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Kullapanich C, Dubbs JM, Mongkolsuk S. Inactivation of the Agrobacterium tumefaciens ActSR system affects resistance to multiple stresses with increased H 2O 2 sensitivity due to reduced expression of hemH. MICROBIOLOGY-SGM 2020; 165:1117-1134. [PMID: 31339484 DOI: 10.1099/mic.0.000838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Agrobacterium tumefaciens ActSR two-component regulatory system is a member of a homologous group of global redox-responsive regulatory systems that adjust the expression of energy-consuming and energy-supplying metabolic pathways in order to maintain cellular redox balance. In this study, the transcriptional organization of the hrpB-actSR locus was determined and the effect of actSR system inactivation on stress resistance was investigated. It was found that hrpB is transcribed as a monocistronic mRNA and actS is transcribed along with actR as a bicistronic mRNA, while actR is also transcribed as a monocistronic message. Each message is initiated from a separate promoter. Inactivation of actR resulted in decreased resistance to membrane stress (sodium dodecyl sulfate), acid stress (pH 5.5), iron starvation (bipyridyl) and iron excess (FeCl3), and antibiotic stress (tetracycline and ciprofloxacin). Resistance to oxidative stress in the form of organic peroxide (cumene hydroperoxide) increased, while resistance to inorganic peroxide (H2O2) decreased. An actR insertion mutant displayed reduced catalase activity, even though transcription of katA and catE remained unchanged. Complementation of the actR inactivation mutant with plasmid-encoded actR or overexpression of hemH, encoding ferrochelatase, restored wild-type catalase activity and H2O2 resistance levels. Gel mobility shift and hemH promoter-lacZ fusion results indicated that ActR is a positive regulator of hemH that binds directly to the hemH promoter region. Thus, inactivation of the A. tumefaciens ActSR system affects resistance to multiple stresses, including reduced resistance to H2O2 resulting from a reduction in catalase activity due to reduced expression of hemH.
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Affiliation(s)
- Chitrasak Kullapanich
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - James M Dubbs
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Center of Excellence on Environmental Health and Toxicology, EHT Ministry of Education, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
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Moinier D, Byrne D, Amouric A, Bonnefoy V. The Global Redox Responding RegB/RegA Signal Transduction System Regulates the Genes Involved in Ferrous Iron and Inorganic Sulfur Compound Oxidation of the Acidophilic Acidithiobacillus ferrooxidans. Front Microbiol 2017; 8:1277. [PMID: 28747899 PMCID: PMC5506826 DOI: 10.3389/fmicb.2017.01277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/26/2017] [Indexed: 12/02/2022] Open
Abstract
The chemical attack of ore by ferric iron and/or sulfuric acid releases valuable metals. The products of these reactions are recycled by iron and sulfur oxidizing microorganisms. These acidophilic chemolithotrophic prokaryotes, among which Acidithiobacillus ferrooxidans, grow at the expense of the energy released from the oxidation of ferrous iron and/or inorganic sulfur compounds (ISCs). In At. ferrooxidans, it has been shown that the expression of the genes encoding the proteins involved in these respiratory pathways is dependent on the electron donor and that the genes involved in iron oxidation are expressed before those responsible for ISCs oxidation when both iron and sulfur are present. Since the redox potential increases during iron oxidation but remains stable during sulfur oxidation, we have put forward the hypothesis that the global redox responding two components system RegB/RegA is involved in this regulation. To understand the mechanism of this system and its role in the regulation of the aerobic respiratory pathways in At. ferrooxidans, the binding of different forms of RegA (DNA binding domain, wild-type, unphosphorylated and phosphorylated-like forms of RegA) on the regulatory region of different genes/operons involved in ferrous iron and ISC oxidation has been analyzed. We have shown that the four RegA forms are able to bind specifically the upstream region of these genes. Interestingly, the phosphorylation of RegA did not change its affinity for its cognate DNA. The transcriptional start site of these genes/operons has been determined. In most cases, the RegA binding site(s) was (were) located upstream from the −35 (or −24) box suggesting that RegA does not interfere with the RNA polymerase binding. Based on the results presented in this report, the role of the RegB/RegA system in the regulation of the ferrous iron and ISC oxidation pathways in At. ferrooxidans is discussed.
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Affiliation(s)
- Danielle Moinier
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille UniversitéMarseille, France
| | - Deborah Byrne
- Protein Expression Facility, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille UniversitéMarseille, France
| | - Agnès Amouric
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille UniversitéMarseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille UniversitéMarseille, France
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Mashruwala AA, Boyd JM. The Staphylococcus aureus SrrAB Regulatory System Modulates Hydrogen Peroxide Resistance Factors, Which Imparts Protection to Aconitase during Aerobic Growth. PLoS One 2017; 12:e0170283. [PMID: 28099473 PMCID: PMC5242492 DOI: 10.1371/journal.pone.0170283] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/03/2017] [Indexed: 01/09/2023] Open
Abstract
The SrrAB two-component regulatory system (TCRS) positively influences the transcription of genes involved in aerobic respiration in response to changes in respiratory flux. Hydrogen peroxide (H2O2) can arise as a byproduct of spontaneous interactions between dioxygen and components of respiratory pathways. H2O2 damages cellular factors including protein associated iron-sulfur cluster prosthetic groups. We found that a Staphylococcus aureus strain lacking the SrrAB two-component regulatory system (TCRS) is sensitive to H2O2 intoxication. We tested the hypothesis that SrrAB manages the mutually inclusive expression of genes required for aerobic respiration and H2O2 resistance. Consistent with our hypothesis, a ΔsrrAB strain had decreased transcription of genes encoding for H2O2 resistance factors (kat, ahpC, dps). SrrAB was not required for the inducing the transcription of these genes in cells challenged with H2O2. Purified SrrA bound to the promoter region for dps suggesting that SrrA directly influences dps transcription. The H2O2 sensitivity of the ΔsrrAB strain was alleviated by iron chelation or deletion of the gene encoding for the peroxide regulon repressor (PerR). The positive influence of SrrAB upon H2O2 metabolism bestowed protection upon the solvent accessible iron-sulfur (FeS) cluster of aconitase from H2O2 poisoning. SrrAB also positively influenced transcription of scdA (ytfE), which encodes for a FeS cluster repair protein. Finally, we found that SrrAB positively influences H2O2 resistance only during periods of high dioxygen-dependent respiratory activity. SrrAB did not influence H2O2 resistance when cellular respiration was diminished as a result of decreased dioxygen availability, and negatively influenced it in the absence of respiration (fermentative growth). We propose a model whereby SrrAB-dependent regulatory patterns facilitate the adaptation of cells to changes in dioxygen concentrations, and thereby aids in the prevention of H2O2 intoxication during respiratory growth upon dixoygen.
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Affiliation(s)
- Ameya A. Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
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Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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Coulson TJD, Patten CL. The TyrR transcription factor regulates the divergent akr-ipdC operons of Enterobacter cloacae UW5. PLoS One 2015; 10:e0121241. [PMID: 25811953 PMCID: PMC4374768 DOI: 10.1371/journal.pone.0121241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/30/2015] [Indexed: 12/11/2022] Open
Abstract
The TyrR transcription factor regulates genes involved in the uptake and biosynthesis of aromatic amino acids in Enterobacteriaceae. Genes may be positively or negatively regulated depending on the presence or absence of each aromatic amino acid, all three of which function as cofactors for TyrR. In this report we detail the transcriptional control of two divergently transcribed genes, akr and ipdC, by TyrR, elucidated by promoter fusion expression assays and electrophoretic mobility shift assays to assess protein-DNA interactions. Expression of both genes was shown to be controlled by TyrR via interactions with two TyrR boxes located within the akr-ipdC intergenic region. Expression of ipdC required TyrR bound to the proximal strong box, and is strongly induced by phenylalanine, and to a lesser extent by tryptophan and tyrosine. Down-regulation of akr was reliant on interactions with the weak box, and may also require a second, as yet unidentified protein for further repression. Tyrosine enhanced repression of akr. Electrophoretic mobility shift assays demonstrated that TyrR interacts with both the strong and weak boxes, and that binding of the weak box in vitro requires an intact adjacent strong box. While the strong box shows a high degree of conservation with the TyrR binding site consensus sequence, the weak box has atypical spacing of the two half sites comprising the palindromic arms. Site-directed mutagenesis demonstrated sequence-specific interaction between TyrR and the weak box. This is the first report of TyrR-controlled expression of two divergent protein-coding genes, transcribed from independent promoters. Moreover, the identification of a predicted aldo-keto reductase as a member of the TyrR regulon further extends the function of the TyrR regulon.
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Affiliation(s)
| | - Cheryl L. Patten
- Department of Biology, University of New Brunswick, Fredericton, Canada
- * E-mail:
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Imam S, Noguera DR, Donohue TJ. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 2014; 10:e1004837. [PMID: 25503406 PMCID: PMC4263372 DOI: 10.1371/journal.pgen.1004837] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 10/20/2014] [Indexed: 12/18/2022] Open
Abstract
Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis. Photosynthetic organisms are among the most abundant life forms on earth. Their unique ability to harvest solar energy and use it to fix atmospheric carbon dioxide is at the foundation of the global food chain. This paper reports the first comprehensive analysis of networks that control expression of photosynthesis genes using Rhodobacter sphaeroides, a microbe that has been studied for decades as a model of solar energy capture and other aspects of the photosynthetic lifestyle. We find a previously unappreciated complexity in the level of control of photosynthetic genes, while identifying new links between photosynthesis and central processes like iron availability. This organism is an ancestor of modern day plants, so our data can inform studies in other photosynthetic organisms and improve our ability to harness solar energy for food and industrial processes.
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Affiliation(s)
- Saheed Imam
- Program in Cellular and Molecular Biology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Bueno E, Mesa S, Bedmar EJ, Richardson DJ, Delgado MJ. Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. Antioxid Redox Signal 2012; 16:819-52. [PMID: 22098259 PMCID: PMC3283443 DOI: 10.1089/ars.2011.4051] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, CSIC, Granada, Spain
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Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology. J Bacteriol 2009; 191:4341-52. [PMID: 19411327 DOI: 10.1128/jb.00243-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus. Specific binding, as shown by competition experiments, requires the phosphorylation of PrrA. The binding affinity of PrrA for site 2 was found to increase 4- to 10-fold when spermidine was added to the binding reaction. The presence of extracellular concentrations of spermidine in growing cultures of R. sphaeroides gave rise to a twofold increase in the expression of the photosynthesis genes pucB and pufB, as well as the RSP3361 gene, under aerobic growth conditions, as shown by the use of lacZ transcriptional fusions, and led to the production of light-harvesting spectral complexes. In addition, we show that negative supercoiling positively regulates the expression of the RSP3361 gene, as well as pucB. We show the importance of supercoiling through an evaluation of the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as using the DNA gyrase inhibitor novobiocin. We propose that polyamines and DNA supercoiling act synergistically to regulate expression of the RSP3361 gene, partly by affecting the affinity of PrrA binding to the PrrA site 2 within the RSP3361 gene.
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