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Lobertti CA, Cabezudo I, Gizzi FO, Blancato V, Magni C, Furlán RLE, García Véscovi E. An allosteric inhibitor of the PhoQ histidine kinase with therapeutic potential against Salmonella infection. J Antimicrob Chemother 2024:dkae151. [PMID: 38853496 DOI: 10.1093/jac/dkae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/30/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND The upsurge of antimicrobial resistance demands innovative strategies to fight bacterial infections. With traditional antibiotics becoming less effective, anti-virulence agents or pathoblockers, arise as an alternative approach that seeks to disarm pathogens without affecting their viability, thereby reducing selective pressure for the emergence of resistance mechanisms. OBJECTIVES To elucidate the mechanism of action of compound N'-(thiophen-2-ylmethylene)benzohydrazide (A16B1), a potent synthetic hydrazone inhibitor against the Salmonella PhoP/PhoQ system, essential for virulence. MATERIALS AND METHODS The measurement of the activity of PhoP/PhoQ-dependent and -independent reporter genes was used to evaluate the specificity of A16B1 to the PhoP regulon. Autokinase activity assays with either the native or truncated versions of PhoQ were used to dissect the A16B1 mechanism of action. The effect of A16B1 on Salmonella intramacrophage replication was assessed using the gentamicin protection assay. The checkerboard assay approach was used to analyse potentiation effects of colistin with the hydrazone. The Galleria mellonella infection model was chosen to evaluate A16B1 as an in vivo therapy against Salmonella. RESULTS A16B1 repressed the Salmonella PhoP/PhoQ system activity, specifically targeting PhoQ within the second transmembrane region. A16B1 demonstrates synergy with the antimicrobial peptide colistin, reduces the intramacrophage proliferation of Salmonella without being cytotoxic and enhances the survival of G. mellonella larvae systemically infected with Salmonella. CONCLUSIONS A16B1 selectively inhibits the activity of the Salmonella PhoP/PhoQ system through a novel inhibitory mechanism, representing a promising synthetic hydrazone compound with the potential to function as a Salmonella pathoblocker. This offers innovative prospects for combating Salmonella infections while mitigating the risk of antimicrobial resistance emergence.
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Affiliation(s)
- Carlos A Lobertti
- Instituto de Biología Molecular y Celular de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Bioquímicas y Farmacéuticas, Departamento de Microbiología, Universidad Nacional de Rosario, Rosario S2000EZP, Argentina
| | - Ignacio Cabezudo
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario 2000, Argentina
| | - Fernán O Gizzi
- Instituto de Biología Molecular y Celular de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Bioquímicas y Farmacéuticas, Departamento de Microbiología, Universidad Nacional de Rosario, Rosario S2000EZP, Argentina
| | - Víctor Blancato
- Instituto de Biología Molecular y Celular de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Bioquímicas y Farmacéuticas, Departamento de Microbiología, Universidad Nacional de Rosario, Rosario S2000EZP, Argentina
| | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Bioquímicas y Farmacéuticas, Departamento de Microbiología, Universidad Nacional de Rosario, Rosario S2000EZP, Argentina
| | - Ricardo L E Furlán
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario 2000, Argentina
| | - Eleonora García Véscovi
- Instituto de Biología Molecular y Celular de Rosario Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Bioquímicas y Farmacéuticas, Departamento de Microbiología, Universidad Nacional de Rosario, Rosario S2000EZP, Argentina
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2
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Li M, Tang H, Qing R, Wang Y, Liu J, Wang R, Lyu S, Ma L, Xu P, Zhang S, Tao F. Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code. Nat Commun 2024; 15:4293. [PMID: 38858360 PMCID: PMC11164701 DOI: 10.1038/s41467-024-48513-9] [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: 08/11/2023] [Accepted: 05/03/2024] [Indexed: 06/12/2024] Open
Abstract
Membrane proteins are critical to biological processes and central to life sciences and modern medicine. However, membrane proteins are notoriously challenging to study, mainly owing to difficulties dictated by their highly hydrophobic nature. Previously, we reported QTY code, which is a simple method for designing water-soluble membrane proteins. Here, we apply QTY code to a transmembrane receptor, histidine kinase CpxA, to render it completely water-soluble. The designed CpxAQTY exhibits expected biophysical properties and highly preserved native molecular function, including the activities of (i) autokinase, (ii) phosphotransferase, (iii) phosphatase, and (iv) signaling receptor, involving a water-solubilized transmembrane domain. We probe the principles underlying the balance of structural stability and activity in the water-solubilized transmembrane domain. Computational approaches suggest that an extensive and dynamic hydrogen-bond network introduced by QTY code and its flexibility may play an important role. Our successful functional preservation further substantiates the robustness and comprehensiveness of QTY code.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanze Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jiongqin Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rui Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Lyu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lina Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Lu J, Han M, Yu HH, Bergen PJ, Liu Y, Zhao J, Wickremasinghe H, Jiang X, Hu Y, Du H, Zhu Y, Velkov T. Lipid A Modification and Metabolic Adaptation in Polymyxin-Resistant, New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0085223. [PMID: 37432123 PMCID: PMC10433984 DOI: 10.1128/spectrum.00852-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 07/12/2023] Open
Abstract
Polymyxins are last-line antibiotics employed against multidrug-resistant (MDR) Klebsiella pneumoniae. Worryingly, polymyxin resistance is rapidly on the rise globally. Polymyxins initially target lipid A of lipopolysaccharides (LPSs) in the cell outer membrane (OM), causing disorganization and cell lysis. While most studies focus on how genetic variations confer polymyxin resistance, the mechanisms of membrane remodeling and metabolic changes in polymyxin-resistant strains remain unclear, thus hampering the development of effective therapies to treat severe K. pneumoniae infections. In the present study, lipid A profiling, OM lipidomics, genomics, and metabolomics were integrated to elucidate the global mechanisms of polymyxin resistance and metabolic adaptation in a polymyxin-resistant strain (strain S01R; MIC of >128 mg/L) obtained from K. pneumoniae strain S01, a polymyxin-susceptible (MIC of 2 mg/L), New Delhi metallo-β-lactamase (NDM)-producing MDR clinical isolate. Genomic analysis revealed a novel in-frame deletion at position V258 of PhoQ in S01R, potentially leading to lipid A modification with 4-amino-4-deoxy-l-arabinose (L-Ara4N) despite the absence of polymyxin B. Comparative metabolomic analysis revealed slightly elevated levels of energy production and amino acid metabolism in S01R compared to their levels in S01. Exposure to polymyxin B (4 mg/L for S01 and 512 mg/L for S01R) substantially altered energy, nucleotide, and amino acid metabolism and resulted in greater accumulation of lipids in both strains. Furthermore, the change induced by polymyxin B treatment was dramatic at both 1 and 4 h in S01 but only significant at 4 h in S01R. Overall, profound metabolic adaptation was observed in S01R following polymyxin B treatment. These findings contribute to our understanding of polymyxin resistance mechanisms in problematic NDM-producing K. pneumoniae strains and may facilitate the discovery of novel therapeutic targets. IMPORTANCE Antimicrobial resistance (AMR) is a major threat to global health. The emergence of resistance to the polymyxins that are the last line of defense in so-called Gram-negative "superbugs" has further increased the urgency to develop novel therapies. There are frequent outbreaks of K. pneumoniae infections in hospitals being reported, and polymyxin usage is increasing remarkably. Importantly, the polymyxin-resistant K. pneumoniae strains are imposing more severe consequences to health systems. Using metabolomics, lipid A profiling, and outer membrane lipidomics, our findings reveal (i) changes in the pentose phosphate pathway and amino acid and nucleotide metabolism in a susceptible strain following polymyxin treatment and (ii) how cellular metabolism, lipid A modification, and outer membrane remodeling were altered in K. pneumoniae following the acquisition of polymyxin resistance. Our study provides, for the first time, mechanistic insights into metabolic responses to polymyxin treatment in a multidrug-resistant, NDM-producing K. pneumoniae clinical isolate with acquired polymyxin resistance. Overall, these results will assist in identifying new therapeutic targets to combat and prevent polymyxin resistance.
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Affiliation(s)
- Jing Lu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Meiling Han
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Heidi H. Yu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Phillip J. Bergen
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yiyun Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jinxin Zhao
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Hasini Wickremasinghe
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Xukai Jiang
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yang Hu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Haiyan Du
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yan Zhu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tony Velkov
- Department of Pharmacology, The Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
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4
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Peng J, Xu Z, Li L, Zhao B, Guo Y. Disruption of the sensor kinase phoQ gene decreases acid resistance in plant growth-promoting rhizobacterium Rahnella aquatilis HX2. J Appl Microbiol 2023; 134:6991427. [PMID: 36748653 DOI: 10.1093/jambio/lxad009] [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: 10/26/2022] [Revised: 12/24/2022] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
AIMS Rahnella aquatilis HX2, a promising plant growth-promoting rhizobacterium (PGPR) in the field, contains genes homologous to the PhoP/PhoQ two-component regulatory system. Although this system regulates stress response in numerous pathogens, PhoP/PhoQ characterization in a PGPR has not received in-depth exploration. METHODS AND RESULTS The phoQ gene was mutated in strain HX2 using an in-frame deletion strategy. Compared to the wild type, the phoQ mutant exhibited increased sensitivity to acidic conditions (pH 4.0) in a chemically defined medium and in mild acidic natural soil (pH 5.7). The phoQ mutant also exhibited increased swimming motility under acidic conditions. Acid resistance was restored in the mutant by introducing the phoQ gene on a plasmid. Three acid resistance genes, add, cfa, and fur were downregulated significantly, whereas the chaperone encoding gene, dnak, was upregulated when the phoQ mutant was exposed to acid stress. CONCLUSIONS This study suggested that the PhoP/PhoQ system positively regulates the acid resistance of R. aquatilis HX2.
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Affiliation(s)
- Jing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Zhongnan Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Lei Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Bingjie Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
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5
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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6
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Ma P, Phillips-Jones MK. Membrane Sensor Histidine Kinases: Insights from Structural, Ligand and Inhibitor Studies of Full-Length Proteins and Signalling Domains for Antibiotic Discovery. Molecules 2021; 26:molecules26165110. [PMID: 34443697 PMCID: PMC8399564 DOI: 10.3390/molecules26165110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 12/19/2022] Open
Abstract
There is an urgent need to find new antibacterial agents to combat bacterial infections, including agents that inhibit novel, hitherto unexploited targets in bacterial cells. Amongst novel targets are two-component signal transduction systems (TCSs) which are the main mechanism by which bacteria sense and respond to environmental changes. TCSs typically comprise a membrane-embedded sensory protein (the sensor histidine kinase, SHK) and a partner response regulator protein. Amongst promising targets within SHKs are those involved in environmental signal detection (useful for targeting specific SHKs) and the common themes of signal transmission across the membrane and propagation to catalytic domains (for targeting multiple SHKs). However, the nature of environmental signals for the vast majority of SHKs is still lacking, and there is a paucity of structural information based on full-length membrane-bound SHKs with and without ligand. Reasons for this lack of knowledge lie in the technical challenges associated with investigations of these relatively hydrophobic membrane proteins and the inherent flexibility of these multidomain proteins that reduces the chances of successful crystallisation for structural determination by X-ray crystallography. However, in recent years there has been an explosion of information published on (a) methodology for producing active forms of full-length detergent-, liposome- and nanodisc-solubilised membrane SHKs and their use in structural studies and identification of signalling ligands and inhibitors; and (b) mechanisms of signal sensing and transduction across the membrane obtained using sensory and transmembrane domains in isolation, which reveal some commonalities as well as unique features. Here we review the most recent advances in these areas and highlight those of potential use in future strategies for antibiotic discovery. This Review is part of a Special Issue entitled “Interactions of Bacterial Molecules with Their Ligands and Other Chemical Agents” edited by Mary K. Phillips-Jones.
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Affiliation(s)
- Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland;
| | - Mary K. Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Correspondence:
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The ChvG-ChvI and NtrY-NtrX Two-Component Systems Coordinately Regulate Growth of Caulobacter crescentus. J Bacteriol 2021; 203:e0019921. [PMID: 34124942 DOI: 10.1128/jb.00199-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Two-component signaling systems (TCSs) are comprised of a sensory histidine kinase and a response regulator protein. In response to environmental changes, sensor kinases directly phosphorylate their cognate response regulator to affect gene expression. Bacteria typically express multiple TCSs that are insulated from one another and regulate distinct physiological processes. There are examples of cross-regulation between TCSs, but this phenomenon remains relatively unexplored. We have identified regulatory links between the ChvG-ChvI (ChvGI) and NtrY-NtrX (NtrYX) TCSs, which control important and often overlapping processes in alphaproteobacteria, including maintenance of the cell envelope. Deletion of chvG and chvI in Caulobacter crescentus limited growth in defined medium, and a selection for genetic suppressors of this growth phenotype uncovered interactions among chvGI, ntrYX, and ntrZ, which encodes a previously uncharacterized periplasmic protein. Significant overlap in the experimentally defined ChvI and NtrX transcriptional regulons provided support for the observed genetic connections between ntrYX and chvGI. Moreover, we present evidence that the growth defect of strains lacking chvGI is influenced by the phosphorylation state of NtrX and, to some extent, by levels of the TonB-dependent receptor ChvT. Measurements of NtrX phosphorylation in vivo indicated that NtrZ is an upstream regulator of NtrY and that NtrY primarily functions as an NtrX phosphatase. We propose a model in which NtrZ functions in the periplasm to inhibit NtrY phosphatase activity; regulation of phosphorylated NtrX levels by NtrZ and NtrY provides a mechanism to modulate and balance expression of the NtrX and ChvI regulons under different growth conditions. IMPORTANCE TCSs enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell envelope function in many alphaproteobacteria. We used Caulobacter crescentus as a model to investigate regulatory connections between ChvGI and NtrYX. Our work defined the ChvI transcriptional regulon in C. crescentus and revealed a genetic interaction between ChvGI and NtrYX, whereby modulation of NtrYX signaling affects the survival of cells lacking ChvGI. In addition, we identified NtrZ as a periplasmic inhibitor of NtrY phosphatase activity in vivo. Our work establishes C. crescentus as an excellent model to investigate multilevel regulatory connections between ChvGI and NtrYX in alphaproteobacteria.
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Interhelical H-Bonds Modulate the Activity of a Polytopic Transmembrane Kinase. Biomolecules 2021; 11:biom11070938. [PMID: 34201916 PMCID: PMC8301901 DOI: 10.3390/biom11070938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DesK is a Histidine Kinase that allows Bacillus subtilis to maintain lipid homeostasis in response to changes in the environment. It is located in the membrane, and has five transmembrane helices and a cytoplasmic catalytic domain. The transmembrane region triggers the phosphorylation of the catalytic domain as soon as the membrane lipids rigidify. In this research, we study how transmembrane inter-helical interactions contribute to signal transmission; we designed a co-expression system that allows studying in vivo interactions between transmembrane helices. By Alanine-replacements, we identified a group of polar uncharged residues, whose side chains contain hydrogen-bond donors or acceptors, which are required for the interaction with other DesK transmembrane helices; a particular array of H-bond- residues plays a key role in signaling, transmitting information detected at the membrane level into the cell to finally trigger an adaptive response.
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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10
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Azam M, Gaind R, Yadav G, Sharma A, Upmanyu K, Jain M, Singh R. Colistin Resistance Among Multiple Sequence Types of Klebsiella pneumoniae Is Associated With Diverse Resistance Mechanisms: A Report From India. Front Microbiol 2021; 12:609840. [PMID: 33692764 PMCID: PMC7937630 DOI: 10.3389/fmicb.2021.609840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Background: The resistance to colistin and carbapenems in Klebsiella pneumoniae infections have been associated with increased morbidity and mortality worldwide. A retrospective observational study was conducted to determine the prevalence and molecular events contributing to colistin resistance. Methods: Clinical samples were screened for colistin resistance and underlying mechanisms were studied by PCR-based amplification and sequence analysis of genes of two-component regulatory system (phoPQ and pmrAB), regulatory transmembrane protein-coding mgrB, and mobilized colistin resistance genes (mcr-1-8). Gene expression of pmrC and pmrK was analyzed by qRT-PCR, and the genetic relationship was assessed by MLST. The putative effect of amino-acid substitutions was predicted by a combination of bioinformatics tools. Results: Of 335 Klebsiella spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). K. pneumoniae isolates belonged to clonal complex-11 (CC11) with sequence types (STs): 14, 16, 43, 54, 147 and 395, whereby four isolates conferred three novel STs (3986, 3987 and 3988) profiles. Sequence analysis revealed non-synonymous potentially deleterious mutations in phoP (T151A), phoQ (del87–90, del263–264, L30Q, and A351D), pmrA (G53S), pmrB (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and mgrB (C28G) genes. The mgrB gene in three strains was disrupted by insertion sequences encoding IS1-like and IS5/IS1182 family-like transposase genes. All 11 isolates showed an elevation in the transcription level of pmrC gene. Mobilized colistin-resistance (mcr) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes blaNDM-1-like, blaOXA-48-like, and blaCTX-M-like were detected in eight, five, and nine isolates, respectively. Conclusion: All the studied colistin- and carbapenem-resistant K. pneumoniae isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.
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Affiliation(s)
- Mudsser Azam
- ICMR-National Institute of Pathology, New Delhi, India
| | - Rajni Gaind
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Gulshan Yadav
- ICMR-National Institute of Pathology, New Delhi, India
| | - Amit Sharma
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Kirti Upmanyu
- ICMR-National Institute of Pathology, New Delhi, India
| | - Manisha Jain
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, New Delhi, India
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11
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Yadavalli SS, Goh T, Carey JN, Malengo G, Vellappan S, Nickels BE, Sourjik V, Goulian M, Yuan J. Functional determinants of a small protein controlling a broadly conserved bacterial sensor kinase. J Bacteriol 2020; 202:JB.00305-20. [PMID: 32482726 PMCID: PMC8404706 DOI: 10.1128/jb.00305-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
The PhoQ/PhoP two-component system plays a vital role in the regulation of Mg2+ homeostasis, resistance to acid and hyperosmotic stress, cationic antimicrobial peptides, and virulence in Escherichia coli, Salmonella and related bacteria. Previous studies have shown that MgrB, a 47 amino acid membrane protein that is part of the PhoQ/PhoP regulon, inhibits the histidine kinase PhoQ. MgrB is part of a negative feedback loop modulating this two-component system that prevents hyperactivation of PhoQ and may also provide an entry point for additional input signals for the PhoQ/PhoP pathway. To explore the mechanism of action of MgrB, we have analyzed the effects of point mutations, C-terminal truncations and transmembrane region swaps on MgrB activity. In contrast with two other known membrane protein regulators of histidine kinases in E. coli, we find that the MgrB TM region is necessary for PhoQ inhibition. Our results indicate that the TM region mediates interactions with PhoQ and that W20 is a key residue for PhoQ/MgrB complex formation. Additionally, mutations of the MgrB cytosolic region suggest that the two N-terminal lysines play an important role in regulating PhoQ activity. Alanine scanning mutagenesis of the periplasmic region of MgrB further indicates that, with the exception of a few highly conserved residues, most residues are not essential for MgrB's function as a PhoQ inhibitor. Our results indicate that the regulatory function of the small protein MgrB depends on distinct contributions from multiple residues spread across the protein. Interestingly, the TM region also appears to interact with other non-cognate histidine kinases in a bacterial two-hybrid assay, suggesting a potential route for evolving new small protein modulators of histidine kinases.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ted Goh
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA
- Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jeffrey N Carey
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Sangeevan Vellappan
- Molecular Biosciences Graduate Program, Rutgers University, Piscataway NJ 08854
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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12
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Kowallis KA, Duvall SW, Zhao W, Childers WS. Manipulation of Bacterial Signaling Using Engineered Histidine Kinases. Methods Mol Biol 2020; 2077:141-163. [PMID: 31707657 DOI: 10.1007/978-1-4939-9884-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two-component systems allow bacteria to respond to changes in environmental or cytosolic conditions through autophosphorylation of a histidine kinase (HK) and subsequent transfer of the phosphate group to its downstream cognate response regulator (RR). The RR then elicits a cellular response, commonly through regulation of transcription. Engineering two-component system signaling networks provides a strategy to study bacterial signaling mechanisms related to bacterial cell survival, symbiosis, and virulence, and to develop sensory devices in synthetic biology. Here we focus on the principles for engineering the HK to identify unknown signal inputs, test signal transmission mechanisms, design small molecule sensors, and rewire two-component signaling networks.
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Affiliation(s)
| | - Samuel W Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zhao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA. .,Chevron Science Center, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Jacob-Dubuisson F, Mechaly A, Betton JM, Antoine R. Structural insights into the signalling mechanisms of two-component systems. Nat Rev Microbiol 2019; 16:585-593. [PMID: 30008469 DOI: 10.1038/s41579-018-0055-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two-component systems reprogramme diverse aspects of microbial physiology in response to environmental cues. Canonical systems are composed of a transmembrane sensor histidine kinase and its cognate response regulator. They catalyse three reactions: autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. Elucidating signal transduction between sensor and output domains is highly challenging given the size, flexibility and dynamics of histidine kinases. However, recent structural work has provided snapshots of the catalytic mechanisms of the three enzymatic reactions and described the conformation and dynamics of the enzymatic moiety in the kinase-competent and phosphatase-competent states. Insight into signalling mechanisms across the membrane is also starting to emerge from new crystal structures encompassing both sensor and transducer domains of sensor histidine kinases. In this Progress article, we highlight such important advances towards understanding at the molecular level the signal transduction mechanisms mediated by these fascinating molecular machines.
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Affiliation(s)
- Françoise Jacob-Dubuisson
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France.
| | - Ariel Mechaly
- Institut Pasteur, Plateforme de Cristallographie, CNRS-UMR3528, Paris, France
| | - Jean-Michel Betton
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Paris, France
| | - Rudy Antoine
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France
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14
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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15
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Yoshitani K, Ishii E, Taniguchi K, Sugimoto H, Shiro Y, Akiyama Y, Kato A, Utsumi R, Eguchi Y. Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control. Biosci Biotechnol Biochem 2019; 83:684-694. [PMID: 30632929 DOI: 10.1080/09168451.2018.1562879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The PhoQ/PhoP two-component signal transduction system is conserved in various Gram-negative bacteria and is often involved in the expression of virulence in pathogens. The small inner membrane protein SafA activates PhoQ in Escherichia coli independently from other known signals that control PhoQ activity. We have previously shown that SafA directly interacts with the sensor domain of the periplasmic region of PhoQ (PhoQ-SD) for activation, and that a D179R mutation in PhoQ-SD attenuates PhoQ activation by SafA. In this study, structural comparison of wild-type PhoQ-SD and D179R revealed a difference in the cavity (SD (sensory domain) pocket) found in the central core of this domain. This was the only structural difference between the two proteins. Site-directed mutagenesis of the residues surrounding the SD pocket has supported the SD pocket as a site involved in PhoQ activity. Furthermore, the SD pocket has also been shown to be involved in SafA-mediated PhoQ control.
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Affiliation(s)
- Kohei Yoshitani
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan.,b Department of Biosystems Science , Institute for Frontier Life and Medical Sciences, Kyoto University , Kyoto , Japan
| | - Eiji Ishii
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan.,b Department of Biosystems Science , Institute for Frontier Life and Medical Sciences, Kyoto University , Kyoto , Japan
| | - Katsuhide Taniguchi
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan
| | - Hiroshi Sugimoto
- c SR Life Science Instrumentation Team , RIKEN SPring-8 Center , Sayo , Japan.,d Graduate School of Life Science , University of Hyogo , Hyogo , Japan
| | - Yoshitsugu Shiro
- d Graduate School of Life Science , University of Hyogo , Hyogo , Japan
| | - Yoshinori Akiyama
- b Department of Biosystems Science , Institute for Frontier Life and Medical Sciences, Kyoto University , Kyoto , Japan
| | - Akinori Kato
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan
| | - Ryutaro Utsumi
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan.,e Department of Biomolecular Science and Reaction , The Institute of Scientific and Industrial Research, Osaka University , Osaka , Japan
| | - Yoko Eguchi
- a Department of Bioscience , Graduate School of Agriculture, Kindai University , Nara , Japan.,f Department of Science and Technology on Food Safety, Faculty of Biology-Oriented Science and Technology , Kindai University , Wakayama , Japan
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16
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Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell 2018; 34:792-806.e5. [PMID: 30449325 PMCID: PMC6248889 DOI: 10.1016/j.ccell.2018.09.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 02/08/2023]
Abstract
Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.
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Affiliation(s)
- Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Tarjani M Thaker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kate Senger
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Noelyn M Kljavin
- Molecular Oncology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037, India
| | - Sameer Phalke
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Prasanna Kumar
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc., Foster City, CA 94404, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ravi Gupta
- Bioinformatics Department, MeGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Arati Khanna-Gupta
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Sally E Trabucco
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ryan J Hartmaier
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ashish Singh
- Department of Medical Oncology, Christian Medical College and Hospital, Vellore 632004, India
| | | | | | - Amit Dutt
- ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Vijay Patil
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | - Amit Joshi
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | | | - James Ziai
- Pathology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Vedam Ramprasad
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA.
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17
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Gushchin I, Gordeliy V. Transmembrane Signal Transduction in Two-Component Systems: Piston, Scissoring, or Helical Rotation? Bioessays 2017; 40. [PMID: 29280502 DOI: 10.1002/bies.201700197] [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: 10/15/2017] [Revised: 11/30/2017] [Indexed: 11/10/2022]
Abstract
Allosteric and transmembrane (TM) signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four-helical TM bundles, focusing on histidine kinases and chemoreceptors found in two-component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system NpSRII:NpHtrII. We show that TM helices can flex at multiple points and argue that the various conformational changes are not mutually exclusive, and often are observed concomitantly, throughout the TM domain or in its part. The piston and scissoring motions are the most prominent motions in the structures, but more research is needed for definitive conclusions.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.,Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany
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18
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Abstract
The PhoQ/PhoP two-component system plays an essential role in the response of enterobacteria to the environment of their mammalian hosts. It is known to sense several stimuli that are potentially associated with the host, including extracellular magnesium limitation, low pH, and the presence of cationic antimicrobial peptides. Here, we show that the PhoQ/PhoP two-component systems of Escherichia coli and Salmonella can also perceive an osmotic upshift, another key stimulus to which bacteria become exposed within the host. In contrast to most previously established stimuli of PhoQ, the detection of osmotic upshift does not require its periplasmic sensor domain. Instead, we show that the activity of PhoQ is affected by the length of the transmembrane (TM) helix as well as by membrane lateral pressure. We therefore propose that osmosensing relies on a conformational change within the TM domain of PhoQ induced by a perturbation in cell membrane thickness and lateral pressure under hyperosmotic conditions. Furthermore, the response mediated by the PhoQ/PhoP two-component system was found to improve bacterial growth recovery under hyperosmotic stress, partly through stabilization of the sigma factor RpoS. Our findings directly link the PhoQ/PhoP two-component system to bacterial osmosensing, suggesting that this system can mediate a concerted response to most of the established host-related cues.
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19
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Abriata LA, Albanesi D, Dal Peraro M, de Mendoza D. Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor. Acc Chem Res 2017; 50:1359-1366. [PMID: 28475313 DOI: 10.1021/acs.accounts.6b00593] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Histidine kinases (HK) are the sensory proteins of two-component systems, responsible for a large fraction of bacterial responses to stimuli and environmental changes. Prototypical HKs are membrane-bound proteins that phosphorylate cognate response regulator proteins in the cytoplasm upon signal detection in the membrane or periplasm. HKs stand as potential drug targets but also constitute fascinating systems for studying proteins at work, specifically regarding the chemistry and mechanics of signal detection, transduction through the membrane, and regulation of catalytic outputs. In this Account, we focus on Bacillus subtilis DesK, a membrane-bound HK part of a two-component system that maintains appropriate membrane fluidity at low growth temperatures. Unlike most HKs, DesK has no extracytoplasmic signal-sensing domains; instead, sensing is carried out by 10 transmembrane helices (coming from two protomers) arranged in an unknown structure. The fifth transmembrane helix from each protomer connects, without any of the intermediate domains found in other HKs, into the dimerization and histidine phosphotransfer (DHp) domain located in the cytoplasm, which is followed by the ATP-binding domains (ABD). Throughout the years, genetic, biochemical, structural, and computational studies on wild-type, mutant, and truncated versions of DesK allowed us to dissect several aspects of DesK's functioning, pushing forward a more general understanding of its own structure/function relationships as well as those of other HKs. We have shown that the sensing mechanism is rooted in temperature-dependent membrane properties, most likely a combination of thickness, fluidity, and water permeability, and we have proposed possible mechanisms by which DesK senses these properties and transduces the signals. X-ray structures and computational models have revealed structural features of TM and cytoplasmic regions in DesK's kinase- and phosphatase-competent states. Biochemical and genetic experiments and molecular simulations further showed that reversible formation of a two-helix coiled coil in the fifth TM segment and the N-terminus of the cytoplasmic domain is essential for the sensing and signal transduction mechanisms. Together with other structural and functional works, the emerging picture suggests that diverse HKs possess distinct sensing and transduction mechanisms but share as rather general features (i) a symmetric phosphatase state and an asymmetric kinase state and (ii) similar functional outputs on the conserved DHp and ABD domains, achieved through different mechanisms that depend on the nature of the initial signal. We here advance (iii) an important role for TM prolines in transducing the initial signals to the cytoplasmic coiled coils, based on simulations of DesK's TM helices and our previous work on a related HK, PhoQ. Lastly, evidence for DesK, PhoQ, BvgS, and DctB HKs shows that (iv) overall catalytic output is tuned by a delicate balance between hydration potentials, coiled coil stability, and exposure of hydrophobic surface patches at their cytoplasmic coiled coils and at the N-terminal and C-terminal sides of their TM helices. This balance is so delicate that small perturbations, either physiological signals or induced by mutations, lead to large remodeling of the underlying conformational landscape achieving clear-cut changes in catalytic output, mirroring the required response speed of these systems for proper biological function.
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Affiliation(s)
- Luciano A. Abriata
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Daniela Albanesi
- Laboratorio
de Fisiología Microbiana, Instituto de Biología Molecular
y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio
CONICET Rosario, 2000 Rosario, Argentina
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Diego de Mendoza
- Laboratorio
de Fisiología Microbiana, Instituto de Biología Molecular
y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio
CONICET Rosario, 2000 Rosario, Argentina
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20
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Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare JP, Remeeva A, Polovinkin V, Utrobin P, Balandin T, Engelhard M, Büldt G, Gordeliy V. New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex. Sci Rep 2017; 7:41811. [PMID: 28165484 PMCID: PMC5292967 DOI: 10.1038/srep41811] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/01/2016] [Indexed: 01/29/2023] Open
Abstract
The complex of two membrane proteins, sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII), mediates negative phototaxis in halobacteria N. pharaonis. Upon light activation NpSRII triggers a signal transduction chain homologous to the two-component system in eubacterial chemotaxis. Here we report on crystal structures of the ground and active M-state of the complex in the space group I212121. We demonstrate that the relative orientation of symmetrical parts of the dimer is parallel (“U”-shaped) contrary to the gusset-like (“V”-shaped) form of the previously reported structures of the NpSRII/NpHtrII complex in the space group P21212, although the structures of the monomers taken individually are nearly the same. Computer modeling of the HAMP domain in the obtained “V”- and “U”-shaped structures revealed that only the “U”-shaped conformation allows for tight interactions of the receptor with the HAMP domain. This is in line with existing data and supports biological relevance of the “U” shape in the ground state. We suggest that the “V”-shaped structure may correspond to the active state of the complex and transition from the “U” to the “V”-shape of the receptor-transducer complex can be involved in signal transduction from the receptor to the signaling domain of NpHtrII.
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Affiliation(s)
- A Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Jägerstraße 17-19, 52056 Aachen, Germany
| | - E Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France
| | - V Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - S Grudinin
- CNRS, Laboratoire Jean Kuntzmann, BP 53, Grenoble Cedex 9, France.,NANO-D, INRIA Grenoble-Rhone-Alpes Research Center, 38334 Saint Ismier Cedex, Montbonnot, France
| | - I Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - J P Klare
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.,Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany
| | - A Remeeva
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - V Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France
| | - P Utrobin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - T Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - M Engelhard
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - G Büldt
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - V Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Jägerstraße 17-19, 52056 Aachen, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
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21
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Zschiedrich CP, Keidel V, Szurmant H. Molecular Mechanisms of Two-Component Signal Transduction. J Mol Biol 2016; 428:3752-75. [PMID: 27519796 DOI: 10.1016/j.jmb.2016.08.003] [Citation(s) in RCA: 342] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/30/2016] [Accepted: 08/01/2016] [Indexed: 02/03/2023]
Abstract
Two-component systems (TCS) comprising sensor histidine kinases and response regulator proteins are among the most important players in bacterial and archaeal signal transduction and also occur in reduced numbers in some eukaryotic organisms. Given their importance to cellular survival, virulence, and cellular development, these systems are among the most scrutinized bacterial proteins. In the recent years, a flurry of bioinformatics, genetic, biochemical, and structural studies have provided detailed insights into many molecular mechanisms that underlie the detection of signals and the generation of the appropriate response by TCS. Importantly, it has become clear that there is significant diversity in the mechanisms employed by individual systems. This review discusses the current knowledge on common themes and divergences from the paradigm of TCS signaling. An emphasis is on the information gained by a flurry of recent structural and bioinformatics studies.
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Affiliation(s)
- Christopher P Zschiedrich
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E Second Street, Pomona, CA 91766, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Victoria Keidel
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E Second Street, Pomona, CA 91766, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hendrik Szurmant
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E Second Street, Pomona, CA 91766, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA.
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22
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Heininger A, Yusuf R, Lawrence RJ, Draheim RR. Identification of transmembrane helix 1 (TM1) surfaces important for EnvZ dimerisation and signal output. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1868-75. [PMID: 27155567 DOI: 10.1016/j.bbamem.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 02/06/2023]
Abstract
The Escherichia coli sensor kinase EnvZ modulates porin expression in response to various stimuli, including extracellular osmolarity, the presence of procaine and interaction with an accessory protein, MzrA. Two major outer membrane porins, OmpF and OmpC, act as passive diffusion-limited pores that allow compounds, including certain classes of antibiotics such as β-lactams and fluoroquinolones, to enter the bacterial cell. Even though the mechanisms by which EnvZ detects and processes the presence of various stimuli are a fundamental component of microbial physiology, they are not yet fully understood. Here, we assess the role of TM1 during signal transduction in response to the presence of extracellular osmolarity. Various mechanisms of transmembrane communication have been proposed including rotation of individual helices within the transmembrane domain, dynamic movement of the membrane-distal portion of the cytoplasmic domain and regulated intra-protein unfolding. To assess these possibilities, we have created a library of single-Cys-containing EnvZ proteins in order to facilitate sulfhydryl-reactivity experimentation. Our results demonstrate that the major TM1-TM1' interface falls along a single surface consisting of residue positions 19, 23, 26, 30 and 34. In addition, we show that Cys substitutions within the N- and C-terminal regions of TM1 result in drastic changes to EnvZ signal output. Finally, we demonstrate that core residues within TM1 are responsible for both TM1 dimerisation and maintenance of steady-state signal output. Overall, our results suggest that no major rearrangement of the TM1-TM1' interface occurs during transmembrane communication in response to extracellular osmolarity. We conclude by discussing these results within the frameworks of several proposed models for transmembrane communication.
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Affiliation(s)
- Annika Heininger
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, D-60438 Frankfurt, Germany.
| | - Rahmi Yusuf
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, England, UK.
| | - Robert J Lawrence
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, England, UK.
| | - Roger R Draheim
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, England, UK; Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth PO1 2DT, England, UK.
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23
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Koler M, Frank V, Amartely H, Friedler A, Vaknin A. Dynamic Clustering of the Bacterial Sensory Kinase BaeS. PLoS One 2016; 11:e0150349. [PMID: 26950881 PMCID: PMC4780735 DOI: 10.1371/journal.pone.0150349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/14/2016] [Indexed: 11/29/2022] Open
Abstract
Several bacterial sensory-kinase receptors form clusters on the cell membrane. However, the dynamics of sensory-kinase clustering are largely unclear. Using measurements of fluorescence anisotropy and time-lapse imaging of Escherichia coli cells, we demonstrate that copper ions trigger self-association of BaeS receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. Copper ions did not trigger self-association of other fluorescently tagged sensory kinases, and other divalent metal ions could not elicit self-association of BaeS. The histidine residues in the BaeS periplasmic domain are essential for copper binding in vitro and are important for the copper-induced BaeS responses in vivo. BaeS clustering was triggered also under conditions that directly triggered BaeS-dependent transcriptional responses. Thus, clustering of sensory kinase receptors can be dynamic and context dependent and can be triggered by specific environmental cues.
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Affiliation(s)
- Moriah Koler
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Vered Frank
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Hadar Amartely
- The Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
- * E-mail:
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24
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Kaneti G, Meir O, Mor A. Controlling bacterial infections by inhibiting proton-dependent processes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:995-1003. [PMID: 26522076 DOI: 10.1016/j.bbamem.2015.10.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/20/2015] [Accepted: 10/27/2015] [Indexed: 12/15/2022]
Abstract
Bacterial resistance to antibiotics is recognized as one of the greatest threats in modern healthcare, taking a staggering toll worldwide. New approaches for controlling bacterial infections must be designed, eventually combining multiple strategies for complimentary therapies. This review explores an old/new paradigm for multi-targeted antibacterial therapy, focused at disturbing bacterial cytoplasmic membrane functions at sub minimal inhibitory concentrations, namely through superficial physical alterations of the bilayer, thereby perturbing transmembrane signals transduction. Such a paradigm may have the advantage of fighting the infection while avoiding many of the known resistance mechanisms. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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Affiliation(s)
- Galoz Kaneti
- Department of Biotechnology & Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ohad Meir
- Department of Biotechnology & Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Amram Mor
- Department of Biotechnology & Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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25
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Bhate MP, Molnar KS, Goulian M, DeGrado WF. Signal transduction in histidine kinases: insights from new structures. Structure 2015; 23:981-94. [PMID: 25982528 DOI: 10.1016/j.str.2015.04.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/22/2015] [Accepted: 03/30/2015] [Indexed: 10/23/2022]
Abstract
Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last 5 years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric to symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented, and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering, and thermodynamics paves the way for a deeper molecular understanding of HK signal transduction.
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Affiliation(s)
- Manasi P Bhate
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA
| | - Kathleen S Molnar
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Goulian
- Department of Biology and Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, 555 Mission Bay Boulevard South, Box 3122, San Francisco, CA 94158, USA.
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26
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Liu J, Yang J, Wen J, Yang Y, Wei X, Zhang X, Wang YP. Mutational analysis of dimeric linkers in peri- and cytoplasmic domains of histidine kinase DctB reveals their functional roles in signal transduction. Open Biol 2015; 4:140023. [PMID: 24898140 PMCID: PMC4077058 DOI: 10.1098/rsob.140023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Membrane-associated histidine kinases (HKs) in two-component systems respond to environmental stimuli by autophosphorylation and phospho-transfer. HK typically contains a periplasmic sensor domain that regulates the cytoplasmic kinase domain through a conserved cytoplasmic linker. How signal is transduced from the ligand-binding site across the membrane barrier remains unclear. Here, we analyse two linker regions of a typical HK, DctB. One region connects the first transmembrane helix with the periplasmic Per-ARNT-Sim domains, while the other one connects the second transmembrane helix with the cytoplasmic kinase domains. We identify a leucine residue in the first linker region to be essential for the signal transduction and for maintaining the delicate balance of the dimeric interface, which is key to its activities. We also show that the other linker, belonging to the S-helix coiled-coil family, plays essential roles in signal transduction inside the cell. Furthermore, by combining mutations with opposing activities in the two regions, we show that these two signalling transduction elements are integrated to produce a combined effect on the final activity of DctB.
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Affiliation(s)
- Jiwei Liu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jin Wen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yun Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaolu Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaodong Zhang
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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27
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Colistin resistance mechanisms in Klebsiella pneumoniae strains from Taiwan. Antimicrob Agents Chemother 2015; 59:2909-13. [PMID: 25691646 DOI: 10.1128/aac.04763-14] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 11/20/2022] Open
Abstract
Colistin is one of the antibiotics of last resort for the treatment of carbapenem-resistant Klebsiella pneumoniae infection. This study showed that capsular type K64 (50%) and ST11 (53.9%) are the prevalent capsular and sequence types in the colistin-resistant strains in Taiwan. The interruption of transcripts (38.5%) and amino acid mutation (15.4%) in mgrB are the major mechanisms contributing to colistin resistance. In addition, novel single amino acid changes in MgrB (Stop48Tyr) and PhoQ (Leu26Pro) were observed to contribute to colistin resistance.
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28
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Botelho SC, Enquist K, von Heijne G, Draheim RR. Differential repositioning of the second transmembrane helices from E. coli Tar and EnvZ upon moving the flanking aromatic residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:615-21. [PMID: 25445668 DOI: 10.1016/j.bbamem.2014.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/29/2014] [Accepted: 11/17/2014] [Indexed: 01/04/2023]
Abstract
Aromatic tuning, i.e. repositioning aromatic residues found at the cytoplasmic end of transmembrane (TM) domains within bacterial receptors, has been previously shown to modulate signal output from the aspartate chemoreceptor (Tar) and the major osmosensor EnvZ of Escherichia coli. In the case of Tar, changes in signal output consistent with the vertical position of the native Trp-Tyr aromatic tandem within TM2 were observed. In contrast, within EnvZ, where a Trp-Leu-Phe aromatic triplet was repositioned, the surface that the triplet resided upon was the major determinant governing signal output. However, these studies failed to determine whether moving the aromatic residues was sufficient to physically reposition the TM helix within a membrane. Recent coarse-grained molecular dynamics (CG-MD) simulations predicted displacement of Tar TM2 upon moving the aromatic residues at the cytoplasmic end of the helix. Here, we demonstrate that repositioning the Trp-Tyr tandem within Tar TM2 displaces the C-terminal boundary of the helix relative to the membrane. In a similar analysis of EnvZ, an abrupt initial displacement of TM2 was observed but no subsequent movement was seen, suggesting that the vertical position of TM2 is not governed by the location of the Trp-Leu-Phe triplet. Our results also provide another set of experimental data, i.e. the resistance of EnvZ TM2 to being displaced upon aromatic tuning, which could be useful for subsequent refinement of the initial CG-MD simulations. Finally, we discuss the limitations of these methodologies, how moving flanking aromatic residues might impact steady-state signal output and the potential to employ aromatic tuning in other bacterial membrane-spanning receptors.
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Affiliation(s)
- Salomé C Botelho
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Karl Enquist
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Roger R Draheim
- Division of Pharmacy, Durham University, Queen's Campus, Stockton-on-Tees TS17 6BH, England, UK; Wolfson Research Institute for Health and Wellbeing, Durham University, Queen's Campus, Stockton-on-Tees, TS17 6BH, England, UK.
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29
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Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure 2014; 22:1239-1251. [PMID: 25087511 PMCID: PMC4322757 DOI: 10.1016/j.str.2014.04.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/17/2014] [Accepted: 04/29/2014] [Indexed: 01/16/2023]
Abstract
Bacteria transduce signals across the membrane using two-component systems (TCSs), consisting of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In gram-negative bacteria, the PhoPQ TCS senses cations and antimicrobial peptides, yet little is known about the structural changes involved in transmembrane signaling. We construct a model of PhoQ signal transduction using Bayesian inference, based on disulfide crosslinking data and homologous crystal structures. The data are incompatible with a single conformation but are instead consistent with two interconverting structures. These states differ in membrane depth of the periplasmic acidic patch and the reciprocal displacement of diagonal helices along the dimer interface. Studies of multiple histidine kinases suggest this repacking might be a common mode of signal transduction in sensor His-kinase receptors. Because a similar scissors model has been ruled out in CheA-linked chemoreceptors, the evidence suggests that sensor His-kinase and CheA-linked receptors possess different signaling mechanisms.
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Affiliation(s)
- Kathleen S Molnar
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group19104, USA, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Massimiliano Bonomi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Graham D Clinthorne
- Pharmacological Sciences Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel Gonzalez
- Biochemistry and Molecular Biophysics Graduate Group19104, USA, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shalom D Goldberg
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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30
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Maity AK, Bandyopadhyay A, Chaudhury P, Banik SK. Role of functionality in two-component signal transduction: a stochastic study. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032713. [PMID: 24730880 DOI: 10.1103/physreve.89.032713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Indexed: 06/03/2023]
Abstract
We present a stochastic formalism for signal transduction processes in a bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of a phosphotransfer mechanism between the cognate partners of a two-component system, viz., the sensor kinase and the response regulator. Based on the difference in functionality of the sensor kinase, the noisy phosphotransfer mechanism has been studied for monofunctional and bifunctional two-component systems using the formalism of the linear noise approximation. Steady-state analysis of both models quantifies different physically realizable quantities, e.g., the variance, the Fano factor (variance/mean), and mutual information. The resultant data reveal that both systems reliably transfer information of extracellular environment under low external stimulus and in a high-kinase-and-phosphatase regime. We extend our analysis further by studying the role of the two-component system in downstream gene regulation.
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Affiliation(s)
- Alok Kumar Maity
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Arnab Bandyopadhyay
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
| | - Pinaki Chaudhury
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Suman K Banik
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
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31
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Maity AK, Bandyopadhyay A, Chattopadhyay S, Chaudhuri JR, Metzler R, Chaudhury P, Banik SK. Quantification of noise in bifunctionality-induced post-translational modification. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032716. [PMID: 24125303 DOI: 10.1103/physreve.88.032716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 03/07/2013] [Indexed: 06/02/2023]
Abstract
We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of a bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctuations due to autophosphorylation, kinase, and phosphatase activity of the sensor kinase have been considered in the model via Langevin equations, which are then solved within the framework of linear noise approximation. The resultant analytical expression of phosphorylated response regulators are then used to quantify the noise profile of biologically motivated single and branched pathways. Enhancement and reduction of noise in terms of extra phosphate outflux and influx, respectively, have been analyzed for the branched system. Furthermore, the role of fluctuations of the network output in the regulation of a promoter with random activation-deactivation dynamics has been analyzed.
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Affiliation(s)
- Alok Kumar Maity
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
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32
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Viarengo G, Sciara MI, Salazar MO, Kieffer PM, Furlán RLE, García Véscovi E. Unsaturated long chain free fatty acids are input signals of the Salmonella enterica PhoP/PhoQ regulatory system. J Biol Chem 2013; 288:22346-58. [PMID: 23782700 DOI: 10.1074/jbc.m113.472829] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Salmonella enterica serovar Typhimurium PhoP/PhoQ system has largely been studied as a paradigmatic two-component regulatory system not only to dissect structural and functional aspects of signal transduction in bacteria but also to gain knowledge about the versatile devices that have evolved allowing a pathogenic bacterium to adjust to or counteract environmental stressful conditions along its life cycle. Mg(2+) limitation, acidic pH, and the presence of cationic antimicrobial peptides have been identified as cues that the sensor protein PhoQ can monitor to reprogram Salmonella gene expression to cope with extra- or intracellular challenging conditions. In this work, we show for the first time that long chain unsaturated free fatty acids (LCUFAs) present in Salmonella growth medium are signals specifically detected by PhoQ. We demonstrate that LCUFAs inhibit PhoQ autokinase activity, turning off the expression of the PhoP-dependent regulon. We also show that LCUFAs exert their action independently of their cellular uptake and metabolic utilization by means of the β-oxidative pathway. Our findings put forth the complexity of input signals that can converge to finely tune the activity of the PhoP/PhoQ system. In addition, they provide a new potential biochemical platform for the development of antibacterial strategies to fight against Salmonella infections.
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Affiliation(s)
- Gastón Viarengo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Predio CCT-CONICET-Rosario, Ocampo y Esmeralda, 2000 Rosario, Argentina
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Abstract
A recurring theme in biological circuits is the existence of components that are antagonistically bifunctional, in the sense that they simultaneously have two opposing effects on the same target or biological process. Examples include bifunctional enzymes that carry out two opposing reactions such as phosphorylating and dephosphorylating the same target, regulators that activate and also repress a gene in circuits called incoherent feedforward loops, and cytokines that signal immune cells to both proliferate and die. Such components are termed "paradoxical", and in this review we discuss how they can provide useful features to cell circuits that are otherwise difficult to achieve. In particular, we summarize how paradoxical components can provide robustness, generate temporal pulses, and provide fold-change detection, in which circuits respond to relative rather than absolute changes in signals.
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Affiliation(s)
- Yuval Hart
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Firon A, Tazi A, Da Cunha V, Brinster S, Sauvage E, Dramsi S, Golenbock DT, Glaser P, Poyart C, Trieu-Cuot P. The Abi-domain protein Abx1 interacts with the CovS histidine kinase to control virulence gene expression in group B Streptococcus. PLoS Pathog 2013; 9:e1003179. [PMID: 23436996 PMCID: PMC3578759 DOI: 10.1371/journal.ppat.1003179] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/19/2012] [Indexed: 12/20/2022] Open
Abstract
Group B Streptococcus (GBS), a common commensal of the female genital tract, is the leading cause of invasive infections in neonates. Expression of major GBS virulence factors, such as the hemolysin operon cyl, is regulated directly at the transcriptional level by the CovSR two-component system. Using a random genetic approach, we identified a multi-spanning transmembrane protein, Abx1, essential for the production of the GBS hemolysin. Despite its similarity to eukaryotic CaaX proteases, the Abx1 function is not involved in a post-translational modification of the GBS hemolysin. Instead, we demonstrate that Abx1 regulates transcription of several virulence genes, including those comprising the hemolysin operon, by a CovSR-dependent mechanism. By combining genetic analyses, transcriptome profiling, and site-directed mutagenesis, we showed that Abx1 is a regulator of the histidine kinase CovS. Overexpression of Abx1 is sufficient to activate virulence gene expression through CovS, overcoming the need for an additional signal. Conversely, the absence of Abx1 has the opposite effect on virulence gene expression consistent with CovS locked in a kinase-competent state. Using a bacterial two-hybrid system, direct interaction between Abx1 and CovS was mapped specifically to CovS domains involved in signal processing. We demonstrate that the CovSR two-component system is the core of a signaling pathway integrating the regulation of CovS by Abx1 in addition to the regulation of CovR by the serine/threonine kinase Stk1. In conclusion, our study reports a regulatory function for Abx1, a member of a large protein family with a characteristic Abi-domain, which forms a signaling complex with the histidine kinase CovS in GBS. The gram-positive Streptococcus genus includes three major human pathogens that are members of the normal microflora: Streptococcus pneumoniae (also known as the pneumococcus), Streptococcus pyogenes (Group A Streptococcus), and Streptococcus agalactiae (Group B Streptococcus). Their carriage in the population is highly dynamic and mostly asymptomatic. However, each of these species can cause a wide spectrum of diseases, from local infections to systemic and fatal infections including septicemia and meningitis. Expression of streptococcal virulence-associated genes is tightly regulated at the transcriptional level. However, the signal(s) and the precise molecular events controlling the switch from commensalism to virulence are not yet understood. In this study, we identified and characterized a bacterial protein essential for virulence gene expression in Group B Streptococcus, the main pathogen of neonates. We show that this transmembrane protein, named Abx1, interacts with the histidine kinase CovS to modulate the activity of the major regulator of virulence CovR. We define how a core set of four proteins, Abx1, CovS, CovR, and the serine/threonine kinase Stk1, interact to control the expression of virulence genes in S. agalactiae. We propose that Abx1-like proteins, that are widespread in bacteria, might be part of a conserved mechanism of two-component system regulation.
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Affiliation(s)
- Arnaud Firon
- Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Paris, France.
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Lemmin T, Soto CS, Clinthorne G, DeGrado WF, Dal Peraro M. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations. PLoS Comput Biol 2013; 9:e1002878. [PMID: 23359663 PMCID: PMC3554529 DOI: 10.1371/journal.pcbi.1002878] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/17/2012] [Indexed: 01/26/2023] Open
Abstract
The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM) domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices. Two-component systems (TCSs) are signaling complexes essential for bacterial survival and virulence. PhoQ is the histidine kinase chemoreceptor of the PhoQ-PhoP tandem machine that detects the concentration of cationic species at the inner membrane of Gram-negative bacteria. A full understanding of the PhoQ signal transduction mechanism is currently hindered by the lack of a complete atomistic structure. Here, by using molecular simulations integrated with cross-linking disulfide scanning data, we present the first structural model of the transmembrane (TM) portion of PhoQ from E. coli. Its structural and dynamic features induce a concerted displacement of the TM helices at the periplasmic side, which modulates a rotation at the cytoplasmic end. This supports the idea that signal transduction is promoted through a combination of scissoring and rotational movements of the TM helices. This complex mechanism is the key to understanding how the chemical stimuli sensed by the periplasmic sensor domain trigger, via the relay of the HAMP domain, the histidine auto-phosphorylation and kinase/phosphatase activity at the cytoplasmic end.
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Affiliation(s)
- Thomas Lemmin
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Cinque S. Soto
- Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Graham Clinthorne
- Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California, United States of America
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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Eguchi Y, Ishii E, Yamane M, Utsumi R. The connector SafA interacts with the multi-sensing domain of PhoQ in Escherichia coli. Mol Microbiol 2012; 85:299-313. [DOI: 10.1111/j.1365-2958.2012.08114.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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