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Wölflingseder M, Fengler VH, Standhartinger V, Wagner GE, Reidl J. The regulatory network comprising ArcAB-RpoS-RssB influences motility in Vibrio cholerae. Mol Microbiol 2024; 121:850-864. [PMID: 38323722 DOI: 10.1111/mmi.15235] [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: 07/24/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 02/08/2024]
Abstract
The diarrheal disease cholera is caused by the versatile and responsive bacterium Vibrio cholerae, which is capable of adapting to environmental changes. Among others, the alternative sigma factor RpoS activates response pathways, including regulation of motility- and chemotaxis-related genes under nutrient-poor conditions in V. cholerae. Although RpoS has been well characterised, links between RpoS and other regulatory networks remain unclear. In this study, we identified the ArcAB two-component system to control rpoS transcription and RpoS protein stability in V. cholerae. In a manner similar to that seen in Escherichia coli, the ArcB kinase not only activates the response regulator ArcA but also RssB, the anti-sigma factor of RpoS. Our results demonstrated that, in V. cholerae, RssB is phosphorylated by ArcB, which subsequently activates RpoS proteolysis. Furthermore, ArcA acts as a repressor of rpoS transcription. Additionally, we determined that the cysteine residue at position 180 of ArcB is crucial for signal recognition and activity. Thus, our findings provide evidence linking RpoS response to the anoxic redox control system ArcAB in V. cholerae.
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Affiliation(s)
- Martina Wölflingseder
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Vera H Fengler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Verena Standhartinger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
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2
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya NI, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023; 11:e16309. [PMID: 37849831 PMCID: PMC10578306 DOI: 10.7717/peerj.16309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.
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Affiliation(s)
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Mexico City, Mexico City, México
| | | | | | | | | | | | | | | | | | | | - Bernardo Franco
- Biology, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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3
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The ArcAB Two-Component System: Function in Metabolism, Redox Control, and Infection. Microbiol Mol Biol Rev 2022; 86:e0011021. [PMID: 35442087 PMCID: PMC9199408 DOI: 10.1128/mmbr.00110-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
ArcAB, also known as the Arc system, is a member of the two-component system family of bacterial transcriptional regulators and is composed of sensor kinase ArcB and response regulator ArcA. In this review, we describe the structure and function of these proteins and assess the state of the literature regarding ArcAB as a sensor of oxygen consumption. The bacterial quinone pool is the primary modulator of ArcAB activity, but questions remain for how this regulation occurs. This review highlights the role of quinones and their oxidation state in activating and deactivating ArcB and compares competing models of the regulatory mechanism. The cellular processes linked to ArcAB regulation of central metabolic pathways and potential interactions of the Arc system with other regulatory systems are also reviewed. Recent evidence for the function of ArcAB under aerobic conditions is challenging the long-standing characterization of this system as strictly an anaerobic global regulator, and the support for additional ArcAB functionality in this context is explored. Lastly, ArcAB-controlled cellular processes with relevance to infection are assessed.
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Teran-Melo JL, Peña-Sandoval GR, Silva-Jimenez H, Rodriguez C, Alvarez AF, Georgellis D. Routes of phosphoryl group transfer during signal transmission and signal decay in the dimeric sensor histidine kinase ArcB. J Biol Chem 2018; 293:13214-13223. [PMID: 29945971 PMCID: PMC6109937 DOI: 10.1074/jbc.ra118.003910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/14/2018] [Indexed: 11/06/2022] Open
Abstract
The Arc (anoxic redox control) two-component system of Escherichia coli, comprising ArcA as the response regulator and ArcB as the sensor histidine kinase, modulates the expression of numerous genes in response to respiratory growth conditions. Under reducing growth conditions, ArcB autophosphorylates at the expense of ATP, and transphosphorylates ArcA via a His292 → Asp576 → His717 → Asp54 phosphorelay, whereas under oxidizing growth conditions, ArcB catalyzes the dephosphorylation of ArcA-P by a reverse Asp54 → His717 → Asp576 → Pi phosphorelay. However, the exact phosphoryl group transfer routes and the molecular mechanisms determining their directions are unclear. Here, we show that, during signal propagation, the His292 → Asp576 and Asp576 → His717 phosphoryl group transfers within ArcB dimers occur intra- and intermolecularly, respectively. Moreover, we report that, during signal decay, the phosphoryl group transfer from His717 to Asp576 takes place intramolecularly. In conclusion, we present a mechanism that dictates the direction of the phosphoryl group transfer within ArcB dimers and that enables the discrimination of the kinase and phosphatase activities of ArcB.
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Affiliation(s)
- Juan L Teran-Melo
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Gabriela R Peña-Sandoval
- the Unidad Académica de Agricultura, Universidad Autónoma de Nayarit, 63190 Tepic, Nayarit, Mexico, and
| | - Hortencia Silva-Jimenez
- the Area de Oceanografía Química, Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - Claudia Rodriguez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Adrián F Alvarez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Dimitris Georgellis
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico,
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Núñez-Oreza LA, Georgellis D, Álvarez AF. ArcB: El sensor del estado redox en bacterias. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2014. [DOI: 10.1016/s1405-888x(14)72088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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6
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Sharma P, Stagge S, Bekker M, Bettenbrock K, Hellingwerf KJ. Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone. PLoS One 2013; 8:e75412. [PMID: 24116043 PMCID: PMC3792059 DOI: 10.1371/journal.pone.0075412] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/14/2013] [Indexed: 01/15/2023] Open
Abstract
Expression of the catabolic network in Escherichia coli is predominantly regulated, via oxygen availability, by the two-component system ArcBA. It has been shown that the kinase activity of ArcB is controlled by the redox state of two critical pairs of cysteines in dimers of the ArcB sensory kinase. Among the cellular components that control the redox state of these cysteines of ArcB are the quinones from the cytoplasmic membrane of the cell, which function in ‘respiratory’ electron transfer. This study is an effort to understand how the redox state of the quinone pool(s) is sensed by the cell via the ArcB kinase. We report the relationship between growth, quinone content, ubiquinone redox state, the level of ArcA phosphorylation, and the level of ArcA-dependent gene expression, in a number of mutants of E. coli with specific alterations in their set of quinones, under a range of physiological conditions. Our results provide experimental evidence for a previously formulated hypothesis that not only ubiquinone, but also demethylmenaquinone, can inactivate kinase activity of ArcB. Also, in a mutant strain that only contains demethylmenaquinone, the extent of ArcA phosphorylation can be modulated by the oxygen supply rate, which shows that demethylmenaquinone can also inactivate ArcB in its oxidized form. Furthermore, in batch cultures of a strain that contains ubiquinone as its only quinone species, we observed that the ArcA phosphorylation level closely followed the redox state of the ubiquinone/ubiquinol pool, much more strictly than it does in the wild type strain. Therefore, at low rates of oxygen supply in the wild type strain, the activity of ArcB may be inhibited by demethylmenaquinone, in spite of the fact that the ubiquinones are present in the ubiquinol form.
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Affiliation(s)
- Poonam Sharma
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
| | - Stefan Stagge
- MPI für Dynamik Komplexer Technischer Systeme, Experimentelle Systembiologie, Magdeburg, Germany
| | - Martijn Bekker
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
| | - Katja Bettenbrock
- MPI für Dynamik Komplexer Technischer Systeme, Experimentelle Systembiologie, Magdeburg, Germany
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, and Netherlands Institute for Systems Biology, Amsterdam, the Netherlands
- * E-mail:
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Ubiquinone and menaquinone electron carriers represent the yin and yang in the redox regulation of the ArcB sensor kinase. J Bacteriol 2013; 195:3054-61. [PMID: 23645604 DOI: 10.1128/jb.00406-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Arc two-component system, comprising the ArcB sensor kinase and the ArcA response regulator, modulates the expression of numerous genes in response to respiratory growth conditions. Under aerobic growth conditions, the ubiquinone electron carriers were proposed to silence the kinase activity of ArcB by oxidizing two cytosol-located redox-active cysteine residues that participate in intermolecular disulfide bond formation. Here, we confirm the role of the ubiquinone electron carriers as the silencing signal of ArcB in vivo, we show that the redox potential of ArcB is about -41 mV, and we demonstrate that the menaquinols are required for proper ArcB activation upon a shift from aerobic to anaerobic growth conditions. Thus, an essential link in the Arc signal transduction pathway connecting the redox state of the quinone pool to the transcriptional apparatus is elucidated.
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