculosis and guides the design of screening platforms for PhoP inhibitors.
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Affiliation(s)
- Xiaoyuan He
- Department of Biochemistry &Molecular Biology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, USA
| | - Liqin Wang
- Department of Biochemistry &Molecular Biology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, USA
| | - Shuishu Wang
- Department of Biochemistry &Molecular Biology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, USA
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30
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Park AK, Lee JH, Chi YM, Park H. Structural characterization of the full-length response regulator spr1814 in complex with a phosphate analogue reveals a novel conformational plasticity of the linker region. Biochem Biophys Res Commun 2016; 473:625-9. [PMID: 27038544 DOI: 10.1016/j.bbrc.2016.03.144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/29/2016] [Indexed: 01/04/2023]
Abstract
Spr1814 of Streptococcus pneumoniae is a response regulator (RR) that belongs to the NarL/FixJ subfamily and has a four-helix helix-turn-helix DNA-binding domain. Here, the X-ray crystal structure of the full-length spr1814 in complex with a phosphate analogue beryllium fluoride (BeF3(-)) was determined at 2.0 Å. This allows for a structural comparison with the previously reported full-length unphosphorylated spr1814. The phosphorylation of conserved aspartic acid residue of N-terminal receiver domain triggers a structural perturbation at the α4-β5-α5 interface, leading to the domain reorganization of spr1814, and this is achieved by a rotational change in the C-terminal DNA-binding domain.
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Affiliation(s)
- Ae Kyung Park
- Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, South Korea; Division of Polar Life Sciences, Korea Polar Research Institute, Yeonsu-gu, Incheon 406-840, South Korea
| | - Jeong Hye Lee
- Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, South Korea.
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Yeonsu-gu, Incheon 406-840, South Korea.
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31
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Khosa S, Hoeppner A, Gohlke H, Schmitt L, Smits SHJ. Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance. PLoS One 2016; 11:e0149903. [PMID: 26930060 PMCID: PMC4773095 DOI: 10.1371/journal.pone.0149903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/05/2016] [Indexed: 01/22/2023] Open
Abstract
Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria. Interestingly, several clinically relevant and human pathogenic strains are inherently resistant towards lantibiotics. The expression of the genes responsible for lantibiotic resistance is regulated by a specific two-component system consisting of a histidine kinase and a response regulator. Here, we focused on a response regulator involved in lantibiotic resistance, NsrR from Streptococcus agalactiae, and determined the crystal structures of its N-terminal receiver domain and C-terminal DNA-binding effector domain. The C-terminal domain exhibits a fold that classifies NsrR as a member of the OmpR/PhoB subfamily of regulators. Amino acids involved in phosphorylation, dimerization, and DNA-binding were identified and demonstrated to be conserved in lantibiotic resistance regulators. Finally, a model of the full-length NsrR in the active and inactive state provides insights into protein dimerization and DNA-binding.
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Affiliation(s)
- Sakshi Khosa
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
- * E-mail:
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Abstract
Two-component regulatory systems (2CRSs) are widely used by bacteria to sense and respond to environmental stimuli with coordinated changes in gene expression. Systems are normally comprised of a sensory kinase protein that activates a transcriptional regulator by phosphorylation. Mycobacteria have few 2CRSs, but they are of key importance for bacterial survival and play important roles in pathogenicity. Mycobacterium tuberculosis has 12 paired two-component regulatory systems (which include a system with two regulators and one sensor, and a split sensor system), as well as four orphan regulators. Several systems are involved in virulence, and disruption of different systems leads to attenuation or hypervirulence. PhoPR plays a major role in regulating cell wall composition, and its inactivation results in sufficient attenuation of M. tuberculosis that deletion strains are live vaccine candidates. MprAB controls the stress response and is required for persistent infections. SenX3-RegX3 is required for control of aerobic respiration and phosphate uptake, and PrrAB is required for adaptation to intracellular infection. MtrAB is an essential system that controls DNA replication and cell division. The remaining systems (KdpDE, NarL, TrcRS, TcrXY, TcrA, PdtaRS, and four orphan regulators) are less well understood. The structure and binding motifs for several regulators have been characterized, revealing variations in function and operation. The sensors are less well characterized, and stimuli for many remain to be confirmed. This chapter reviews our current understanding of the role of two-component systems in mycobacteria, in particular M. tuberculosis.
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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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34
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Ahmad A, Cai Y, Chen X, Shuai J, Han A. Conformational Dynamics of Response Regulator RegX3 from Mycobacterium tuberculosis. PLoS One 2015. [PMID: 26201027 PMCID: PMC4511772 DOI: 10.1371/journal.pone.0133389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Two-component signal transduction systems (TCS) are vital for adaptive responses to various environmental stresses in bacteria, fungi and even plants. A TCS typically comprises of a sensor histidine kinase (SK) with its cognate response regulator (RR), which often has two domains—N terminal receiver domain (RD) and C terminal effector domain (ED). The histidine kinase phosphorylates the RD to activate the ED by promoting dimerization. However, despite significant progress on structural studies, how RR transmits activation signal from RD to ED remains elusive. Here we analyzed active to inactive transition process of OmpR/PhoB family using an active conformation of RegX3 from Mycobacterium tuberculosis as a model system by computational approaches. An inactive state of RegX3 generated from 150 ns molecular dynamic simulation has rotameric conformations of Thr79 and Tyr98 that are generally conserved in inactive RRs. Arg81 in loop β4α4 acts synergistically with loop β1α1 to change its interaction partners during active to inactive transition, potentially leading to the N-terminal movement of RegX3 helix α1. Global conformational dynamics of RegX3 is mainly dependent on α4β5 region, in particular seven ‘hot-spot’ residues (Tyr98 to Ser104), adjacent to which several coevolved residues at dimeric interface, including Ile76-Asp96, Asp97-Arg111 and Glu24-Arg113 pairs, are critical for signal transduction. Taken together, our computational analyses suggest a molecular linkage between Asp phosphorylation, proximal loops and α4β5α5 dimeric interface during RR active to inactive state transition, which is not often evidently defined from static crystal structures.
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Affiliation(s)
- Ashfaq Ahmad
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Xingqiang Chen
- Department of Physics, Xiamen University, Siming, Xiamen, China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Siming, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
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Maule AF, Wright DP, Weiner JJ, Han L, Peterson FC, Volkman BF, Silvaggi NR, Ulijasz AT. The aspartate-less receiver (ALR) domains: distribution, structure and function. PLoS Pathog 2015; 11:e1004795. [PMID: 25875291 PMCID: PMC4395418 DOI: 10.1371/journal.ppat.1004795] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 03/09/2015] [Indexed: 01/07/2023] Open
Abstract
Two-component signaling systems are ubiquitous in bacteria, Archaea and plants and play important roles in sensing and responding to environmental stimuli. To propagate a signaling response the typical system employs a sensory histidine kinase that phosphorylates a Receiver (REC) domain on a conserved aspartate (Asp) residue. Although it is known that some REC domains are missing this Asp residue, it remains unclear as to how many of these divergent REC domains exist, what their functional roles are and how they are regulated in the absence of the conserved Asp. Here we have compiled all deposited REC domains missing their phosphorylatable Asp residue, renamed here as the Aspartate-Less Receiver (ALR) domains. Our data show that ALRs are surprisingly common and are enriched for when attached to more rare effector outputs. Analysis of our informatics and the available ALR atomic structures, combined with structural, biochemical and genetic data of the ALR archetype RitR from Streptococcus pneumoniae presented here suggest that ALRs have reorganized their active pockets to instead take on a constitutive regulatory role or accommodate input signals other than Asp phosphorylation, while largely retaining the canonical post-phosphorylation mechanisms and dimeric interface. This work defines ALRs as an atypical REC subclass and provides insights into shared mechanisms of activation between ALR and REC domains.
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Affiliation(s)
- Andrew F. Maule
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - David P. Wright
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
| | - Joshua J. Weiner
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Lanlan Han
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
- * E-mail: (ATU); (NRS)
| | - Andrew T. Ulijasz
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
- * E-mail: (ATU); (NRS)
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36
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Kadowaki T, Nishiyama Y, Hisabori T, Hihara Y. Identification of OmpR-family response regulators interacting with thioredoxin in the Cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2015; 10:e0119107. [PMID: 25774906 PMCID: PMC4361706 DOI: 10.1371/journal.pone.0119107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/28/2015] [Indexed: 12/23/2022] Open
Abstract
The redox state of the photosynthetic electron transport chain is known to act as a signal to regulate the transcription of key genes involved in the acclimation responses to environmental changes. We hypothesized that the protein thioredoxin (Trx) acts as a mediator connecting the redox state of the photosynthetic electron transport chain and transcriptional regulation, and established a screening system to identify transcription factors (TFs) that interact with Trx. His-tagged TFs and S-tagged mutated form of Trx, TrxMC35S, whose active site cysteine 35 was substituted with serine to trap the target interacting protein, were co-expressed in E. coli cells and Trx-TF complexes were detected by immuno-blotting analysis. We examined the interaction between Trx and ten OmpR family TFs encoded in the chromosome of the cyanobacterium Synechocystis sp. PCC 6803 (S.6803). Although there is a highly conserved cysteine residue in the receiver domain of all OmpR family TFs, only three, RpaA (Slr0115), RpaB (Slr0946) and ManR (Slr1837), were identified as putative Trx targets. The recombinant forms of wild-type TrxM, RpaA, RpaB and ManR proteins from S.6803 were purified following over-expression in E. coli and their interaction was further assessed by monitoring changes in the number of cysteine residues with free thiol groups. An increase in the number of free thiols was observed after incubation of the oxidized TFs with Trx, indicating the reduction of cysteine residues as a consequence of interaction with Trx. Our results suggest, for the first time, the possible regulation of OmpR family TFs through the supply of reducing equivalents from Trx, as well as through the phospho-transfer from its cognate sensor histidine kinase.
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Affiliation(s)
- Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yoshitaka Nishiyama
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
- CREST, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- CREST, Japan Science and Technology Agency (JST), Saitama, Japan
- * E-mail:
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Zhang Y, Luo F, Hikichi Y, Kiba A, Yasuo I, Ohnishi K. The C-terminal extension of PrhG impairs its activation of hrp expression and virulence in Ralstonia solanacearum. FEMS Microbiol Lett 2015; 362:fnv026. [PMID: 25714547 DOI: 10.1093/femsle/fnv026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ralstonia solanacearum is the second most destructive bacterial plant pathogens worldwide and HrpG is the master regulator of its pathogenicity. PrhG is a close paralogue of HrpG and both belong to OmpR/PhoB family of two-component response regulators. Despite a high similarity (72% global identity and 96% similarity in helix-loop-helix domain), they display distinct roles in pathogenicity. HrpG is necessary for the bacterial growth in planta and pathogenicity, while PrhG is dispensable for bacterial growth in planta and contributes little to pathogenicity. The main difference between HrpG and PrhG is the 50-amino-acid-long C-terminal extension in PrhG (amino-acid residues 230-283), which is absent in HrpG. When this extension is deleted, truncated PrhGs (under the control of its native promoter) allowed complete recovery of bacterial growth in planta and wild-type virulence of hrpG mutant. This novel finding demonstrates that the extension region in PrhG is responsible for the functional difference between HrpG and PrhG, which may block the binding of PrhG to target promoters and result in impaired activation of hrp expression by PrhG and reduced virulence of R. solanacearum.
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Affiliation(s)
- Yong Zhang
- Research Center of Bioenergy and Bioremediation, Southwest University, BeiBei District, Chongqing 400715, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, Southwest University, BeiBei District, Chongqing 400715, China
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and Biotechnology, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Akinori Kiba
- Laboratory of Plant Pathology and Biotechnology, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Igarashi Yasuo
- Research Center of Bioenergy and Bioremediation, Southwest University, BeiBei District, Chongqing 400715, China
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan
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He X, Wang S. DNA consensus sequence motif for binding response regulator PhoP, a virulence regulator of Mycobacterium tuberculosis. Biochemistry 2014; 53:8008-20. [PMID: 25434965 PMCID: PMC4283936 DOI: 10.1021/bi501019u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Tuberculosis has reemerged as a serious
threat to human health
because of the increasing prevalence of drug-resistant strains and
synergetic infection with HIV, prompting an urgent need for new and
more efficient treatments. The PhoP–PhoR two-component system
of Mycobacterium tuberculosis plays an important
role in the virulence of the pathogen and thus represents a potential
drug target. To study the mechanism of gene transcription regulation
by response regulator PhoP, we identified a high-affinity DNA sequence
for PhoP binding using systematic evolution of ligands by exponential
enrichment. The sequence contains a direct repeat of two 7 bp motifs
separated by a 4 bp spacer, TCACAGC(N4)TCACAGC. The specificity
of the direct-repeat sequence for PhoP binding was confirmed by isothermal
titration calorimetry and electrophoretic mobility shift assays. PhoP
binds to the direct repeat as a dimer in a highly cooperative manner.
We found many genes previously identified to be regulated by PhoP
that contain the direct-repeat motif in their promoter sequences.
Synthetic DNA fragments at the putative promoter-binding sites bind
PhoP with variable affinity, which is related to the number of mismatches
in the 7 bp motifs, the positions of the mismatches, and the spacer
and flanking sequences. Phosphorylation of PhoP increases the affinity
but does not change the specificity of DNA binding. Overall, our results
confirm the direct-repeat sequence as the consensus motif for PhoP
binding and thus pave the way for identification of PhoP directly
regulated genes in different mycobacterial genomes.
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Affiliation(s)
- Xiaoyuan He
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
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39
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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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40
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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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41
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Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool DA. An asymmetric heterodomain interface stabilizes a response regulator-DNA complex. Nat Commun 2014; 5:3282. [PMID: 24526190 PMCID: PMC4399498 DOI: 10.1038/ncomms4282] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 01/18/2014] [Indexed: 01/08/2023] Open
Abstract
Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter DNA via a phosphorylation-triggered inactive-to-active transition. The molecular basis for formation of stable response regulator-DNA complexes that precede the assembly of RNA polymerases is unclear. Here, we present structures of DNA complexed with the response regulator KdpE, a member of the OmpR/PhoB family. The distinctively asymmetric complex in an active-like conformation reveals a unique intramolecular interface between the receiver domain (RD) and the DNA-binding domain (DBD) of only one of the two response regulators in the complex. Structure-function studies show that this RD-DBD interface is necessary to form stable complexes that support gene expression. The conservation of sequence and structure suggests that these findings extend to a large group of response regulators that act as transcription factors.
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Affiliation(s)
- Anoop Narayanan
- 1] Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA [2]
| | - Shivesh Kumar
- 1] Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA [2] [3]
| | - Amanda N Evrard
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA
| | - Lake N Paul
- Bindley Bioscience Center, Purdue University, 1203 West State Street, West Lafayette, Indiana 47907, USA
| | - Dinesh A Yernool
- 1] Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA [2] Bindley Bioscience Center, Purdue University, 1203 West State Street, West Lafayette, Indiana 47907, USA
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42
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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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43
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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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Micevski D, Dougan DA. Proteolytic regulation of stress response pathways in Escherichia coli. Subcell Biochem 2013; 66:105-28. [PMID: 23479439 DOI: 10.1007/978-94-007-5940-4_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. Indeed proteases play a crucial role in the clearance of unwanted proteins that accumulate during stress, but more importantly, in the activation of various different stress response pathways. In bacteria, the cells response to stress is usually orchestrated by a specific transcription factor (sigma factor). In Escherichia coli there are seven different sigma factors, each of which responds to a particular stress, resulting in the rapid expression of a specific set of genes. The cellular concentration of each transcription factor is tightly controlled, at the level of transcription, translation and protein stability. Here we will focus on the proteolytic regulation of two sigma factors (σ(32) and σ(S)), which control the heat and general stress response pathways, respectively. This review will also briefly discuss the role proteolytic systems play in the clearance of unwanted proteins that accumulate during stress.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, 3086, Australia
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45
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Szurmant H, Hoch JA. Statistical analyses of protein sequence alignments identify structures and mechanisms in signal activation of sensor histidine kinases. Mol Microbiol 2012; 87:707-12. [PMID: 23279101 DOI: 10.1111/mmi.12128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2012] [Indexed: 01/31/2023]
Abstract
Statistical analyses of genome sequence-derived protein sequence data can identify amino acid residues that interact between proteins or between domains of a protein. These statistical methods are based on evolution-directed amino acid variation responding to structural and functional constraints in proteins. The identified residues form a basis for determining structure and folding of proteins as well as inferring mechanisms of protein function. When applied to two-component systems, several research groups have shown they can be used to identify the amino acid interactions between response regulators and histidine kinases and the specificity therein. Recently, statistical studies between the HisKA and HATPase-ATP-binding domains of histidine kinases identified amino acid interactions for both the inactive and the active catalytic states of such kinases. The identified interactions generated a model structure for the domain conformation of the active state. This conformation requires an unwinding of a portion of the C-terminal helix of the HisKA domain that destroys the inactive state residue contacts and suggests how signal-binding determines the equilibrium between the inactive and active states of histidine kinases. The rapidly accumulating protein sequence databases from genome, metagenome and microbiome studies are an important resource for functional and structural understanding of proteins and protein complexes in microbes.
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Affiliation(s)
- Hendrik Szurmant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
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Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems. Proc Natl Acad Sci U S A 2012; 110:E161-9. [PMID: 23256153 DOI: 10.1073/pnas.1212102110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cellular processes require specific interactions between cognate protein partners and concomitant discrimination against noncognate partners. Signal transduction by classical two-component regulatory systems typically entails an intermolecular phosphoryl transfer between a sensor kinase (SK) and a cognate response regulator (RR). Interactions between noncognate partners are rare because SK/RR pairs coevolve unique interfaces that dictate phosphotransfer specificity. Here we report that the in vitro phosphotransfer specificity is relaxed in hybrid two-component systems (HTCSs) from the human gut symbiont Bacteroides thetaiotaomicron, which harbor both the SK and RR in a single polypeptide. In contrast, phosphotransfer specificity is retained in classical two-component regulatory systems from this organism. This relaxed specificity enabled us to rewire a HTCS successfully to transduce signals between noncognate SK/RR pairs. Despite the relaxed specificity between SK and RRs, HTCSs remained insulated from cross-talk with noncognate proteins in vivo. Our data suggest that the high local concentration of the SK and RR present in the same polypeptide maintains specificity while relaxing the constraints on coevolving unique contact interfaces.
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Veerabagu M, Elgass K, Kirchler T, Huppenberger P, Harter K, Chaban C, Mira-Rodado V. The Arabidopsis B-type response regulator 18 homomerizes and positively regulates cytokinin responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:721-31. [PMID: 22775331 DOI: 10.1111/j.1365-313x.2012.05101.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In higher plants, the two-component system (TCS) is a signaling mechanism based on a His-to-Asp phosphorelay. The Arabidopsis TCS involves three different types of proteins, namely the histidine kinases (AHKs), the histidine phosphotransfer proteins (AHPs) and the response regulators (ARRs). The ARRs comprise three different families, namely A, B and C types, according to their protein structure. While some members of the B-type family of ARRs have been studied extensively and reported to act as DNA-binding transcriptional regulators, very limited information is available for other B-type ARRs such as ARR18. In this study, we characterize in detail the molecular and functional properties of ARR18. ARR18 acts as a transcriptional regulator in plant cells and forms homodimers in planta as shown by FRET-FLIM studies. As demonstrated by mutational analysis, the aspartate at position 70 (D70) in the receiver domain of ARR18 acts as crucial phosphorylation site. The modification of D70 affects the response regulator's ability to homodimerize and to activate its target genes. Furthermore, physiological investigations of Arabidopsis lines ectopically expressing ARR18 introduce ARR18 as a new member within the cytokinin-regulated response pathway regulating root elongation.
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Affiliation(s)
- Manikandan Veerabagu
- Center for Plant Molecular Biology-ZMBP, Department of Plant Physiology, University of Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany
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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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Abstract
To exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.
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Affiliation(s)
- Emily J Capra
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
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50
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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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