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Martínez LE, Gómez G, Ramírez N, Franco B, Robleto EA, Pedraza-Reyes M. 8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis. Antioxidants (Basel) 2024; 13:332. [PMID: 38539865 PMCID: PMC10968225 DOI: 10.3390/antiox13030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.
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Affiliation(s)
- Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Gerardo Gómez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Norma Ramírez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Bernardo Franco
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, NV 89557, USA;
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
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Marcos-Fernández R, Blanco-Míguez A, Ruiz L, Margolles A, Ruas-Madiedo P, Sánchez B. Towards the isolation of more robust next generation probiotics: The first aerotolerant Bifidobacterium bifidum strain. Food Res Int 2023; 165:112481. [PMID: 36869494 DOI: 10.1016/j.foodres.2023.112481] [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: 03/18/2022] [Revised: 11/20/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
This work reports on the first described aerotolerant Bifidobacterium bifidum strain, Bifidobacterium bifidum IPLA60003, which has the ability to form colonies on the surface of agar plates under aerobic conditions, a weird phenotype that to our knowledge has never been observed in B. bifidum. The strain IPLA60003 was generated after random UV mutagenesis from an intestinal isolate. It incorporates 26 single nucleotide polymorphisms that activate the expression of native oxidative-defense mechanisms such as the alkyl hydroxyperoxide reductase, the glycolytic pathway and several genes coding for enzymes involved in redox reactions. In the present work, we discuss the molecular mechanisms underlying the aerotolerance phenotype of B. bifidum IPLA60003, which will open new strategies for the selection and inclusion of probiotic gut strains and next generation probiotics into functional foods.
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Affiliation(s)
- Raquel Marcos-Fernández
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Aitor Blanco-Míguez
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Borja Sánchez
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
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Bacillus subtilis Stressosome Sensor Protein Sequences Govern the Ability To Distinguish among Environmental Stressors and Elicit Different σ B Response Profiles. mBio 2022; 13:e0200122. [PMID: 36409125 PMCID: PMC9765535 DOI: 10.1128/mbio.02001-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteria use a variety of systems to sense stress and mount an appropriate response to ensure fitness and survival. Bacillus subtilis uses stressosomes-cytoplasmic multiprotein complexes-to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σB. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σB response profiles with respect to timing and intensity when facing an identical stressor. Here, we use a similar approach to address the question of whether the σB responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σB with characteristic transient response timing irrespective of stressor but show various response magnitudes. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative, and acid stress, implying that RsbR proteins can distinguish among stressors. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argue that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σB response timing. IMPORTANCE Bacterial survival depends on appropriate responses to diverse stressors. The general stress-response system in the environmental model bacterium Bacillus subtilis is constantly poised for an immediate response and uses unusual stress-sensing protein complexes called stressosomes. Stressosomes typically contain four different types of putative sensing protein. We asked whether each type of sensor has a distinct role in mediating response dynamics to different environmental stressors. We find that one sensor type always mediates a transient response, while the others show distinct response magnitude and timing to different stressors. We also find that a transient response is exceptional, as several engineered hybrid proteins did not show strong transient responses. Our work reveals functional distinctions among subunits of the stressosome complex and represents a step toward understanding how the general stress response of B. subtilis ensures its survival in natural environmental settings.
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The Catalase KatA Contributes to Microaerophilic H2O2 Priming to Acquire an Improved Oxidative Stress Resistance in Staphylococcus aureus. Antioxidants (Basel) 2022; 11:antiox11091793. [PMID: 36139867 PMCID: PMC9495333 DOI: 10.3390/antiox11091793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus has to cope with oxidative stress during infections. In this study, S. aureus was found to be resistant to 100 mM H2O2 during aerobic growth. While KatA was essential for this high aerobic H2O2 resistance, the peroxiredoxin AhpC contributed to detoxification of 0.4 mM H2O2 in the absence of KatA. In addition, the peroxiredoxins AhpC, Tpx and Bcp were found to be required for detoxification of cumene hydroperoxide (CHP). The high H2O2 tolerance of aerobic S. aureus cells was associated with priming by endogenous H2O2 levels, which was supported by an oxidative shift of the bacillithiol redox potential to −291 mV compared to −310 mV in microaerophilic cells. In contrast, S. aureus could be primed by sub-lethal doses of 100 µM H2O2 during microaerophilic growth to acquire an improved resistance towards the otherwise lethal triggering stimulus of 10 mM H2O2. This microaerophilic priming was dependent on increased KatA activity, whereas aerobic cells showed constitutive high KatA activity. Thus, KatA contributes to the high H2O2 resistance of aerobic cells and to microaerophilic H2O2 priming in order to survive the subsequent lethal triggering doses of H2O2, allowing the adaptation of S. aureus under infections to different oxygen environments.
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Senges CHR, Warmuth HL, Vázquez-Hernández M, Uzun HD, Sagurna L, Dietze P, Schmidt C, Mücher B, Herlitze S, Krämer U, Ott I, Pomorski TG, Bandow JE. Effects of 4-Br-A23187 on Bacillus subtilis cells and unilamellar vesicles reveal it to be a potent copper ionophore. Proteomics 2022; 22:e2200061. [PMID: 35666003 PMCID: PMC10140759 DOI: 10.1002/pmic.202200061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/19/2022] [Accepted: 06/03/2022] [Indexed: 11/12/2022]
Abstract
Ionophores are small molecules or peptides that transport metal ions across biological membranes. Their transport capabilities are typically characterized in vitro using vesicles and single ion species. It is difficult to infer from these data which effects ionophores have on living cells in a complex environment (e.g. culture medium), since net ion movement is influenced by many factors including ion composition of the medium, concentration gradients, pH gradient, and protein-mediated transport processes across the membrane. To gain insights into the antibacterial mechanism of action of the semisynthetic polyether ionophore 4-Br-A23187, known to efficiently transport zinc and manganese in vitro, we investigated its effects on the gram-positive model organism Bacillus subtilis. In addition to monitoring cellular ion concentrations, the physiological impact of treatment was assessed on the proteome level. 4-Br-A23187 treatment resulted in an increase in intracellular copper levels, the extent of which depended on the copper concentration of the medium. Effects of copper accumulation mirrored by the proteomic response included oxidative stress, disturbance of proteostasis, metal and sulfur homeostasis. The antibiotic effect of 4-Br-A23187 is further aggravated by a decrease in intracellular manganese and magnesium. A liposome model confirmed that 4-Br-A23187 acts as copper ionophore in vitro. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Helen L Warmuth
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Melissa Vázquez-Hernández
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Huriye Deniz Uzun
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Leonie Sagurna
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Pascal Dietze
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Claudia Schmidt
- Inorganic and Organometallic Medicinal Chemistry, Faculty of Life Sciences, Technical University Braunschweig, 38106, Braunschweig, Germany.,Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Brix Mücher
- Department of Zoology and Neurobiology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Stefan Herlitze
- Department of Zoology and Neurobiology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
| | - Ingo Ott
- Inorganic and Organometallic Medicinal Chemistry, Faculty of Life Sciences, Technical University Braunschweig, 38106, Braunschweig, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801, Bochum, Germany
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García-Descalzo L, García-López E, Cid C. Comparative Proteomic Analysis of Psychrophilic vs. Mesophilic Bacterial Species Reveals Different Strategies to Achieve Temperature Adaptation. Front Microbiol 2022; 13:841359. [PMID: 35591995 PMCID: PMC9111180 DOI: 10.3389/fmicb.2022.841359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
The old debate of nature (genes) vs. nurture (environmental variables) is once again topical concerning the effect of climate change on environmental microorganisms. Specifically, the Polar Regions are experiencing a drastic increase in temperature caused by the rise in greenhouse gas emissions. This study, in an attempt to mimic the molecular adaptation of polar microorganisms, combines proteomic approaches with a classical microbiological analysis in three bacterial species Shewanella oneidensis, Shewanella frigidimarina, and Psychrobacter frigidicola. Both shewanellas are members of the same genus but they live in different environments. On the other hand, Shewanella frigidimarina and Psychrobacter frigidicola share the same natural environment but belong to a different genus. The comparison of the strategies employed by each bacterial species estimates the contribution of genome vs. environmental variables in the adaptation to temperature. The results show a greater versatility of acclimatization for the genus Shewanella with respect to Psychrobacter. Besides, S. frigidimarina was the best-adapted species to thermal variations in the temperature range 4–30°C and displayed several adaptation mechanisms common with the other two species. Regarding the molecular machinery used by these bacteria to face the consequences of temperature changes, chaperones have a pivoting role. They form complexes with other proteins in the response to the environment, establishing cooperation with transmembrane proteins, elongation factors, and proteins for protection against oxidative damage.
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Affiliation(s)
- Laura García-Descalzo
- Centro de Astrobiología, Department of Planetology and Habitability, CSIC-INTA, Madrid, Spain
| | - Eva García-López
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
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Tn
FLXopen
: Markerless Transposons for Functional Fluorescent Fusion Proteins and Protein Interaction Prediction. Microbiol Spectr 2022; 10:e0242821. [PMID: 35499319 PMCID: PMC9241775 DOI: 10.1128/spectrum.02428-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence microscopy of cells expressing proteins translationally linked to a fluorophore can be a powerful tool to investigate protein localization dynamics in vivo. One major obstacle to reliably analyze biologically relevant localization is the construction of a fusion protein that is both fluorescent and functional. Here, we develop a strategy to construct fluorescent fusions at theoretically any location in the protein by using TnFLXopen random transposon mutagenesis to randomly insert a gene encoding a fluorescent protein. Moreover, insertions within a target gene are enriched by an inducible gene-trap strategy and selection by fluorescence activated cell sorting. Using this approach, we isolate a variety of fluorescent fusions to FtsZ that exhibit ring-like localization and a fusion to the flagellar stator protein that both is functional for supporting motility and localizes as fluorescent puncta. Finally, we further modify TnFLXopen to insert the coding sequence for the C-terminal half of mVenus for use in bimolecular fluorescence complementation (BiFC) and the in vivo detection of protein-protein interaction candidates. As proof-of-concept, the DivIVA polar scaffolding protein was fused to the N terminus of mVenus, the C terminus of mVenus was delivered by transposition, and a combination of fluorescence activated cell sorter (FACS) sorting and whole-genome sequencing identified the known self-interaction of DivIVA as well as other possible candidate interactors. We suggest that the FACS selection is a viable alternative to antibiotic selection in transposon mutagenesis that can generate new fluorescent tools for in vivo protein characterization. IMPORTANCE Transposon mutagenesis is a powerful tool for random mutagenesis, as insertion of a transposon and accompanying antibiotic resistance cassette often disrupt gene function. Here, we present a series of transposons with fluorescent protein genes which, when integrated in frame, may be selected with a fluorescence activated cell sorter (FACS). An open reading frame runs continuously through the transposon such that fluorescent protein fusions may be inserted theoretically anywhere in the primary sequence and potentially preserve function of the target protein. Finally, the transposons were further modified to randomly insert a partial fluorescent protein compatible with bimolecular fluorescence complementation (BiFC) to identify protein interaction candidates.
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Roth M, Jaquet V, Lemeille S, Bonetti EJ, Cambet Y, François P, Krause KH. Transcriptomic Analysis of E. coli after Exposure to a Sublethal Concentration of Hydrogen Peroxide Revealed a Coordinated Up-Regulation of the Cysteine Biosynthesis Pathway. Antioxidants (Basel) 2022; 11:antiox11040655. [PMID: 35453340 PMCID: PMC9026346 DOI: 10.3390/antiox11040655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a key defense component of host-microbe interaction. However, H2O2 concentrations generated by immune cells or epithelia are usually insufficient for bacterial killing and rather modulate bacterial responses. Here, we investigated the impact of sublethal H2O2 concentration on gene expression of E. coli BW25113 after 10 and 60 min of exposure. RNA-seq analysis revealed that approximately 12% of bacterial genes were strongly dysregulated 10 min following exposure to 2.5 mM H2O2. H2O2 exposure led to the activation of a specific antioxidant response and a general stress response. The latter was characterized by a transient down-regulation of genes involved in general metabolism, such as nucleic acid biosynthesis and translation, with a striking and coordinated down-regulation of genes involved in ribosome formation, and a sustained up-regulation of the SOS response. We confirmed the rapid transient and specific response mediated by the transcription factor OxyR leading to up-regulation of antioxidant systems, including the catalase-encoding gene (katG), that rapidly degrade extracellular H2O2 and promote bacterial survival. We documented a strong and transient up-regulation of genes involved in sulfur metabolism and cysteine biosynthesis, which are under the control of the transcription factor CysB. This strong specific transcriptional response to H2O2 exposure had no apparent impact on bacterial survival, but possibly replenishes the stores of oxidized cysteine and glutathione. In summary, our results demonstrate that different stress response mechanisms are activated by H2O2 exposure and highlight the cysteine synthesis as an antioxidant response in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- Correspondence: ; Tel.: +41-223-794-257
| | - Vincent Jaquet
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Sylvain Lemeille
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Yves Cambet
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
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Constructing of Bacillus subtilis-Based Lux-Biosensors with the Use of Stress-Inducible Promoters. Int J Mol Sci 2021; 22:ijms22179571. [PMID: 34502476 PMCID: PMC8431380 DOI: 10.3390/ijms22179571] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we present a new lux-biosensor based on Bacillus subtilis for detecting of DNA-tropic and oxidative stress-causing agents. Hybrid plasmids pNK-DinC, pNK-AlkA, and pNK-MrgA have been constructed, in which the Photorhabdus luminescens reporter genes luxABCDE are transcribed from the stress-inducible promoters of B. subtilis: the SOS promoter PdinC, the methylation-specific response promoter PalkA, and the oxidative stress promoter PmrgA. The luminescence of B. subtilis-based biosensors specifically increases in response to the appearance in the environment of such common toxicants as mitomycin C, methyl methanesulfonate, and H2O2. Comparison with Escherichia coli-based lux-biosensors, where the promoters PdinI, PalkA, and Pdps were used, showed generally similar characteristics. However, for B. subtilis PdinC, a higher response amplitude was observed, and for B. subtilis PalkA, on the contrary, both the amplitude and the range of detectable toxicant concentrations were decreased. B. subtilis PdinC and B. subtilis PmrgA showed increased sensitivity to the genotoxic effects of the 2,2'-bis(bicyclo [2.2.1] heptane) compound, which is a promising propellant, compared to E. coli-based lux-biosensors. The obtained biosensors are applicable for detection of toxicants introduced into soil. Such bacillary biosensors can be used to study the differences in the mechanisms of toxicity against Gram-positive and Gram-negative bacteria.
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10
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SigB regulates stress resistance, glucose starvation, MnSOD production, biofilm formation, and root colonization in Bacillus cereus 905. Appl Microbiol Biotechnol 2021; 105:5943-5957. [PMID: 34350477 DOI: 10.1007/s00253-021-11402-y] [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: 01/26/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 10/20/2022]
Abstract
Bacillus cereus 905, originally isolated from wheat rhizosphere, exhibits strong colonization ability on wheat roots. Our previous studies showed that root colonization is contributed by the ability of the bacterium to efficiently utilize carbon sources and form biofilms and that the sodA2 gene-encoded manganese-containing superoxide dismutase (MnSOD2) plays an indispensable role in the survival of B. cereus 905 in the wheat rhizosphere. In this investigation, we further demonstrated that the ability of B. cereus 905 to resist adverse environmental conditions is partially attributed to activation of the alternative sigma factor σB, encoded by the sigB gene. The sigB mutant experienced a dramatic reduction in survival when cells were exposed to ethanol, acid, heat, and oxidative stress or under glucose starvation. Analysis of the sodA2 gene transcription revealed a partial, σB-dependent induction of the gene during glucose starvation or when treated with paraquat. In addition, the sigB mutant displayed a defect in biofilm formation under stress conditions. Finally, results from the root colonization assay indicated that sigB and sodA2 collectively contribute to B. cereus 905 colonization on wheat roots. Our study suggests a diverse role of SigB in rhizosphere survival and root colonization of B. cereus 905 under stress conditions. KEY POINTS : • SigB confers resistance to environmental stresses in B. cereus 905. • SigB plays a positive role in glucose utilization and biofilm formation in B. cereus. • SigB and SodA2 collectively contribute to colonization on wheat roots by B. cereus.
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11
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Wan F, Feng X, Yin J, Gao H. Distinct H 2O 2-Scavenging System in Yersinia pseudotuberculosis: KatG and AhpC Act Together to Scavenge Endogenous Hydrogen Peroxide. Front Microbiol 2021; 12:626874. [PMID: 34025596 PMCID: PMC8139631 DOI: 10.3389/fmicb.2021.626874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/22/2021] [Indexed: 01/09/2023] Open
Abstract
To colonize in the digestive tract of animals and humans, Yersinia pseudotuberculosis has to deal with reactive oxygen species (ROS) produced by host cells and microbiota. However, an understanding of the ROS-scavenging systems and their regulation in this bacterium remains largely elusive. In this study, we identified OxyR as the master transcriptional regulator mediating cellular responses to hydrogen peroxide (H2O2) in Y. pseudotuberculosis through genomics and transcriptomics analyses. OxyR activates transcription of diverse genes, especially the core members of its regulon, including those encoding catalases, peroxidases, and thiol reductases. The data also suggest that sulfur species and manganese may play a particular role in the oxidative stress response of Y. pseudotuberculosis. Among the three H2O2-scavenging systems in Y. pseudotuberculosis, catalase/peroxidase KatE functions as the primary scavenger for high levels of H2O2; NADH peroxidase alkyl hydroperoxide reductase (AhpR) and catalase KatG together are responsible for removing low levels of H2O2. The simultaneous loss of both AhpC (the peroxidatic component of AhpR) and KatG results in activation of OxyR. Moreover, we found that AhpC, unlike its well-characterized Escherichia coli counterpart, has little effect on protecting cells against toxicity of organic peroxides. These findings provide not only novel insights into the structural and functional diversity of bacterial H2O2-scavenging systems but also a basic understanding of how Y. pseudotuberculosis copes with oxidative stress.
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Affiliation(s)
- Fen Wan
- College of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xue Feng
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhenjiang University of Technology, Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, China
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12
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Ichikawa S, Tsuge Y, Karita S. Metabolome Analysis of Constituents in Membrane Vesicles for Clostridium thermocellum Growth Stimulation. Microorganisms 2021; 9:microorganisms9030593. [PMID: 33805707 PMCID: PMC8002186 DOI: 10.3390/microorganisms9030593] [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: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 11/24/2022] Open
Abstract
The cultivation of the cellulolytic bacterium, Clostridium thermocellum, can have cost-effective cellulosic biomass utilizations, such as consolidated bioprocessing, simultaneous biological enzyme production and saccharification. However, these processes require a longer cultivation term of approximately 1 week. We demonstrate that constituents of the C. thermocellum membrane vesicle fraction significantly promoted the growth rate of C. thermocellum. Similarly, cell-free Bacillus subtilis broth was able to increase C. thermocellum growth rate, while several B. subtilis single-gene deletion mutants, e.g., yxeJ, yxeH, ahpC, yxdK, iolF, decreased the growth stimulation ability. Metabolome analysis revealed signal compounds for cell–cell communication in the C. thermocellum membrane vesicle fraction (ethyl 2-decenoate, ethyl 4-decenoate, and 2-dodecenoic acid) and B. subtilis broth (nicotinamide, indole-3-carboxaldehyde, urocanic acid, nopaline, and 6-paradol). These findings suggest that the constituents in membrane vesicles from C. thermocellum and B. subtilis could promote C. thermocellum growth, leading to improved efficiency of cellulosic biomass utilization.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
- Correspondence: ; Tel.: +89-59-231-9254; Fax: +89-59-231-9352
| | - Yoichiro Tsuge
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan;
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13
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Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [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: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
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14
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Hong SH, Singh S, Tripathi BN, Mondal S, Lee S, Jung HS, Cho C, Kaur S, Kim JH, Lee S, Bai HW, Bae HJ, Lee SY, Lee SS, Chung BY. Functional properties and the oligomeric state of alkyl hydroperoxide reductase subunit F (AhpF) in Pseudomonas aeruginosa. PROTOPLASMA 2020; 257:807-817. [PMID: 31909437 DOI: 10.1007/s00709-019-01465-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Alkyl hydroperoxide reductase subunit F (AhpF) is a well-known flavoprotein that transfers electrons from pyridine nucleotides to the peroxidase protein AhpC via redox-active disulfide centers to detoxify hydrogen peroxide. However, study of AhpF has historically been limited to particular eubacteria, and the connection between the functional and structural properties of AhpF remains unknown. The present study demonstrates the dual function of Pseudomonas aeruginosa AhpF (PaAhpF) as a reductase and a molecular chaperone. It was observed that the functions of PaAhpF are closely linked with its structural status. The reductase and foldase chaperone function of PaAhpF predominated for its low-molecular-weight (LMW) form, whereas the holdase chaperone function of PaAhpF was found associated with its high-molecular-weight (HMW) complex. Further, the present study also demonstrates the multiple function of PaAhpF in controlling oxidative and heat stresses in P. aeruginosa resistance to oxidative and heat stress.
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Affiliation(s)
- Sung Hyun Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Sudhir Singh
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Bhumi Nath Tripathi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, 484887, India
| | - Suvendu Mondal
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Sangmin Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, South Korea
| | - Chuloh Cho
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
| | - Shubhpreet Kaur
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
| | - Sungbeom Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyoung-Woo Bai
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyeun-Jong Bae
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju, 52828, South Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea.
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, South Korea.
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, South Korea.
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15
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Nguyen HTM, Akanuma G, Hoa TTM, Nakai Y, Kimura K, Yamamoto K, Inaoka T. Ribosome Reconstruction during Recovery from High-Hydrostatic-Pressure-Induced Injury in Bacillus subtilis. Appl Environ Microbiol 2019; 86:e01640-19. [PMID: 31604775 PMCID: PMC6912085 DOI: 10.1128/aem.01640-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetative cells of Bacillus subtilis can recover from injury after high-hydrostatic-pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that substantial numbers of ribosomal genes and translation-related genes (e.g., translation initiation factors) were upregulated during the growth arrest phase after HHP treatment. The transcript levels of cold shock-responsive genes, whose products play key roles in efficient translation, and heat shock-responsive genes, whose products mediate correct protein folding or degrade misfolded proteins, were also upregulated. In contrast, the transcript level of hpf, whose product (Hpf) is involved in ribosome inactivation through the dimerization of 70S ribosomes, was downregulated during the growth arrest phase. Sucrose density gradient sedimentation analysis revealed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed. We also found that cell growth after HHP-induced injury was apparently inhibited by the addition of Mn2+ or Zn2+ to the recovery medium. Ribosome reconstruction in the HHP-injured cells was also significantly delayed in the presence of Mn2+ or Zn2+ Moreover, Zn2+, but not Mn2+, promoted dimer formation of 70S ribosomes in the HHP-injured cells. Disruption of the hpf gene suppressed the Zn2+-dependent accumulation of ribosome dimers, partially relieving the inhibitory effect of Zn2+ on the growth recovery of HHP-treated cells. In contrast, it was likely that Mn2+ prevented ribosome reconstruction without stimulating ribosome dimerization. Our results suggested that both Mn2+ and Zn2+ can prevent ribosome reconstruction, thereby delaying the growth recovery of HHP-injured B. subtilis cells.IMPORTANCE HHP treatment is used as a nonthermal processing technology in the food industry to inactivate bacteria while retaining high quality of foods under suppressed chemical reactions. However, some populations of bacterial cells may survive the inactivation. Although the survivors are in a transient nongrowing state due to HHP-induced injury, they can recover from the injury and then start growing, depending on the postprocessing conditions. The recovery process in terms of cellular components after the injury remains unclear. Transcriptome analysis using vegetative cells of Bacillus subtilis revealed that the translational machinery can preferentially be reconstructed after HHP treatment. We found that both Mn2+ and Zn2+ prolonged the growth-arrested stage of HHP-injured cells by delaying ribosome reconstruction. It is likely that ribosome reconstruction is crucial for the recovery of growth ability in HHP-injured cells. This study provides further understanding of the recovery process in HHP-injured B. subtilis cells.
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Affiliation(s)
- Huyen Thi Minh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | | | - Tu Thi Minh Hoa
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Yuji Nakai
- Institute of Regional Innovation, Hirosaki University, Aomori, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kazutaka Yamamoto
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Takashi Inaoka
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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16
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Clemente A, Ramsden JJ, Wright A, Iza F, Morrissey JA, Li Puma G, Malik DJ. Staphylococcus aureus resists UVA at low irradiance but succumbs in the presence of TiO2 photocatalytic coatings. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 193:131-139. [PMID: 30851512 DOI: 10.1016/j.jphotobiol.2019.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Accepted: 02/25/2019] [Indexed: 11/25/2022]
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17
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Kiran MD, Bala S, Hirshberg M, Balaban N. YhgC protects Bacillus anthracis from oxidative stress. Int J Artif Organs 2018. [DOI: 10.1177/039139881003300905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bacillus anthracis can cause lethal inhalational anthrax and can be used as a bioweapon due to its ability to form spores and to survive under various environmental stress conditions. YhgC in bacilli are structural homologues of TRAP, a protein involved in stress response in staphylococci. To test the role of YhgC in B. anthracis, YhgC gene was deleted in B. anthracis strain Sterne and parent and mutant strains tested. Immunolocalization studies indicated that YhgC is clustered both on the cell surface and within the cytoplasm. Phenotypic analyses indicated that YhgC is an important factor for oxidative stress tolerance and for macrophage infection in vitro. Accordingly, transcriptomics studies indicated that yhgC has a profound effect on genes encoding for stress response regulatory proteins where it negatively regulates the expression of genes encoding for Class I and Class III stress response proteins belonging to the regulons hrcA (hrcA, grpE, dnaK, dnaJ, groEL and groES) and ctsR (ctsR, mcsA, mcsB, clpC/mecB, clpP1). Proteomics studies also indicated that YhgC positively regulates the expression of ClpP-2 and camelysin, which are proteins involved in adaptive responses and pathogenesis in various Gram-positive bacteria. Put together, these results suggest that YhgC is important for the survival of B. anthracis under oxidative stress conditions and thus inhibition of YhgC may compromise the ability of the bacteria to survive within the host.
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Affiliation(s)
- Madanahally D. Kiran
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA - USA
- IQUUM Inc, Marlborough MA - USA
| | - Shashi Bala
- University of Massachusetts Medical School, Worcester, MA - USA
| | - Miriam Hirshberg
- EMBL Outstation – Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge - United Kingdom
| | - Naomi Balaban
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA - USA
- Yale University, Department of Chemical Engineering, New Haven, CT - USA
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18
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Reuß DR, Altenbuchner J, Mäder U, Rath H, Ischebeck T, Sappa PK, Thürmer A, Guérin C, Nicolas P, Steil L, Zhu B, Feussner I, Klumpp S, Daniel R, Commichau FM, Völker U, Stülke J. Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism. Genome Res 2016; 27:289-299. [PMID: 27965289 PMCID: PMC5287234 DOI: 10.1101/gr.215293.116] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/01/2016] [Indexed: 11/24/2022]
Abstract
Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium, Bacillus subtilis, whose genomes have been reduced by ∼36%. These strains are fully viable, and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism. A comparison of gene counts and resource allocation demonstrates drastic differences in the two parameters, with 50% of the genes using as little as 10% of translation capacity, whereas the 6% essential genes require 57% of the translation resources. Taken together, the results are a valuable resource on gene dispensability in B. subtilis, and they suggest the roads to further genome reduction to approach the final aim of a minimal cell in which all functions are understood.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Praveen Kumar Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Cyprien Guérin
- MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pierre Nicolas
- MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Stefan Klumpp
- Institute for Nonlinear Dynamics, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
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19
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Zwick JV, Noble S, Ellaicy YK, Coe GD, Hakey DJ, King AN, Sadauskas AJ, Faulkner MJ. AhpA is a peroxidase expressed during biofilm formation in Bacillus subtilis. Microbiologyopen 2016; 6. [PMID: 27683249 PMCID: PMC5300871 DOI: 10.1002/mbo3.403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 11/10/2022] Open
Abstract
Organisms growing aerobically generate reactive oxygen species such as hydrogen peroxide. These reactive oxygen molecules damage enzymes and DNA, potentially causing cell death. In response, Bacillus subtilis produces at least nine potential peroxide-scavenging enzymes; two belong to the alkylhydroperoxide reductase (Ahp) class of peroxidases. Here, we explore the role of one of these Ahp homologs, AhpA. While previous studies demonstrated that AhpA can scavenge peroxides and thus defend cells against peroxides, they did not clarify when during growth the cell produces AhpA. The results presented here show that the expression of ahpA is regulated in a manner distinct from that of the other peroxide-scavenging enzymes in B. subtilis. While the primary Ahp, AhpC, is expressed during exponential growth and stationary phase, these studies demonstrate that the expression of ahpA is dependent on the transition-state regulator AbrB and the sporulation and biofilm formation transcription factor Spo0A. Furthermore, these results show that ahpA is specifically expressed during biofilm formation, and not during sporulation or stationary phase, suggesting that derepression of ahpA by AbrB requires a signal other than those present upon entry into stationary phase. Despite this expression pattern, ahpA mutant strains still form and maintain robust biofilms, even in the presence of peroxides. Thus, the role of AhpA with regard to protecting cells within biofilms from environmental stresses is still uncertain. These studies highlight the need to further study the Ahp homologs to better understand how they differ from one another and the unique roles they may play in oxidative stress resistance.
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Affiliation(s)
- Joelie V Zwick
- Department of Biology, Bradley University, Peoria, IL, USA
| | - Sarah Noble
- Department of Biology, Bradley University, Peoria, IL, USA
| | | | | | - Dylan J Hakey
- Department of Biology, Bradley University, Peoria, IL, USA
| | - Alyssa N King
- Department of Biology, Bradley University, Peoria, IL, USA
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20
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Singh S, Dwivedi SK, Singh VS, Tripathi AK. Expression of alkyl hydroperoxide reductase is regulated negatively by OxyR1 and positively by RpoE2 sigma factor in Azospirillum brasilense Sp7. MICROBIOLOGY-SGM 2016; 162:1870-1883. [PMID: 27557935 DOI: 10.1099/mic.0.000363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OxyR proteins are LysR-type transcriptional regulators, which play an important role in responding to oxidative stress in bacteria. Azospirillum brasilense Sp7 harbours two copies of OxyR. The inactivation of the oxyR1, the gene organized divergently to ahpC in A. brasilense Sp7, led to an increased tolerance to alkyl hydroperoxides, which was corroborated by an increase in alkyl hydroperoxide reductase (AhpC) activity, enhanced expression of ahpC :lacZ fusion and increased synthesis of AhpC protein in the oxyR1::km mutant. The upstream region of ahpC promoter harboured a putative OxyR binding site, T-N11-A. Mutation of T, A or both in the T-N11-Amotif caused derepression of ahpC in A. brasilense suggesting that T-N11-A might be the binding site for a negative regulator. Retardation of the electrophoretic mobility of the T-N11-A motif harbouring oxyR1-ahpC intergenic DNA by recombinant OxyR1, under reducing as well as oxidizing conditions, indicated that OxyR1 acts as a negative regulator of ahpC in A. brasilense. Sequence of the promoter of ahpC, predicted on the basis of transcriptional start site, and an enhanced expression of ahpC:lacZ fusion in chrR2::km mutant background suggested that ahpC promoter was RpoE2 dependent. Thus, this study shows that in A. brasilense Sp7, ahpC expression is regulated negatively by OxyR1 but is regulated positively by RpoE2, an oxidative-stress-responsive sigma factor. It also shows that OxyR1 regulates the expression RpoE1, which is known to play an important role during photooxidative stress in A. brasilense.
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Affiliation(s)
- Sudhir Singh
- Laboratory of Bacterial Genetics, Faculty of Science, School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Susheel Kumar Dwivedi
- Laboratory of Bacterial Genetics, Faculty of Science, School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Vijay Shankar Singh
- Laboratory of Bacterial Genetics, Faculty of Science, School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Anil Kumar Tripathi
- Laboratory of Bacterial Genetics, Faculty of Science, School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
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21
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Shrivastava AK, Pandey S, Yadav S, Mishra Y, Singh PK, Rai R, Singh S, Rai S, Rai LC. Comparative proteomics of wild type, An+ahpC and An∆ahpC strains of Anabaena sp. PCC7120 demonstrates AhpC mediated augmentation of photosynthesis, N2-fixation and modulation of regulatory network of antioxidative proteins. J Proteomics 2016; 140:81-99. [PMID: 27102494 DOI: 10.1016/j.jprot.2016.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 12/30/2022]
Abstract
UNLABELLED Alkylhydroperoxide reductase (AhpC), a 1-Cys peroxiredoxin is well known for maintaining the cellular homeostasis. Present study employs proteome approach to analyze and compare alterations in proteome of Anabaena PCC7120 in overexpressing (An+ahpC), deletion (An∆ahpC) and its wild type. 2-DE based analysis revealed that the major portion of identified protein belongs to energy metabolism, protein folding, modification and stress related proteins and carbohydrate metabolism. The two major traits discernible from An+ahpC were (i) augmentation of photosynthesis and nitrogen fixation (ii) modulation of regulatory network of antioxidative proteins. Increased accumulation of proteins of light reaction, dark reaction, pentose phosphate pathway and electron transfer agent FDX for nitrogenase in An+ahpC and their simultaneous downregulation in AnΔahpC demonstrates its role in augmenting photosynthesis and nitrogen fixation. Proteomic data was nicely corroborated with physiological, biochemical parameters displaying upregulation of nitrogenase (1.6 fold) PSI (1.08) and PSII (2.137) in An+ahpC. Furthermore, in silico analysis not only attested association of AhpC with peroxiredoxins but also with other players of antioxidative defense system viz. thioredoxin and thioredoxin reductase. Above mentioned findings are in agreement with 33-40% and 40-60% better growth performance of An+ahpC over wild type and An∆ahpC respectively under abiotic stresses, suggesting its role in maintenance of metabolic machinery under stress. SIGNIFICANCE Present work explores key role of AhpC in mitigating stress in Anabaena PCC7120 through combined proteomic, biochemical and in silico investigations. This study is the first attempt to analyze and compare alterations in proteome of Anabaena PCC7120 following addition (overexpressing strain An+ahpC) and deletion (mutant An∆ahpC) of AhpC against its wild type. The effort resulted in two major traits in An+ahpC as (i) augmentation of photosynthesis and nitrogen fixation (ii) modulation of regulatory network of antioxidative proteins.
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Affiliation(s)
- Alok K Shrivastava
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sarita Pandey
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Yogesh Mishra
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Prashant K Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ruchi Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Snigdha Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Insights into the Function of a Second, Nonclassical Ahp Peroxidase, AhpA, in Oxidative Stress Resistance in Bacillus subtilis. J Bacteriol 2016; 198:1044-57. [PMID: 26787766 DOI: 10.1128/jb.00679-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 01/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Organisms growing aerobically generate reactive oxygen-containing molecules, such as hydrogen peroxide (H2O2). These reactive oxygen molecules damage enzymes and DNA and may even cause cell death. In response, Bacillus subtilis produces at least nine potential peroxide-scavenging enzymes, two of which appear to be the primary enzymes responsible for detoxifying peroxides during vegetative growth: a catalase (encoded by katA) and an alkylhydroperoxide reductase (Ahp, encoded by ahpC). AhpC uses two redox-active cysteine residues to reduce peroxides to nontoxic molecules. A specialized thioredoxin-like protein, AhpF, is then required to restore oxidized AhpC back to its reduced state. Curiously, B. subtilis has two genes encoding Ahp: ahpC and ahpA. Although AhpC is well characterized, very little is known about AhpA. In fact, numerous bacterial species have multiple ahp genes; however, these additional Ahp proteins are generally uncharacterized. We seek to understand the role of AhpA in the bacterium's defense against toxic peroxide molecules in relation to the roles previously assigned to AhpC and catalase. Our results demonstrate that AhpA has catalytic activity similar to that of the primary enzyme, AhpC. Furthermore, our results suggest that a unique thioredoxin redox protein, AhpT, may reduce AhpA upon its oxidation by peroxides. However, unlike AhpC, which is expressed well during vegetative growth, our results suggest that AhpA is expressed primarily during postexponential growth. IMPORTANCE B. subtilis appears to produce nine enzymes designed to protect cells against peroxides; two belong to the Ahp class of peroxidases. These studies provide an initial characterization of one of these Ahp homologs and demonstrate that the two Ahp enzymes are not simply replicates of each other, suggesting that they instead are expressed at different times during growth of the cells. These results highlight the need to further study the Ahp homologs to better understand how they differ from one another and to identify their function, if any, in protection against oxidative stress. Through these studies, we may better understand why bacteria have multiple enzymes designed to scavenge peroxides and thus have a more accurate understanding of oxidative stress resistance.
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Gambino M, Marzano V, Villa F, Vitali A, Vannini C, Landini P, Cappitelli F. Effects of sublethal doses of silver nanoparticles on Bacillus subtilis
planktonic and sessile cells. J Appl Microbiol 2015; 118:1103-15. [DOI: 10.1111/jam.12779] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/10/2015] [Accepted: 02/14/2015] [Indexed: 01/01/2023]
Affiliation(s)
- M. Gambino
- Department of Biosciences; Università degli Studi di Milano; Milan Italy
| | - V. Marzano
- Institute of Chemistry of Molecular Recognition; Consiglio Nazionale delle Ricerche (CNR); Rome Italy
| | - F. Villa
- Department of Food, Environmental and Nutritional Sciences; Università degli Studi di Milano; Milan Italy
| | - A. Vitali
- Institute of Chemistry of Molecular Recognition; Consiglio Nazionale delle Ricerche (CNR); Rome Italy
| | - C. Vannini
- Department of Biotecnology and Life Science; Università degli Studi dell'Insubria; Varese Italy
| | - P. Landini
- Department of Biosciences; Università degli Studi di Milano; Milan Italy
| | - F. Cappitelli
- Department of Food, Environmental and Nutritional Sciences; Università degli Studi di Milano; Milan Italy
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Maaβ S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics 2014; 13:2260-76. [PMID: 24878497 PMCID: PMC4159648 DOI: 10.1074/mcp.m113.035741] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Systems biology based on high quality absolute quantification data, which are mandatory for the simulation of biological processes, successively becomes important for life sciences. We provide protein concentrations on the level of molecules per cell for more than 700 cytosolic proteins of the Gram-positive model bacterium Bacillus subtilis during adaptation to changing growth conditions. As glucose starvation and heat stress are typical challenges in B. subtilis' natural environment and induce both, specific and general stress and starvation proteins, these conditions were selected as models for starvation and stress responses. Analyzing samples from numerous time points along the bacterial growth curve yielded reliable and physiologically relevant data suitable for modeling of cellular regulation under altered growth conditions. The analysis of the adaptational processes based on protein molecules per cell revealed stress-specific modulation of general adaptive responses in terms of protein amount and proteome composition. Furthermore, analysis of protein repartition during glucose starvation showed that biomass seems to be redistributed from proteins involved in amino acid biosynthesis to enzymes of the central carbon metabolism. In contrast, during heat stress most resources of the cell, namely those from amino acid synthetic pathways, are used to increase the amount of chaperones and proteases. Analysis of dynamical aspects of protein synthesis during heat stress adaptation revealed, that these proteins make up almost 30% of the protein mass accumulated during early phases of this stress.
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Affiliation(s)
- Sandra Maaβ
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Gerhild Wachlin
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Christine Eymann
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Vincent Fromion
- §INRA, Mathématique Informatique et Génome UR1077, 78350 Jouy-en-Josas, France
| | - Katharina Riedel
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany;
| | - Michael Hecker
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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25
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Zuo F, Yu R, Khaskheli GB, Ma H, Chen L, Zeng Z, Mao A, Chen S. Homologous overexpression of alkyl hydroperoxide reductase subunit C (ahpC) protects Bifidobacterium longum strain NCC2705 from oxidative stress. Res Microbiol 2014; 165:581-9. [PMID: 24953679 DOI: 10.1016/j.resmic.2014.05.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/14/2014] [Accepted: 05/30/2014] [Indexed: 11/30/2022]
Abstract
The ability to manage reactive oxygen species (ROS) effectively is crucial for the survival of gut bifidobacteria under conditions of oxidative stress. Alkyl hydroperoxide reductase catalytic subunit C (ahpC) of Bifidobacterium longum responds to various oxidative stresses. In this study, an ahpC-overexpressing transformant of B. longum strain NCC2705 was constructed to investigate the role and function of ahpC in oxidative stresses inflicted by treatments with hydrogen peroxide (H2O2), cumene hydroperoxide, and aerobic oxygen. Results indicated that in B. longum, AhpC is the primary scavenger of endogenous H2O2 generated by aerobic metabolism, but it is unable to detoxify high concentrations of exogenous H2O2. The ahpC-overexpressing B. longum strain showed increased resistance to organic hydroperoxide killing, increased viability under aerobic growth, but decreased resistance to exogenous H2O2 in comparison to the control strain. Analysis of genes from the oxidative stress-defense pathway encoding oxygen-independent coproporphyrinogen III oxidase (HemN), NADH oxidase (Nox) and thioredoxin reductase-like protein (TrxB) showed increased transcript levels in the ahpC-overexpressing vs. control strain. These findings suggest that elevated ahpC expression facilitates or activates the different electron donor-dependent ROS-elimination pathways in B. longum's response to oxidative stress.
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Affiliation(s)
- FangLei Zuo
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
| | - Rui Yu
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
| | - Gul Bahar Khaskheli
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
| | - HuiQin Ma
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China.
| | - LiLi Chen
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
| | - Zhu Zeng
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China.
| | - AiJun Mao
- Beijing Agricultural Function Microbial Engineering and Technology Center, No. 1 Li'ersi Industrial Area, Zhangjiawan Town, Tongzhou District, Beijing 101113, PR China.
| | - ShangWu Chen
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Qinghua East Road, Haidian District, Beijing 100083, PR China; Beijing Agricultural Function Microbial Engineering and Technology Center, No. 1 Li'ersi Industrial Area, Zhangjiawan Town, Tongzhou District, Beijing 101113, PR China.
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26
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Raatschen N, Wenzel M, Ole Leichert LI, Düchting P, Krämer U, Bandow JE. Extracting iron and manganese from bacteria with ionophores - a mechanism against competitors characterized by increased potency in environments low in micronutrients. Proteomics 2013; 13:1358-70. [PMID: 23412951 DOI: 10.1002/pmic.201200556] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 01/24/2013] [Accepted: 01/31/2013] [Indexed: 11/10/2022]
Abstract
To maintain their metal ion homeostasis, bacteria critically depend on membrane integrity and controlled ion translocation. Terrestrial Streptomyces species undermine the function of the cytoplasmic membrane as diffusion barrier for metal cations in competitors using ionophores. Although the properties of the divalent cation ionophores calcimycin and ionomycin have been characterized to some extent in vitro, their effects on bacterial ion homeostasis, the factors leading to bacterial cell death, and their ecological role are poorly understood. To gain insight into their antibacterial mechanism, we determined the metal ion composition of the soil bacterium Bacillus subtilis after treatment with calcimycin and ionomycin. Within 15 min the cells lost approximately half of their cellular iron and manganese content whereas calcium levels increased. The proteomic response of B. subtilis provided evidence that disturbance of metal cation homeostasis is accompanied by intracellular oxidative stress, which was confirmed with a ROS-specific fluorescent probe. B. subtilis showed enhanced sensitivity to the ionophores in medium lacking iron or manganese. Furthermore, in the presence of ionophores bacteria were sensitive to high calcium levels. These findings suggest that divalent cation ionophores are particularly effective against competing microorganisms in soils rich in available calcium and low in available iron and manganese.
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Affiliation(s)
- Nadja Raatschen
- Biology of Microorganisms, Ruhr University Bochum, Bochum, Germany
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27
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Al Dahouk S, Jubier-Maurin V, Neubauer H, Köhler S. Quantitative analysis of the Brucella suis proteome reveals metabolic adaptation to long-term nutrient starvation. BMC Microbiol 2013; 13:199. [PMID: 24007556 PMCID: PMC3844638 DOI: 10.1186/1471-2180-13-199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the infection process, bacteria are confronted with various stress factors including nutrient starvation. In an in vitro model, adaptation strategies of nutrient-starved brucellae, which are facultative intracellular pathogens capable of long-term persistence, were determined. RESULTS Long-term nutrient starvation in a medium devoid of carbon and nitrogen sources resulted in a rapid decline in viability of Brucella suis during the first three weeks, followed by stabilization of the number of viable bacteria for a period of at least three weeks thereafter. A 2D-Difference Gel Electrophoresis (DIGE) approach allowed the characterization of the bacterial proteome under these conditions. A total of 30 proteins showing altered concentrations in comparison with bacteria grown to early stationary phase in rich medium were identified. More than half of the 27 significantly regulated proteins were involved in bacterial metabolism with a marked reduction of the concentrations of enzymes participating in amino acid and nucleic acid biosynthesis. A total of 70% of the significantly regulated proteins showed an increased expression, including proteins involved in the adaptation to harsh conditions, in regulation, and in transport. CONCLUSIONS The adaptive response of Brucella suis most likely contributes to the long-term survival of the pathogen under starvation conditions, and may play a key role in persistence.
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Affiliation(s)
- Sascha Al Dahouk
- Federal Institute for Risk Assessment, Diedersdorfer Weg 1, D-12277, Berlin Germany.
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28
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Puri RV, Singh N, Gupta RK, Tyagi AK. Endonuclease IV Is the major apurinic/apyrimidinic endonuclease in Mycobacterium tuberculosis and is important for protection against oxidative damage. PLoS One 2013; 8:e71535. [PMID: 23936515 PMCID: PMC3731287 DOI: 10.1371/journal.pone.0071535] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/29/2013] [Indexed: 11/23/2022] Open
Abstract
During the establishment of an infection, bacterial pathogens encounter oxidative stress resulting in the production of DNA lesions. Majority of these lesions are repaired by base excision repair (BER) pathway. Amongst these, abasic sites are the most frequent lesions in DNA. Class II apurinic/apyrimidinic (AP) endonucleases play a major role in BER of damaged DNA comprising of abasic sites. Mycobacterium tuberculosis, a deadly pathogen, resides in the human macrophages and is continually subjected to oxidative assaults. We have characterized for the first time two AP endonucleases namely Endonuclease IV (End) and Exonuclease III (XthA) that perform distinct functions in M.tuberculosis. We demonstrate that M.tuberculosis End is a typical AP endonuclease while XthA is predominantly a 3′→5′ exonuclease. The AP endonuclease activity of End and XthA was stimulated by Mg2+ and Ca2+ and displayed a preferential recognition for abasic site paired opposite to a cytosine residue in DNA. Moreover, End exhibited metal ion independent 3′→5′ exonuclease activity while in the case of XthA this activity was metal ion dependent. We demonstrate that End is not only a more efficient AP endonuclease than XthA but it also represents the major AP endonuclease activity in M.tuberculosis and plays a crucial role in defense against oxidative stress.
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Affiliation(s)
- Rupangi Verma Puri
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Nisha Singh
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Rakesh K. Gupta
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
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29
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Contributions of individual σB-dependent general stress genes to oxidative stress resistance of Bacillus subtilis. J Bacteriol 2012; 194:3601-10. [PMID: 22582280 DOI: 10.1128/jb.00528-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The general stress regulon of Bacillus subtilis comprises approximately 200 genes and is under the control of the alternative sigma factor σ(B). The activation of σ(B) occurs in response to multiple physical stress stimuli as well as energy starvation conditions. The expression of the general stress proteins provides growing and stationary nonsporulating vegetative cells with nonspecific and broad stress resistance. A previous comprehensive phenotype screening analysis of 94 general stress gene mutants in response to severe growth-inhibiting stress stimuli, including ethanol, NaCl, heat, and cold, indicated that secondary oxidative stress may be a common component of severe physical stress. Here we tested the individual contributions of the same set of 94 mutants to the development of resistance against exposure to the superoxide-generating agent paraquat and hydrogen peroxide (H(2)O(2)). In fact, 62 mutants displayed significantly decreased survival rates in response to paraquat and/or H(2)O(2) stress compared to the wild type at a confidence level of an α value of ≤ 0.01. Thus, we were able to assign 47 general stress genes to survival against superoxide, 6 genes to protection from H(2)O(2) stress, and 9 genes to the survival against both. Furthermore, we show that a considerable overlap exists between the phenotype clusters previously assumed to be involved in oxidative stress management and the actual group of oxidative-stress-sensitive mutants. Our data provide information that many general stress proteins with still unknown functions are implicated in oxidative stress resistance and further support the notion that different severe physical stress stimuli elicit a common secondary oxidative stress.
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30
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Reder A, Albrecht D, Gerth U, Hecker M. Cross-talk between the general stress response and sporulation initiation inBacillus subtilis- the σBpromoter ofspo0Erepresents an AND-gate. Environ Microbiol 2012; 14:2741-56. [DOI: 10.1111/j.1462-2920.2012.02755.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Integration of σB activity into the decision-making process of sporulation initiation in Bacillus subtilis. J Bacteriol 2011; 194:1065-74. [PMID: 22210769 DOI: 10.1128/jb.06490-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spo0A∼P is the master regulator of sporulation in Bacillus subtilis. Activity of Spo0A is regulated by a phosphorelay integrating multiple positive and negative signals by the action of kinases and phosphatases. The phosphatase Spo0E specifically inactivates the response regulator Spo0A∼P by dephosphorylation. We identified a σ(B)-type promoter adjacent to spo0E that is activated by the general stress response sigma factor σ(B) and is responsible for spo0E induction in vivo. Ectopic expression of σ(B) and subsequent induction of spo0E cause a σ(B)-dependent block of sporulation-specific transcription of the spo0A and spoIIE genes and produces a sporulation-deficient phenotype. This effect could be erased by a deletion of the σ(B) promoter of spo0E and thus solely addresses σ(B) activity. Here, a molecular mechanism is shown that integrates σ(B) activity into the decision-making process of sporulation and provides a link to interconnect these two dominant and probably mutually exclusive adaptive responses in the regulatory network of B. subtilis.
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Nannapaneni P, Hertwig F, Depke M, Hecker M, Mäder U, Völker U, Steil L, van Hijum SAFT. Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. MICROBIOLOGY-SGM 2011; 158:696-707. [PMID: 22174379 DOI: 10.1099/mic.0.055434-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The structure of the SigB-dependent general stress regulon of Bacillus subtilis has previously been characterized by proteomics approaches as well as DNA array-based expression studies. However, comparing the SigB targets published in three previous major transcriptional profiling studies it is obvious that although each of them identified well above 100 target genes, only 67 were identified in all three studies. These substantial differences can likely be attributed to the different strains, growth conditions, microarray platforms and experimental setups used in the studies. In order to gain a better understanding of the structure of this important regulon, a targeted DNA microarray analysis covering most of the known SigB-inducing conditions was performed, and the changes in expression kinetics of 252 potential members of the SigB regulon and appropriate control genes were recorded. Transcriptional data for the B. subtilis wild-type strain 168 and its isogenic sigB mutant BSM29 were analysed using random forest, a machine learning algorithm, by incorporating the knowledge from previous studies. This analysis revealed a strictly SigB-dependent expression pattern for 166 genes following ethanol, butanol, osmotic and oxidative stress, low-temperature growth and heat shock, as well as limitation of oxygen or glucose. Kinetic analysis of the data for the wild-type strain identified 30 additional members of the SigB regulon, which were also subject to control by additional transcriptional regulators, thus displaying atypical SigB-independent induction patterns in the mutant strain under some of the conditions tested. For 19 of these 30 SigB regulon members, published reports support control by secondary regulators along with SigB. Thus, this microarray-based study assigns a total of 196 genes to the SigB-dependent general stress regulon of B. subtilis.
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Affiliation(s)
- Priyanka Nannapaneni
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Falk Hertwig
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Maren Depke
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Ulrike Mäder
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Leif Steil
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
| | - Sacha A F T van Hijum
- NIZO Food Research, PO Box 20, 6710 BA Ede, The Netherlands.,Radboud University Nijmegen Medical Centre, Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.,Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
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Oxygen exposure increases resistance of Desulfovibrio vulgaris Hildenborough to killing by hydrogen peroxide. Antonie van Leeuwenhoek 2011; 101:303-11. [DOI: 10.1007/s10482-011-9634-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 08/22/2011] [Indexed: 11/30/2022]
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34
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Schweder T. Bioprocess monitoring by marker gene analysis. Biotechnol J 2011; 6:926-33. [PMID: 21786424 DOI: 10.1002/biot.201100248] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 11/11/2022]
Abstract
The optimization and the scale up of industrial fermentation processes require an efficient and possibly comprehensive analysis of the physiology of the production system throughout the process development. Furthermore, to ensure a good quality control of established bioprocesses, on-line analysis techniques for the determination of marker gene expression are of interest to monitor the productivity and the safety of bioprocesses. A prerequisite for such analyses is the knowledge of genes, the expression of which is critical either for the productivity or for the performance of the bioprocess. This work reviews marker genes that are specific indicators for stress- and nutrient-limitation conditions or for the physiological status of the bacterial production hosts Bacillus subtilis, Bacillus licheniformis and Escherichia coli. The suitability of existing gene expression analysis techniques for bioprocess monitoring is discussed. Analytical approaches that enable a robust and sensitive determination of selected marker mRNAs or proteins are presented.
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Affiliation(s)
- Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany.
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35
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Adaptation to cold and proteomic responses of the psychrotrophic biopreservative Lactococcus piscium strain CNCM I-4031. Appl Environ Microbiol 2010; 76:8011-8. [PMID: 20935127 DOI: 10.1128/aem.01331-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is considerable interest in the use of psychrotrophic bacteria for food biopreservation and in the understanding of cold adaptation mechanisms. The psychrotrophic biopreservative Lactococcus piscium strain CNCM I-4031 was studied for its growth behavior and proteomic responses after cold shock and during cold acclimation. Growth kinetics highlighted the absence of growth latency after cold shock, suggesting a very high promptness in cold adaptation, a behavior that has never been described before for lactic acid bacteria (LAB). A comparative proteomic analysis was applied with two-dimensional gel electrophoresis (2-DE), and upregulated proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Both cold shock and cold acclimation triggered the upregulation of proteins involved in general and oxidative stress responses and fatty acid and energetic metabolism. However, 2-DE profiles and upregulated proteins were different under both conditions, suggesting a sequence of steps in cold adaptation. In addition, the major 7-kDa Csp protein was identified in the L. piscium CNCM I-4031 genome but was not cold regulated. The implication of the identified cold shock proteins and cold acclimation proteins in efficient cold adaptation, the possible regulation of a histidyl phosphocarrier protein, and the roles of a constitutive major 7-kDa Csp are discussed.
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36
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Evidence that Vibrio vulnificus ahpC2 is essential for survival under high salinity by modulating intracellular level of ROS. J Microbiol 2010; 48:129-33. [PMID: 20221741 DOI: 10.1007/s12275-009-0227-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/09/2009] [Indexed: 12/19/2022]
Abstract
Expression of ahpC2 encoding an alkyl hydroperoxide reductase of Vibrio vulnificus, a foodborne pathogen, was incrementally induced depending on NaCl concentrations in the culture. Growth of the ahpC2 mutant was significantly impaired with longer lag phase and lower growth rate when cultured under high salinity. ROS was accumulated in V. vulnificus cells when stressed by exposure to high salinity, and the ahpC2 mutant accumulated higher level of ROS as compared with the parental wild type. Consequently, the combined results suggest that AhpC2 contributes to the growth of V. vulnificus under high salinity by scavenging ROS in cells.
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37
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Abstract
The spore-forming bacterium and model prokaryotic genetic system, Bacillus subtilis, is extremely useful in the study of oxidative stress management through proteomic and genome-wide transcriptomic analyses, as well as through detailed structural studies of the regulatory factors that govern the oxidative stress response. The factors that sense oxidants and induce expression of protective activities include the PerR and OhrR proteins, which show acute discrimination for their peroxide stimuli, whereas the general stress control factor, the RNA polymerase sigma(B) subunit and the thiol-based sensor Spx, govern the protective response to oxidants under multiple stress conditions. Some specific and some redundant protective mechanisms are mobilized at different stages of the Bacillus developmental cycle to deal with vulnerable cells in stationary-phase conditions and during spore germination and outgrowth. An important unknown is the nature and influence of the low-molecular-weight thiols that mediate the buffering of the redox environment.
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Affiliation(s)
- Peter Zuber
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, Beaverton, Oregon 97006, USA.
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38
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Wasim M, Bible AN, Xie Z, Alexandre G. Alkyl hydroperoxide reductase has a role in oxidative stress resistance and in modulating changes in cell-surface properties in Azospirillum brasilense Sp245. MICROBIOLOGY-SGM 2009; 155:1192-1202. [PMID: 19332821 DOI: 10.1099/mic.0.022541-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An ahpC mutant derivative of Azospirillum brasilense Sp245 (strain SK586) that encodes an alkyl hydroperoxide reductase was found to be more sensitive to oxidative stress caused by organic hydroperoxides compared with the wild-type. In addition, the ahpC mutant strain had multiple defects in a large array of cellular functions that were consistent with alteration of cell-surface properties, such as cell morphology in stationary phase, Calcofluor White-, Congo Red- and lectin-binding abilities, as well as cell-to-cell aggregation and flocculation. All phenotypes of the ahpC mutant were complemented by in trans expression of AhpC, and overexpression of AhpC in the wild-type strain was found to affect the same set of phenotypes, suggesting that the pleiotropic effects were caused by the ahpC mutation. SK586 was also found to be fully motile, but it lost motility at a higher rate than the wild-type during growth, such that most SK586 cells were non-motile in stationary phase. Despite these defects, the mutant did not differ from the wild-type in short-term colonization of sterile wheat roots when inoculated alone, and in competition with the wild-type strain; this implied that AhpC activity may not endow the cells with a competitive advantage in colonization under these conditions. Although the exact function of AhpC in affecting these phenotypes remains to be determined, changes in cell morphology, surface properties, cell-to-cell aggregation and flocculation are common adaptive responses to various stresses in bacteria, and the data obtained here suggest that AhpC contributes to modulating such stress responses in A. brasilense.
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Affiliation(s)
- Mariam Wasim
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Amber N Bible
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37922, USA
| | - Zhihong Xie
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37922, USA
| | - Gladys Alexandre
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37922, USA.,Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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AhpC (alkyl hydroperoxide reductase) from Anabaena sp. PCC 7120 protects Escherichia coli from multiple abiotic stresses. Biochem Biophys Res Commun 2009; 381:606-11. [PMID: 19248767 DOI: 10.1016/j.bbrc.2009.02.100] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 02/20/2009] [Indexed: 11/23/2022]
Abstract
Alkyl hydroperoxide reductase (AhpC) is known to detoxify peroxides and reactive sulfur species (RSS). However, the relationship between its expression and combating of abiotic stresses is still not clear. To investigate this relationship, the genes encoding the alkyl hydroperoxide reductase (ahpC) from Anabaena sp. PCC 7120 were introduced into E. coli using pGEX-5X-2 vector and their possible functions against heat, salt, carbofuron, cadmium, copper and UV-B were analyzed. The transformed E. coli cells registered significantly increase in growth than the control cells under temperature (47 degrees C), NaCl (6% w/v), carbofuron (0.025mgml(-1)), CdCl(2) (4mM), CuCl(2) (1mM), and UV-B (10min) exposure. Enhanced expression of ahpC gene as measured by semi-quantitative RT-PCR under aforementioned stresses at different time points demonstrated its role in offering tolerance against multiple abiotic stresses.
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40
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Reder A, Höper D, Weinberg C, Gerth U, Fraunholz M, Hecker M. The Spx paralogue MgsR (YqgZ) controls a subregulon within the general stress response ofBacillus subtilis. Mol Microbiol 2008; 69:1104-20. [DOI: 10.1111/j.1365-2958.2008.06332.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Abstract
Peroxiredoxins constitute an important component of the bacterial defense against toxic peroxides. These enzymes use reactive cysteine thiols to reduce peroxides with electrons ultimately derived from reduced pyridine dinucleotides. Studies examining the regulation and physiological roles of AhpC, Tpx, Ohr and OsmC reveal the multilayered nature of bacterial peroxide defense. AhpC is localized in the cytoplasm and has a wide substrate range that includes H2O2, organic peroxides and peroxynitrite. This enzyme functions in both the control of endogenous peroxides, as well as in the inducible defense response to exogenous peroxides or general stresses. Ohr, OsmC and Tpx are organic peroxide specific. Tpx is localized to the periplasm and can be involved in either constitutive peroxide defense or participate in oxidative stress inducible responses depending on the organism. Ohr is an organic peroxide specific defense system that is under the control of the organic peroxide sensing repressor OhrR. In some organisms Ohr homologs are regulated in response to general stress. Clear evidence indicates that AhpC, Tpx and Ohr are involved in virulence. The role of OsmC is less clear. Regulation of OsmC expression is not oxidative stress inducible, but is controlled by multiple general stress responsive regulators.
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Affiliation(s)
- James M Dubbs
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
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42
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La Carbona S, Sauvageot N, Giard JC, Benachour A, Posteraro B, Auffray Y, Sanguinetti M, Hartke A. Comparative study of the physiological roles of three peroxidases (NADH peroxidase, Alkyl hydroperoxide reductase and Thiol peroxidase) in oxidative stress response, survival inside macrophages and virulence of Enterococcus faecalis. Mol Microbiol 2007; 66:1148-63. [PMID: 17971082 DOI: 10.1111/j.1365-2958.2007.05987.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The opportunistic pathogen Enterococcus faecalis is well equipped with peroxidatic activities. It harbours three loci encoding a NADH peroxidase, an alkyl hydroperoxide reductase and a protein (EF2932) belonging to the AhpC/TSA family. We present results demonstrating that ef2932 does encode a thiol peroxidase (Tpx) and show that it is part of the regulon of the hydrogen peroxide regulator HypR. Characterization of unmarked deletion mutants showed that all three peroxidases are important for the defence against externally provided H(2)O(2). Exposure to internal generated H(2)O(2) by aerobic growth on glycerol, lactose, galactose or ribose showed that Npr was absolutely required for aerobic growth on glycerol and optimal growth on the other substrates. Growth on glycerol was also dependent on Ahp. Addition of catalase restored growth of the mutants, and therefore, extracellular H(2)O(2) concentrations have been determined. This showed that the time point of growth arrest of the Deltanpr mutant correlated with the highest H(2)O(2) concentration measured. Analysis of the survival of the different strains inside peritoneal macrophages revealed that Tpx was the most important antioxidant activity for protecting the cells against the hostile phagocyte environment. Finally, the Deltatpx and the triple mutant showed attenuated virulence in a mouse peritonitis model.
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Affiliation(s)
- Stephanie La Carbona
- Laboratoire de Microbiologie de l'Université de Caen, EA956 USC INRA2017, 14032 CAEN cedex, France
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43
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Cosgrove K, Coutts G, Jonsson IM, Tarkowski A, Kokai-Kun JF, Mond JJ, Foster SJ. Catalase (KatA) and alkyl hydroperoxide reductase (AhpC) have compensatory roles in peroxide stress resistance and are required for survival, persistence, and nasal colonization in Staphylococcus aureus. J Bacteriol 2006; 189:1025-35. [PMID: 17114262 PMCID: PMC1797328 DOI: 10.1128/jb.01524-06] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxidative-stress resistance in Staphylococcus aureus is linked to metal ion homeostasis via several interacting regulators. In particular, PerR controls the expression of a regulon of genes, many of which encode antioxidants. Two PerR regulon members, ahpC (alkylhydroperoxide reductase) and katA (catalase), show compensatory regulation, with independent and linked functions. An ahpC mutation leads to increased H2O2 resistance due to greater katA expression via relief of PerR repression. Moreover, AhpC provides residual catalase activity present in a katA mutant. Mutation of both katA and ahpC leads to a severe growth defect under aerobic conditions in defined media (attributable to lack of catalase activity). This results in the inability to scavenge exogenous or endogenously produced H2O2, resulting in accumulation of H2O2 in the medium. This leads to DNA damage, the likely cause of the growth defect. Surprisingly, the katA ahpC mutant is not attenuated in two independent models of infection, which implies reduced oxygen availability during infection. In contrast, both AhpC and KatA are required for environmental persistence (desiccation) and nasal colonization. Thus, oxidative-stress resistance is an important factor in the ability of S. aureus to persist in the hospital environment and so contribute to the spread of human disease.
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Affiliation(s)
- Kate Cosgrove
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
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44
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Geiman DE, Raghunand TR, Agarwal N, Bishai WR. Differential gene expression in response to exposure to antimycobacterial agents and other stress conditions among seven Mycobacterium tuberculosis whiB-like genes. Antimicrob Agents Chemother 2006; 50:2836-41. [PMID: 16870781 PMCID: PMC1538666 DOI: 10.1128/aac.00295-06] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The seven Mycobacterium tuberculosis whiB-like genes encode small proteins postulated to be transcriptional regulators. A systematic real-time reverse transcription-PCR analysis following exposure to antibiotics and a variety of growth and in vitro stress conditions indicates differential, and in some cases dramatic, transcription modulations for the different M. tuberculosis whiB family members. This information together with biochemical analyses of the whiB1 to whiB7 gene products will be important for understanding the biology of this novel family of proteins in mycobacteria and related actinomycetes.
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Affiliation(s)
- Deborah E Geiman
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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45
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Wiegeshoff F, Beckering CL, Debarbouille M, Marahiel MA. Sigma L is important for cold shock adaptation of Bacillus subtilis. J Bacteriol 2006; 188:3130-3. [PMID: 16585774 PMCID: PMC1446980 DOI: 10.1128/jb.188.8.3130-3133.2006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although sigma factor-dependent transcriptional regulation was shown to be essential for adaptation to different environmental stimuli, no such sigma factor has been related to the regulation of the cold shock response in Bacillus subtilis. In this study, we present genetic evidence for participation of sigma(L) (sigma(54)) and the two sigma(L)-dependent transcriptional enhancers BkdR and YplP in the cold shock response of Bacillus subtilis JH642. Single-gene deletion of either sigL, bkdR, or yplP resulted in a cold-sensitive phenotype.
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Affiliation(s)
- Frank Wiegeshoff
- Philipps-Universität Marburg, FB Chemie-Biochemie, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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46
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Pané-Farré J, Jonas B, Förstner K, Engelmann S, Hecker M. The sigmaB regulon in Staphylococcus aureus and its regulation. Int J Med Microbiol 2006; 296:237-58. [PMID: 16644280 DOI: 10.1016/j.ijmm.2005.11.011] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 10/05/2005] [Accepted: 11/01/2005] [Indexed: 11/30/2022] Open
Abstract
The Staphylococcus aureus genome codes for a sigma factor that shows close sequence similarity to the alternative sigma factor sigmaB of Bacillus subtilis. However, of the proteins controlling the activity of sigmaB in B. subtilis only RsbU, RsbV, and RsbW are encoded in the staphylococcal genome. Therefore, the regulation of the sigmaB activity must differ between these two bacterial species. The present study was designed (i) to describe the sigmaB regulon and (ii) to identify stimuli leading to an activation of sigmaB-dependent transcription. All conditions under which sigmaB was activated in S. aureus (heat shock, addition of MnCl2 or NaCl, alkaline shock) required the presence of RsbU, a positive regulator of sigmaB. In contrast to B. subtilis, a drop in the cellular ATP level caused by the addition of carbonyl cyanide m-chlorophenylhydrazone did not lead to an activation of sigmaB in S. aureus. Moreover, ethanol, a strong inductor of sigmaB activity in B. subtilis, also failed to induce sigmaB in S. aureus. Expression of sigB and sigmaB-dependent genes was enhanced following entry into stationary phase of cells grown in complex medium (LB medium). Our DNA microarray data indicated that 122 genes are positively regulated by sigmaB under alkaline stress conditions. Interestingly, only 12% of these genes have an orthologue in the B. subtilis sigmaB regulon, suggesting that the function of the sigmaB regulon in S. aureus is different from that in B. subtilis. We could show that sigmaB of S. aureus, in contrast to B. subtilis, may have a function in more basic cellular processes such as cell envelope composition, membrane transport processes and intermediary metabolism. sigmaB-dependent genes identified by the DNA microarray approach were subjected to detailed transcriptional analyses using primer extension and Northern blot techniques. These analyses confirmed our DNA microarray data and furthermore revealed different regulatory groups of sigmaB-dependent genes.
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Affiliation(s)
- Jan Pané-Farré
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, F.-L.-Jahn-Str. 15, D-17487 Greifswald, Germany
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47
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Paterson GK, Blue CE, Mitchell TJ. An operon in Streptococcus pneumoniae containing a putative alkylhydroperoxidase D homologue contributes to virulence and the response to oxidative stress. Microb Pathog 2006; 40:152-60. [PMID: 16542815 DOI: 10.1016/j.micpath.2005.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 12/08/2005] [Accepted: 12/12/2005] [Indexed: 11/19/2022]
Abstract
Analysis of the pneumococcal genome sequences from strains R6 and TIGR4 identified a putative alkylhydroperoxidase homologue RT-PCR showed this gene to be expressed in an operon with the downstream open reading frame. No probable function for this second gene is suggested although it appears to be an integral membrane protein. An allelic replacement mutant lacking this two-gene operon in strain D39 was attenuated in competitive infections with the wild type parent. This operon is, therefore, a novel pneumococcal virulence determinant. In line with a role in the response to oxidative stress, this mutant showed enhanced resistance to killing by hydrogen peroxide, a phenotype shared by alkylhydroperoxidase mutants in other bacterial species. The analysis of non-polar single mutants shows that both genes contribute to these phenotypes. Finally, an important role in pneumococcal biology is suggested by the presence of this operon in all 20 clinical isolates examined and the highly conserved sequence of the two genes.
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Affiliation(s)
- Gavin K Paterson
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow, Scotland G12 8QQ, UK
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48
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Yan G, Hua Z, Du G, Chen J. Adaptive response of Bacillus sp. F26 to hydrogen peroxide and menadione. Curr Microbiol 2006; 52:238-42. [PMID: 16502296 DOI: 10.1007/s00284-005-0313-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 12/12/2005] [Indexed: 01/24/2023]
Abstract
The adaptive and cross-protection responses to oxidants were investigated in Bacillus sp. F26. The cells were treated with sublethal concentrations of either H(2)O(2) or menadione (a superoxide-generating agent) to induce an adaptive response. The results showed that the cells treated with menadione exhibited cross-protection against, but in another case, those cells treated with H(2)O(2) did not show significant resistance to menadione. It suggests that Bacillus sp. F26 possesses two separate adaptive responses that respond to the two different kinds of oxidants. The adaptability is regarded as that which is accompanied by the inductions of some antioxidant enzymes. It was found that catalase (CAT) production was increased about 1.6-fold after treatment with 600 microM: H(2)O(2), whereas the presence of 50 microM: menadione induced CAT, superoxide dismutase (SOD), glucose-6-phosphate dehydrogenase (G6PD), and glutathione reductase (GR) by 2-, 2-, 2-, and 1.6-fold, respectively. The results can be used to explain why menadione-treated cells have higher adaptability to lethal concentrations of oxidants than that of those H(2)O(2)-treated. In addition, it was found that growing Bacillus sp. F26 in high-salinity media causes it to become more resistant to H(2)O(2) and menadione stress, which may be partially due to the induction of CAT and SOD production under high NaCl concentration.
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Affiliation(s)
- Guoliang Yan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Southern Yangtze University, Wuxi, 214036, People's Republic of China
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49
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Fuangthong M, Mongkolsuk S. Isolation and characterization of a multiple peroxide resistant mutant from Xanthomonas campestris pv. phaseoli. FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1997.tb10427.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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50
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Hauser F, Lindemann A, Vuilleumier S, Patrignani A, Schlapbach R, Fischer HM, Hennecke H. Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region. Mol Genet Genomics 2005; 275:55-67. [PMID: 16328374 DOI: 10.1007/s00438-005-0059-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 10/08/2005] [Indexed: 10/25/2022]
Abstract
The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genome.
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Affiliation(s)
- F Hauser
- Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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