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Jung JH, Jeong S, Im S, Kim MK, Seo HS, Lim S. Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C. Front Microbiol 2021; 12:659233. [PMID: 34394020 PMCID: PMC8363230 DOI: 10.3389/fmicb.2021.659233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Deinococcus radiodurans known for its extraordinary resistance to ionizing radiation contains bacterial phytochrome (BphP), a member of the family of red/far-red light-sensing proteins. In this study, we constructed a bphP mutant strain (ΔbphP) to investigate the role of D. radiodurans BphP (DrBphP) in the DNA damage response. When cells were incubated under light and dark conditions following exposure to DNA damaging agents, such as γ- and UV-radiation and mitomycin C (MMC), no significant difference in cell survival was observed between the wild-type D. radiodurans strain (WT) and ΔbphP. However, when continuously exposed to MMC under light conditions, the WT strain notably exhibited increased survival compared to cells grown in the dark. The increased survival was not observed in the ΔbphP strain. These results are indicative of the protective role of light-activated DrBphP in the presence of MMC. Site-directed mutagenesis revealed that the conserved amino acids Cys-24 and His-532 involved in chromophore binding and signal transduction, respectively, were essential for the protective function of DrBphP. Inactivation of the cognate response regulator (RR; DrBphR) of DrBphP increased MMC resistance in the dark. In trans complementation of the bphP bphR double mutant strain (ΔbphPR) with DrBphR decreased MMC resistance. Considering that DrBphP acts as a light-activated phosphatase that dephosphorylates DrBphR, it appears that phosphorylated DrBphR exerts a negative effect on cell survival in the presence of MMC. DrBphP overexpression resulted in an increase in MMC resistance of ΔbphPR, implying that other RRs might be involved in the DrBphP-mediated signaling pathway. A mutant lacking the dr_0781 gene (Δdr_0781) demonstrated the same MMC phenotype as ΔbphR. Survival was further increased in the bphR dr_0781 double mutant strain compared to each single mutant ΔbphR or Δdr_0781, suggesting that DR_0781 is also involved in the DrBphP-dependent MMC sensitivity. This study uncovered a previously unknown phenomenon of red/far-red light-dependent DNA damage survival mediated by BphP by identifying the conditions under which DrBphP exhibits a fitness advantage.
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Affiliation(s)
- Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Soyoung Jeong
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Seonghun Im
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Ho Seong Seo
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
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2
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Multamäki E, Nanekar R, Morozov D, Lievonen T, Golonka D, Wahlgren WY, Stucki-Buchli B, Rossi J, Hytönen VP, Westenhoff S, Ihalainen JA, Möglich A, Takala H. Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. Nat Commun 2021; 12:4394. [PMID: 34285211 PMCID: PMC8292422 DOI: 10.1038/s41467-021-24676-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.
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Affiliation(s)
- Elina Multamäki
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Rahul Nanekar
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Dmitry Morozov
- grid.9681.60000 0001 1013 7965Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Topias Lievonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - David Golonka
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Weixiao Yuan Wahlgren
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Brigitte Stucki-Buchli
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jari Rossi
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Vesa P. Hytönen
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Sebastian Westenhoff
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A. Ihalainen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Andreas Möglich
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland ,grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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3
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De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Verméglio A. Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis. Sci Rep 2019; 9:16505. [PMID: 31712689 PMCID: PMC6848086 DOI: 10.1038/s41598-019-52927-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022] Open
Abstract
Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.
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Affiliation(s)
- Gilles De Luca
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Jérôme Lavergne
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France.
| | - André Verméglio
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
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4
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Gourinchas G, Etzl S, Winkler A. Bacteriophytochromes - from informative model systems of phytochrome function to powerful tools in cell biology. Curr Opin Struct Biol 2019; 57:72-83. [PMID: 30878713 DOI: 10.1016/j.sbi.2019.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022]
Abstract
Bacteriophytochromes are a subfamily of the diverse light responsive phytochrome photoreceptors. Considering their preferential interaction with biliverdin IXα as endogenous cofactor, they have recently been used for creating optogenetic tools and engineering fluorescent probes. Ideal absorption characteristics for the activation of bacteriophytochrome-based systems in the therapeutic near-infrared window as well the availability of biliverdin in mammalian tissues have resulted in tremendous progress in re-engineering bacteriophytochromes for diverse applications. At the same time, both the structural analysis and the functional characterization of diverse naturally occurring bacteriophytochrome systems have unraveled remarkable differences in signaling mechanisms and have so far only touched the surface of the evolutionary diversity within the family of bacteriophytochromes. This review highlights recent findings and future challenges.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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5
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Miguel-Romero L, Casino P, Landete JM, Monedero V, Zúñiga M, Marina A. The malate sensing two-component system MaeKR is a non-canonical class of sensory complex for C4-dicarboxylates. Sci Rep 2017; 7:2708. [PMID: 28577341 PMCID: PMC5457438 DOI: 10.1038/s41598-017-02900-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
Microbial colonization of different environments is enabled to a great extent by the plasticity of their sensory mechanisms, among them, the two-component signal transduction systems (TCS). Here, an example of TCS plasticity is presented: the regulation of L-malate catabolism via malic enzyme by MaeRK in Lactobacillales. MaeKR belongs to the citrate family of TCS as the Escherichia coli DcuSR system. We show that the Lactobacillus casei histidine-kinase MaeK is defective in autophosphorylation activity as it lacks a functional catalytic and ATP binding domain. The cognate response regulator MaeR was poorly phosphorylated at its phosphoacceptor Asp in vitro. This phosphorylation, however, enhanced MaeR binding in vitro to its target sites and it was required for induction of regulated genes in vivo. Elucidation of the MaeR structure revealed that response regulator dimerization is accomplished by the swapping of α4-β5-α5 elements between two monomers, generating a phosphoacceptor competent conformation. Sequence and phylogenetic analyses showed that the MaeKR peculiarities are not exclusive to L. casei as they are shared by the rest of orthologous systems of Lactobacillales. Our results reveal MaeKR as a non-canonical TCS displaying distinctive features: a swapped response regulator and a sensor histidine kinase lacking ATP-dependent kinase activity.
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Affiliation(s)
- L Miguel-Romero
- Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain
| | - P Casino
- Departamento de Bioquímica, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - J M Landete
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.,Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - V Monedero
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - M Zúñiga
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - A Marina
- Department of Genomic and Proteomic, Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain. .,Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, -, Spain.
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