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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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Maksimova Y, Zorina A, Nesterova L. Oxidative Stress Response and E. coli Biofilm Formation under the Effect of Pristine and Modified Carbon Nanotubes. Microorganisms 2023; 11:1221. [PMID: 37317195 DOI: 10.3390/microorganisms11051221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/16/2023] Open
Abstract
The article investigates the expression of oxyR and soxS oxidative stress genes in E. coli under the effect of pristine multi-walled carbon nanotubes (MWCNTs) and pristine single-walled carbon nanotubes (SWCNTs), MWCNTs and SWCNTs functionalized with carboxyl groups (MWCNTs-COOH and SWCNTs-COOH, respectively), SWCNTs functionalized with amino groups (SWCNTs-NH2) and SWCNTs functionalized with octadecylamine (SWCNTs-ODA). Significant differences were found in the expression of the soxS gene, while no changes were observed in the expression level of the oxyR gene. The pro-oxidant effect of SWCNTs, SWCNTs-COOH, SWCNTs-NH2, and SWCNTs-ODA is presented, and the contrary antioxidant effect of pristine MWCNTs and MWCNTs-COOH in the presence of methyl viologen hydrate (paraquat) is shown. The article shows that SWCNTs-COOH, SWCNTs-NH2, and SWCNTs-ODA added to the medium generate the production of reactive oxygen species (ROS) in bacterial cells. SWCNTs-COOH intensified the E. coli biofilm formation, and the biofilm biomass exceeded the control by 25 times. Additionally, it is shown that the rpoS expression increased in response to MWCNTs-COOH and SWCNTs-COOH, and the effect of SWCNTs-COOH was more significant. SWCNTs-COOH and SWCNTs-NH2 initiated an increase in ATP concentration in the planktonic cells and a decrease in the biofilm cells. The atomic force microscopy (AFM) method showed that the volume of E. coli planktonic cells after the exposure to carbon nanotubes (CNTs) decreased compared to that without exposure, mainly due to a decrease in cell height. The absence of a strong damaging effect of functionalized SWCNTs on E. coli K12 cells, both in suspension and in biofilms, is shown. Contact with functionalized SWCNTs initiated the aggregation of the polymeric substances of the biofilms; however, the cells did not lyse. Among the studied CNTs, SWCNTs-COOH caused an increased expression of the soxS and rpoS, the formation of ROS, and stimulation of the biofilm formation.
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Affiliation(s)
- Yuliya Maksimova
- Laboratory of Molecular Biotechnology, Institute of Ecology and Genetics of Microorganisms UB RAS, 614081 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 614990 Perm, Russia
| | - Anastasiya Zorina
- Laboratory of Molecular Biotechnology, Institute of Ecology and Genetics of Microorganisms UB RAS, 614081 Perm, Russia
| | - Larisa Nesterova
- Laboratory of Adaptation of Microorganisms, Institute of Ecology and Genetics of Microorganisms UB RAS, 614081 Perm, Russia
- Department of Plant Physiology and Soil Ecology, Perm State University, 614990 Perm, Russia
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OxyR Positively Influences Phaseolotoxin Synthesis and Pyoverdin Production in Pseudomonas savastanoi pv. phaseolicola NPS3121. Microorganisms 2022; 10:microorganisms10112123. [DOI: 10.3390/microorganisms10112123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
Phaseolotoxin is a major virulence factor of the bean pathogen bacterium P. savastanoi pv. phaseolicola. This toxin plays a key role in the development of the halo blight disease in bean plants. So far, the signal transduction pathways involved in the synthesis of phaseolotoxin have not been elucidated. The influence of regulation mechanisms related to the oxidative stress response, in particular the OxyR protein, it has been suggested to be involved in this process.. In this study we evaluated the role of OxyR in P. savastanoi pv. phaseolicola, mainly compared to the synthesis of phaseolotoxin and the virulence of this phytopathogen. Generation of the oxyR-mutant, pathogenicity and virulence tests, and analyses of gene expression by RT-PCR assays were performed. The results showed that OxyR exerts an effect on the synthesis of phaseolotoxin and positively influences the expression of the Pht and Pbo cluster genes. Likewise, OxyR influences the production of pyoverdine by the control of the expression of the genes encoding the PvdS sigma factor, involved in the synthesis of this pigment. This study is the first report on members of the OxyR regulon of P. savastanoi pv. phaseolicola NPS3121.
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Seth D, Hausladen A, Stamler JS. Anaerobic Transcription by OxyR: A Novel Paradigm for Nitrosative Stress. Antioxid Redox Signal 2020; 32:803-816. [PMID: 31691575 PMCID: PMC7074925 DOI: 10.1089/ars.2019.7921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Significance: S-nitrosylation, the post-translational modification by nitric oxide (NO) to form S-nitrosothiols (SNOs), regulates diverse aspects of cellular function, and aberrant S-nitrosylation (nitrosative stress) is implicated in disease, from neurodegeneration to cancer. Essential roles for S-nitrosylation have been demonstrated in microbes, plants, and animals; notably, bacteria have often served as model systems for elucidation of general principles. Recent Advances: Recent conceptual advances include the idea of a molecular code through which proteins sense and differentiate S-nitrosothiol (SNO) from alternative oxidative modifications, providing the basis for specificity in SNO signaling. In Escherichia coli, S-nitrosylation relies on an enzymatic cascade that regulates, and is regulated by, the transcription factor OxyR under anaerobic conditions. S-nitrosylated OxyR activates an anaerobic regulon of >100 genes that encode for enzymes that both mediate S-nitrosylation and protect against nitrosative stress. Critical Issues: Mitochondria originated from endosymbiotic bacteria and generate NO under hypoxic conditions, analogous to conditions in E. coli. Nitrosative stress in mitochondria has been implicated in Alzheimer's and Parkinson's disease, among others. Many proteins that are S-nitrosylated in mitochondria are also S-nitrosylated in E. coli. Insights into enzymatic regulation of S-nitrosylation in E. coli may inform the identification of disease-relevant regulatory machinery in mammalian systems. Future Directions: Using E. coli as a model system, in-depth analysis of the anaerobic response controlled by OxyR may lead to the identification of enzymatic mechanisms regulating S-nitrosylation in particular, and hypoxic signaling more generally, providing novel insights into analogous mechanisms in mammalian cells and within dysfunctional mitochondria that characterize neurodegenerative diseases.
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Affiliation(s)
- Divya Seth
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
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Guo Y, Li Y, Zhan W, Wood TK, Wang X. Resistance to oxidative stress by inner membrane protein ElaB is regulated by OxyR and RpoS. Microb Biotechnol 2019; 12:392-404. [PMID: 30656833 PMCID: PMC6389858 DOI: 10.1111/1751-7915.13369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
C-tail anchored inner membrane proteins are a family of proteins that contain a C-terminal transmembrane domain but lack an N-terminal signal sequence for membrane targeting. They are widespread in eukaryotes and prokaryotes and play critical roles in membrane traffic, apoptosis and protein translocation in eukaryotes. Recently, we identified and characterized in Escherichia coli a new C-tail anchored inner membrane, ElaB, which is regulated by the stationary phase sigma factor RpoS. ElaB is important for resistance to oxidative stress but the exact mechanism is unclear. Here, we show that ElaB functions as part of the adaptive oxidative stress response by maintaining membrane integrity. Production of ElaB is induced by oxidative stress at the transcriptional level. Moreover, elaB expression is also regulated by the key regulator OxyR via an OxyR binding site in the promoter of elaB. OxyR induces the expression of elaB in the exponential growth phase, while excess OxyR reduces elaB expression in an RpoS-dependent way in the stationary phase. In addition, deletion of elaB reduced fitness compared to wild-type cells after prolonged incubation. Therefore, we determined how ElaB is regulated under oxidative stress: RpoS and OxyR coordinately control the expression of inner membrane protein ElaB.
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Affiliation(s)
- Yunxue Guo
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
| | - Yangmei Li
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
| | - Waner Zhan
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
| | - Thomas K. Wood
- Department of Chemical EngineeringPennsylvania State University, University ParkPA16802‐4400USA
- Department of Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkPA16802‐4400USA
| | - Xiaoxue Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
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6
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Guebel DV, Torres NV. Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. Front Microbiol 2018; 9:941. [PMID: 29875739 PMCID: PMC5974110 DOI: 10.3389/fmicb.2018.00941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Background: While in eukaryotes acetylation/deacetylation regulation exerts multiple pleiotropic effects, in Escherichia coli it seems to be more limited and less known. Hence, we aimed to progress in the characterization of this regulation by dealing with three convergent aspects: the effector enzymes involved, the master regulator CRP, and the dependence on glucose availability. Methods: The transcriptional response of E. coli BW25113 was analyzed across 14 relevant scenarios. These conditions arise when the wild type and four isogenic mutants (defective in deacetylase CobB, defective in N(ε)-lysine acetyl transferase PatZ, Q- and R-type mutants of protein CRP) are studied under three levels of glucose availability (glucose-limited chemostat and glucose-excess or glucose-exhausted in batch culture). The Q-type emulates a permanent stage of CRPacetylated, whereas the R-type emulates a permanent stage of CRPdeacetylated. The data were analyzed by an optimized factorial microarray method (Q-GDEMAR). Results: (a) By analyzing one mutant against the other, we were able to unravel the true genes that participate in the interaction between ΔcobB/ΔpatZ mutations and glucose availability; (b) Increasing stages of glucose limitation appear to be associated with the up-regulation of specific sets of target genes rather than with the loss of genes present when glucose is in excess; (c) Both CRPdeacetylated and CRPacetylated produce extensive changes in specific subsets of genes, but their number and identity depend on the glucose availability; (d) In other sub-sets of genes, the transcriptional effect of CRP seems to be independent of its acetylation or deacetylation; (e) Some specific ontology functions can be associated with each of the different sets of genes detected herein. Conclusions: CRP cannot be thought of only as an effector of catabolite repression, because it acts along all the glucose conditions tested (excess, limited, and exhausted), exerting both positive and negative effects through different sets of genes. Acetylation of CRP does not seem to be a binary form of regulation, as there is not a univocal relationship between its activation/inhibitory effect and its acetylation/deacetylation stage. All the combinatorial possibilities are observed. During the exponential growth phase, CRP also exerts a very significant transcriptional effect, mainly on flagellar assembly and chemotaxis (FDR = 7.2 × 10−44).
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Affiliation(s)
| | - Néstor V Torres
- Systems Biology and Mathematical Modelling Group, Department of Biochemistry, Microbiology, Cellular Biology and Genetics, Institute of Biomedical Technologies, Center for Biomedical Research of the Canary Islands, University of La Laguna, San Cristóbal de La Laguna, Spain
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7
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Ma Z, Russo VC, Rabadi SM, Jen Y, Catlett SV, Bakshi CS, Malik M. Elucidation of a mechanism of oxidative stress regulation in Francisella tularensis live vaccine strain. Mol Microbiol 2016; 101:856-78. [PMID: 27205902 DOI: 10.1111/mmi.13426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2016] [Indexed: 12/21/2022]
Abstract
Francisella tularensis causes a lethal human disease known as tularemia. As an intracellular pathogen, Francisella survives and replicates in phagocytic cells, such as macrophages. However, to establish an intracellular niche, Francisella must overcome the oxidative stress posed by the reactive oxygen species (ROS) produced by the infected macrophages. OxyR and SoxR/S are two well-characterized transcriptional regulators of oxidative stress responses in several bacterial pathogens. Only the OxyR homolog is present in F. tularensis, while the SoxR homologs are absent. The functional role of OxyR has not been established in F. tularensis. We demonstrate that OxyR regulates oxidative stress responses and provides resistance against ROS, thereby contributing to the survival of the F. tularensis subsp. holarctica live vaccine strain (LVS) in macrophages and epithelial cells and contributing to virulence in mice. Proteomic analysis reveals the differential production of 128 proteins in the oxyR gene deletion mutant, indicating its global regulatory role in the oxidative stress response of F. tularensis. Moreover, OxyR regulates the transcription of the primary antioxidant enzyme genes by binding directly to their putative promoter regions. This study demonstrates that OxyR is an important virulence factor and transcriptional regulator of the oxidative stress response of the F. tularensis LVS.
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Affiliation(s)
- Zhuo Ma
- Department of Basic and Social Sciences, Albany College of Pharmacy and Health Sciences, Albany, NY, USA
| | - Vincenzo C Russo
- Department of Basic and Social Sciences, Albany College of Pharmacy and Health Sciences, Albany, NY, USA
| | - Seham M Rabadi
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Yu Jen
- Department of Pathology, Westchester Medical Center, Valhalla, NY, USA
| | - Sally V Catlett
- Department of Basic and Social Sciences, Albany College of Pharmacy and Health Sciences, Albany, NY, USA
| | | | - Meenakshi Malik
- Department of Basic and Social Sciences, Albany College of Pharmacy and Health Sciences, Albany, NY, USA
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Shi M, Wan F, Mao Y, Gao H. Unraveling the Mechanism for the Viability Deficiency of Shewanella oneidensis oxyR Null Mutant. J Bacteriol 2015; 197:2179-2189. [PMID: 25897035 PMCID: PMC4455265 DOI: 10.1128/jb.00154-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/16/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED Oxidative stresses triggered by reactive oxygen species (ROS) that damage various cellular components are unavoidable for virtually all living organisms. In defense, microorganisms have evolved sophisticated mechanisms to sense, respond to, and battle against ROS. Shewanella oneidensis, an important research model for applied and environmental microbes, employs OxyR to mediate the response to H2O2 by derepressing the production of the major H2O2 scavenger KatB as a major means toward these goals. Surprisingly, despite enhanced H2O2 degradation, the oxyR mutant carries a viability deficiency phenotype (plating defect), which can be suppressed by the addition of exogenous iron species. Experiments showed that the defect was not due to iron starvation. Rather, multiple lines of evidence suggested that H2O2 generated abiotically in lysogeny broth (LB) is responsible for the defect by quickly killing mutant cells. We then showed that the iron species suppressed the plating defect by two distinct mechanisms, either as an H2O2 scavenger without involving living cells or as an environmental cue to stimulate an OxyR-independent response to help cells cope with oxidative stress. Based on the suppression of the plating defect by overproduction of H2O2 scavengers in vivo, we propose that cellular components that are vulnerable to H2O2 and responsible for the defect may reside outside the cytoplasm. IMPORTANCE In bacteria, OxyR is the major regulator controlling the cellular response to H2O2. The loss of OxyR results in reduced viability in many species, but the underlying mechanism is unknown. We showed in S. oneidensis that this defect was due to H2O2 generated abiotically in LB. We then showed that this defect could be corrected by the addition of Fe(2+) or catalase to the LB or increased intracellular production of catalase. Further analyses revealed that Fe(2+) was able not only to decompose H2O2 directly but also to stimulate the activity of OxyR-independent H2O2-scavenging enzymes. Our data indicate that iron species play a previously underappreciated role in protecting cells from H2O2 in environments.
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Affiliation(s)
- Miaomiao Shi
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Agro-Microbial Research and Utilization, Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fen Wan
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Agro-Microbial Research and Utilization, Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yinting Mao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Agro-Microbial Research and Utilization, Zhejiang Province, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Agro-Microbial Research and Utilization, Zhejiang Province, Hangzhou, Zhejiang, China
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Gama-Castro S, Rinaldi F, López-Fuentes A, Balderas-Martínez YI, Clematide S, Ellendorff TR, Santos-Zavaleta A, Marques-Madeira H, Collado-Vides J. Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau049. [PMID: 24903516 PMCID: PMC4207228 DOI: 10.1093/database/bau049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Given the current explosion of data within original publications generated in the field of genomics, a recognized bottleneck is the transfer of such knowledge into comprehensive databases. We have for years organized knowledge on transcriptional regulation reported in the original literature of Escherichia coli K-12 into RegulonDB (http://regulondb.ccg.unam.mx), our database that is currently supported by >5000 papers. Here, we report a first step towards the automatic biocuration of growth conditions in this corpus. Using the OntoGene text-mining system (http://www.ontogene.org), we extracted and manually validated regulatory interactions and growth conditions in a new approach based on filters that enable the curator to select informative sentences from preprocessed full papers. Based on a set of 48 papers dealing with oxidative stress by OxyR, we were able to retrieve 100% of the OxyR regulatory interactions present in RegulonDB, including the transcription factors and their effect on target genes. Our strategy was designed to extract, as we did, their growth conditions. This result provides a proof of concept for a more direct and efficient curation process, and enables us to define the strategy of the subsequent steps to be implemented for a semi-automatic curation of original literature dealing with regulation of gene expression in bacteria. This project will enhance the efficiency and quality of the curation of knowledge present in the literature of gene regulation, and contribute to a significant increase in the encoding of the regulatory network of E. coli. RegulonDB Database URL:http://regulondb.ccg.unam.mx OntoGene URL:http://www.ontogene.org
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Affiliation(s)
- Socorro Gama-Castro
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Fabio Rinaldi
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Alejandra López-Fuentes
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Yalbi Itzel Balderas-Martínez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Simon Clematide
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Tilia Renate Ellendorff
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Alberto Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Hernani Marques-Madeira
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland
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10
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Donovan GT, Norton JP, Bower JM, Mulvey MA. Adenylate cyclase and the cyclic AMP receptor protein modulate stress resistance and virulence capacity of uropathogenic Escherichia coli. Infect Immun 2013; 81:249-58. [PMID: 23115037 PMCID: PMC3536135 DOI: 10.1128/iai.00796-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/24/2012] [Indexed: 02/07/2023] Open
Abstract
In many bacteria, the second messenger cyclic AMP (cAMP) interacts with the transcription factor cAMP receptor protein (CRP), forming active cAMP-CRP complexes that can control a multitude of cellular activities, including expanded carbon source utilization, stress response pathways, and virulence. Here, we assessed the role of cAMP-CRP as a regulator of stress resistance and virulence in uropathogenic Escherichia coli (UPEC), the principal cause of urinary tract infections worldwide. Deletion of genes encoding either CRP or CyaA, the enzyme responsible for cAMP synthesis, attenuates the ability of UPEC to colonize the bladder in a mouse infection model, dependent on intact innate host defenses. UPEC mutants lacking cAMP-CRP grow normally in the presence of glucose but are unable to utilize alternate carbon sources like amino acids, the primary nutrients available to UPEC within the urinary tract. Relative to the wild-type UPEC isolate, the cyaA and crp deletion mutants are sensitive to nitrosative stress and the superoxide generator methyl viologen but remarkably resistant to hydrogen peroxide (H(2)O(2)) and acid stress. In the mutant strains, H(2)O(2) resistance correlates with elevated catalase activity attributable in part to enhanced translation of the alternate sigma factor RpoS. Acid resistance was promoted by both RpoS-independent and RpoS-dependent mechanisms, including expression of the RpoS-regulated DNA-binding ferritin-like protein Dps. We conclude that balanced input from many cAMP-CRP-responsive elements, including RpoS, is critical to the ability of UPEC to handle the nutrient limitations and severe environmental stresses present within the mammalian urinary tract.
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Affiliation(s)
- Grant T Donovan
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
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11
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Basak S, Jiang R. Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLoS One 2012; 7:e51179. [PMID: 23251448 PMCID: PMC3522674 DOI: 10.1371/journal.pone.0051179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/30/2012] [Indexed: 12/11/2022] Open
Abstract
Oxidative damage to microbial hosts often occurs under stressful conditions during bioprocessing. Classical strain engineering approaches are usually both time-consuming and labor intensive. Here, we aim to improve E. coli performance under oxidative stress via engineering its global regulator cAMP receptor protein (CRP), which can directly or indirectly regulate redox-sensing regulators SoxR and OxyR, and other ~400 genes in E. coli. Error-prone PCR technique was employed to introduce modifications to CRP, and three mutants (OM1~OM3) were identified with improved tolerance via H(2)O(2) enrichment selection. The best mutant OM3 could grow in 12 mM H(2)O(2) with the growth rate of 0.6 h(-1), whereas the growth of wild type was completely inhibited at this H(2)O(2) concentration. OM3 also elicited enhanced thermotolerance at 48°C as well as resistance against cumene hydroperoxide. The investigation about intracellular reactive oxygen species (ROS), which determines cell viability, indicated that the accumulation of ROS in OM3 was always lower than in WT with or without H(2)O(2) treatment. Genome-wide DNA microarray analysis has shown not only CRP-regulated genes have demonstrated great transcriptional level changes (up to 8.9-fold), but also RpoS- and OxyR-regulated genes (up to 7.7-fold). qRT-PCR data and enzyme activity assay suggested that catalase (katE) could be a major antioxidant enzyme in OM3 instead of alkyl hydroperoxide reductase or superoxide dismutase. To our knowledge, this is the first work on improving E. coli oxidative stress resistance by reframing its transcription machinery through its native global regulator. The positive outcome of this approach may suggest that engineering CRP can be successfully implemented as an efficient strain engineering alternative for E. coli.
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Affiliation(s)
- Souvik Basak
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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12
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Peroxide resistance in Escherichia coli serotype O157 : H7 biofilms is regulated by both RpoS-dependent and -independent mechanisms. Microbiology (Reading) 2012; 158:2225-2234. [DOI: 10.1099/mic.0.059535-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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14
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Barth E, Gora KV, Gebendorfer KM, Settele F, Jakob U, Winter J. Interplay of cellular cAMP levels, {sigma}S activity and oxidative stress resistance in Escherichia coli. MICROBIOLOGY-SGM 2009; 155:1680-1689. [PMID: 19372151 DOI: 10.1099/mic.0.026021-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hypochlorous acid (HOCl), the active ingredient of household bleach, functions as a powerful antimicrobial that is used not only in numerous industrial applications but also in mammalian host defence. Here we show that multicopy expression of cpdA, encoding the cAMP phosphodiesterase, leads to a dramatically increased resistance of Escherichia coli to HOCl stress as well as to the unrelated hydrogen peroxide (H(2)O(2)) stress. This general oxidative stress resistance is apparently caused by the CpdA-mediated decrease in cellular cAMP levels, which leads to the partial inactivation of the global transcriptional regulator cAMP receptor protein (CRP). Downregulation of CRP in turn causes the derepression of rpoS, encoding the alternative sigma factor sigma(S), which activates the general stress response in E. coli. We found that these highly oxidative stress-resistant cells have a substantially increased capacity to combat HOCl-mediated insults and to degrade reactive oxygen species. Mutational analysis revealed that the DNA-protecting protein Dps, the catalase KatE, and the exonuclease III XthA play the predominant roles in conferring the high resistance of rpoS-overexpressing strains towards HOCl and H(2)O(2) stress. Our results demonstrate the close regulatory interplay between cellular cAMP levels, sigma(S) activity and oxidative stress resistance in E. coli.
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Affiliation(s)
- Evelyn Barth
- Department Chemie, Biotechnologie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Katherine V Gora
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Katharina M Gebendorfer
- Center for Integrated Protein Science Munich (CiPSM), 81377 Munich, Germany.,Department Chemie, Biotechnologie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Florian Settele
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Jeannette Winter
- Center for Integrated Protein Science Munich (CiPSM), 81377 Munich, Germany.,Department Chemie, Biotechnologie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
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15
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Omsland A, Miranda KM, Friedman RL, Boitano S. Bordetella bronchiseptica responses to physiological reactive nitrogen and oxygen stresses. FEMS Microbiol Lett 2008; 284:92-101. [PMID: 18462394 DOI: 10.1111/j.1574-6968.2008.01181.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bordetella bronchiseptica can establish prolonged airway infection consistent with a highly developed ability to evade mammalian host immune responses. Upon initial interaction with the host upper respiratory tract mucosa, B. bronchiseptica are subjected to antimicrobial reactive nitrogen species (RNS) and reactive oxygen species (ROS), effector molecules of the innate immune system. However, the responses of B. bronchiseptica to redox species at physiologically relevant concentrations (nM-microM) have not been investigated. Using predicted physiological concentrations of nitric oxide (NO), superoxide and hydrogen peroxide (H2O2) on low numbers of CFU of B. bronchiseptica, all redox active species displayed dose-dependent antimicrobial activity. Susceptibility to individual redox active species was significantly increased upon introduction of a second species at subantimicrobial concentrations. An increased bacteriostatic activity of NO was observed relative to H2O2. The understanding of Bordetella responses to physiologically relevant levels of exogenous RNS and ROS will aid in defining the role of endogenous production of these molecules in host innate immunity against Bordetella and other respiratory pathogens.
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Affiliation(s)
- Anders Omsland
- Department of Cell Biology and Anatomy, Arizona Health Sciences Center, University of Arizona, AZ 85724-5030, USA
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16
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Limthammahisorn S, Brady YJ, Arias CR. Gene expression of cold shock and other stress-related genes in Vibrio vulnificus grown in pure culture under shellstock temperature control conditions. J Food Prot 2008; 71:157-64. [PMID: 18236677 DOI: 10.4315/0362-028x-71.1.157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shellstock refrigeration after harvesting is recommended to prevent further increases in Vibrio vulnificus numbers in oysters, but it could potentially induce a cold shock response in this bacterium. V. vulnificus was incubated at 35, 25, 20, and 15 degrees C and then subjected to 7.2 and 4 degrees C for 1 week. A cold-adaptation response that enhanced cell culturability was observed when cells were incubated at 15 degrees C prior to cold shock at 7.2 degrees C. In vitro cold shock gene expression was analyzed by reverse transcriptase PCR (RT-PCR). The expression of cold shock genes csp1 and csp5 (homologous genes to cspA and cspV) remained constant, despite cold shock. However, the transcript of csp3 was constitutively expressed before and after cold shock, with a few exceptions. The synthesis of csp3 mRNA in V. vulnificus C7184Tr (an avirulent strain) was induced only after 15 degrees C incubation and cold shock at 4 degrees C. The expression of csp4 was repressed after cold shock. Our data showed that the csp(s) tested in this study are not cold inducible. The transcripts of two oxidative stress-related genes, oxyR and katG, showed different induction patterns among strains after cold shock, suggesting that V. vulnificus cells encountered oxidative stress during cold shock.
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Affiliation(s)
- Suttinee Limthammahisorn
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama 36849-5419, USA
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17
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Wu HJ, Seib KL, Srikhanta YN, Kidd SP, Edwards JL, Maguire TL, Grimmond SM, Apicella MA, McEwan AG, Jennings MP. PerR controls Mn-dependent resistance to oxidative stress in Neisseria gonorrhoeae. Mol Microbiol 2006; 60:401-16. [PMID: 16573689 DOI: 10.1111/j.1365-2958.2006.05079.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In previous studies it has been established that resistance to superoxide by Neisseria gonorrhoeae is dependent on the accumulation of Mn(II) ions involving the ABC transporter, MntABC. A mutant strain lacking the periplasmic binding protein component (MntC) of this transport system is hypersensitive to killing by superoxide anion. In this study the mntC mutant was found to be more sensitive to H2O2 killing than the wild-type. Analysis of regulation of MntC expression revealed that it was de-repressed under low Mn(II) conditions. The N. gonorrhoeae mntABC locus lacks the mntR repressor typically found associated with this locus in other organisms. A search for a candidate regulator of mntABC expression revealed a homologue of PerR, a Mn-dependent peroxide-responsive regulator found in Gram-positive organisms. A perR mutant expressed more MntC protein than wild-type, and expression was independent of Mn(II), consistent with a role for PerR as a repressor of mntABC expression. The PerR regulon of N. gonorrhoeae was defined by microarray analysis and includes ribosomal proteins, TonB-dependent receptors and an alcohol dehydrogenase. Both the mntC and perR mutants had reduced intracellular survival in a human cervical epithelial cell model.
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Affiliation(s)
- Hsing-Ju Wu
- School of Molecular and Microbial Sciences and Centre for Metals in Biology, The University of Queensland, Brisbane, Australia 4072
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18
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Abstract
Hydrogen peroxide (H2O2) is a well-documented component of living cells. It plays important roles in host defense and oxidative biosynthetic reactions. In addition there is growing evidence that at low levels, H2O2 also functions as a signaling agent, particularly in higher organisms. This review evaluates the evidence that H2O2 functions as a signaling agent in higher organisms in light of the known biology and biochemistry of H2O2. All aerobic organisms studied to date from prokaryotes to humans appear to tightly regulate their intracellular H2O2 concentrations at relatively similar levels. Multiple biochemical strategies for rapidly reacting with these low endogenous levels of H2O2 have been elucidated from the study of peroxidases and catalases. Well-defined biochemical pathways involved in the response to exogenous H2O2 have been described in both prokaryotes and yeast. In animals and plants, regulated enzymatic systems for generating H2O2 have been described. In addition oxidation-dependent steps in signal transduction pathways are being uncovered, and evidence is accumulating regarding the nature of the specific reactive oxygen species involved in each of these pathways. Application of physiologic levels of H2O2 to mammalian cells has been shown to stimulate biological responses and to activate specific biochemical pathways in these cells.
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Affiliation(s)
- James R Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
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Semchyshyn H, Lushchak V, Storey K. Possible Reasons for Difference in Sensitivity to Oxygen of Two Escherichia coli Strains. BIOCHEMISTRY (MOSCOW) 2005; 70:424-31. [PMID: 15892608 DOI: 10.1007/s10541-005-0132-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In preliminary experiments it was found that Escherichia coli strains AB1157 and KS400 are different in their abilities to grow under various oxygen levels in cultivation medium: the first strain does not grow under high oxygen conditions, unlike the second one. To investigate whether the damage to cellular components due to production of reactive oxygen species (ROS) was responsible for this difference, the intensity of free radical oxidation of proteins and lipids as well as the activities of selected antioxidant and associated enzymes (superoxide dismutase, catalase, peroxidase, glutathione reductase, glucose-6-phosphate dehydrogenase) were compared in the two strains. The level of thiobarbituric acid-reactive substances was 1.8-2.5-fold higher in AB1157 than in KS400, but the concentration of carbonyl proteins was lower in the AB1157 strain. In both strains growth under higher oxygen levels resulted in higher superoxide dismutase and peroxidase activities in both exponential and stationary phases. Overall, the activities of antioxidant enzymes were always higher in the KS400 strain than in AB1157. The results for both lipid and protein oxidative damage and antioxidant enzyme activities suggest that the differences in oxygen tolerance between these two strains may be due to their different abilities to cope with ROS.
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Affiliation(s)
- H Semchyshyn
- Department of Biochemistry, Vassyl Stefanyk Precarpathian National University, 76025 Ivano-Frankivsk, Ukraine
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20
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Srinivasa Rao PS, Yamada Y, Leung KY. A major catalase (KatB) that is required for resistance to H2O2 and phagocyte-mediated killing in Edwardsiella tarda. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2635-2644. [PMID: 12949187 DOI: 10.1099/mic.0.26478-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Edwardsiella tarda causes haemorrhagic septicaemia in fish and gastro- and extra-intestinal infections in animals including humans. Resistance to phagocyte-mediated killing is one of the virulence factors of Ed. tarda. The authors' previous studies using TnphoA transposon mutagenesis indicated that katB mutants derived from the strain PPD130/91 are at least 1.6 log higher in LD50 values than the wild-type strain. These findings suggest the involvement of catalase (KatB) in Ed. tarda pathogenesis. In this study, experiments were conducted to characterize the contribution of KatB to Ed. tarda infection. Zymographic analyses indicated that the 22 Ed. tarda strains examined expressed three different types of catalase-peroxidases (Kat1-3) based on their mobility in non-denaturing polyacrylamide gels. KatB (Kat1), the major catalase enzyme, was expressed in eight out of 22 Ed. tarda strains, and was commonly found in virulent strains except AL9379. AL9379 has a mutated katB, which has a base substitution and a deletion that translate into stop codons in the catalase gene. KatB produced by PPD130/91 was located in both periplasmic and cytoplasmic fractions and was constitutively expressed in various growth phases. Kinetics studies indicated that the catalase provided resistance to H2O2- and phagocyte-mediated killing. Infection kinetics studies of katB mutant 34 in gourami fish demonstrated its inability to survive and replicate in phagocyte-rich organs and this prevented the dissemination of infections when compared to the wild-type. Complementation of catalase mutants restored the production of catalase, and led to an increase in the resistance to H2O2- and phagocyte-mediated killing, and a decrease in LD50 values. This study has identified and characterized a major catalase gene (katB) that is required for resistance to H2O2- and phagocyte-mediated killing in Ed. tarda. The results also suggest that catalase may play a role as a virulence factor in Ed. tarda pathogenesis.
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Affiliation(s)
- P S Srinivasa Rao
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Science Drive 4, Singapore 117543
| | - Yoshiyuki Yamada
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Science Drive 4, Singapore 117543
| | - Ka Yin Leung
- Tropical Marine Science Institute, The National University of Singapore, Science Drive 4, Singapore 117543
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Science Drive 4, Singapore 117543
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21
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Loprasert S, Whangsuk W, Sallabhan R, Mongkolsuk S. Regulation of the katG-dpsA operon and the importance of KatG in survival of Burkholderia pseudomallei exposed to oxidative stress. FEBS Lett 2003; 542:17-21. [PMID: 12729890 DOI: 10.1016/s0014-5793(03)00328-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Homologues of the catalase-peroxidase gene katG and the gene for the non-specific DNA binding protein dpsA were identified downstream of oxyR in Burkholderia pseudomallei. Northern experiments revealed that both katG and dpsA are co-transcribed during oxidative stress. Under conditions where the katG promoter is not highly induced, dpsA is transcribed from a second promoter located within the katG-dpsA intergenic region. A katG insertion mutant was found to be hypersensitive to various oxidants. Analysis of katG expression in the oxyR mutant indicates that OxyR is a dual function regulator that represses the expression of katG during normal growth and activates katG during exposure to oxidative stress. Both reduced and oxidized OxyR were shown to bind to the katG promoter.
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Affiliation(s)
- Suvit Loprasert
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, 10210, Bangkok, Thailand.
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22
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Hahn JS, Oh SY, Roe JH. Role of OxyR as a peroxide-sensing positive regulator in Streptomyces coelicolor A3(2). J Bacteriol 2002; 184:5214-22. [PMID: 12218006 PMCID: PMC137946 DOI: 10.1128/jb.184.19.5214-5222.2002] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes encoding a homolog of Escherichia coli OxyR (oxyR) and an alkyl hydroperoxide reductase system (ahpC and ahpD) have been isolated from Streptomyces coelicolor A3(2). The ahpC and ahpD genes constitute an operon transcribed divergently from the oxyR gene. Expression of both ahpCD and oxyR genes was maximal at early exponential phase and decreased rapidly as cells entered mid-exponential phase. Overproduction of OxyR in Streptomyces lividans conferred resistance against cumene hydroperoxide and H2O2. The oxyR mutant produced fewer ahpCD and oxyR transcripts than the wild type, suggesting that OxyR acts as a positive regulator for their expression. Both oxyR and ahpCD transcripts increased more than fivefold within 10 min of H2O2 treatment and decreased to the normal level in 50 min, with kinetics similar to those of the CatR-mediated induction of the catalase A gene (catA) by H2O2. The oxyR mutant failed to induce oxyR and ahpCD genes in response to H2O2, indicating that OxyR is the modulator for the H2O2-dependent induction of these genes. Purified OxyR protein bound specifically to the intergenic region between ahpC and oxyR, suggesting its direct role in regulating these genes. These results demonstrate that in S. coelicolor OxyR mediates H2O2 induction of its own gene and genes for alkyl hydroperoxide reductase system, but not the catalase gene (catA), unlike in Escherichia coli and Salmonella enterica serovar Typhimurium.
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Affiliation(s)
- Ji-Sook Hahn
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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Gabig M, Herman-Antosiewicz A, Kwiatkowska M, Los M, Thomas MS, Wegrzyn G. The cell surface protein Ag43 facilitates phage infection of Escherichia coli in the presence of bile salts and carbohydrates. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1533-42. [PMID: 11988528 DOI: 10.1099/00221287-148-5-1533] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It was found that infection of Escherichia coli by bacteriophage lambda is inhibited in the presence of certain bile salts and carbohydrates when cells are in the "OFF" state for production of the phase-variable cell surface protein antigen 43 (Ag43). The inhibition of phage growth was found to be due to a significant impairment in the process of phage adsorption. Expression of the gene encoding Ag43 (agn43) from a plasmid or inactivation of the oxyR gene (encoding an activator of genes important for defence against oxidative stress) suppressed this inhibition. A mutation, rpoA341, in the gene encoding the alpha subunit of RNA polymerase also facilitated phage adsorption in the presence of bile salts and carbohydrates. The rpoA341 mutation promoted efficient production of Ag43 in a genetic background that would otherwise be in the "OFF" phase for expression of the agn43 gene. Analysis of a reporter gene fusion demonstrated that the promoter for the agn43 gene was more active in the rpoA341 mutant than in the otherwise isogenic rpoA(+) strain. The combined inhibitory action of bile salts and carbohydrates on phage adsorption and the abolition of this inhibition by production of Ag43 was not restricted to lambda, as a similar phenomenon was observed for the coliphages P1 and T4.
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Affiliation(s)
- Magdalena Gabig
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
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Pomposiello PJ, Demple B. Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 2001; 19:109-14. [PMID: 11179804 DOI: 10.1016/s0167-7799(00)01542-0] [Citation(s) in RCA: 276] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Two redox-responsive transcription regulators have been well defined in Escherichia coli and serve as paradigms of redox-operated genetic switches. SoxR contains iron-sulfur centers that activate the protein when they are one-electron oxidized, or nitrosylated by nitric oxide. OxyR contains a pair of redox-active cysteine residues that activate the protein when they are oxidized to form a disulfide bond.
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Affiliation(s)
- P J Pomposiello
- Dept of Cancer Cell Biology, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
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Moreau PL, Gérard F, Lutz NW, Cozzone P. Non-growing Escherichia coli cells starved for glucose or phosphate use different mechanisms to survive oxidative stress. Mol Microbiol 2001; 39:1048-60. [PMID: 11251823 DOI: 10.1046/j.1365-2958.2001.02303.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent data suggest that superoxide dismutases are important in preventing lethal oxidative damage of proteins in Escherichia coli cells incubated under aerobic, carbon starvation conditions. Here, we show that the alkylhydroperoxide reductase AhpCF (AHP) is specifically required to protect cells incubated under aerobic, phosphate (Pi) starvation conditions. Additional loss of the HP-I (KatG) hydroperoxidase activity dramatically accelerated the death rate of AHP-deficient cells. Investigation of the composition of spent culture media indicates that DeltaahpCF katG cells leak nutrients, which suggests that membrane lipids are the principal target of peroxides produced in Pi-starved cells. In fact, the introduction of various mutations inactivating repair activities revealed no obvious role for protein or DNA lesions in the viability of ahp cells. Because the death of ahp cells was directly related to ongoing aerobic glucose metabolism, we wondered how glycolysis, which requires free Pi, could proceed. 31P nuclear magnetic resonance spectra showed that Pi-starved cells consumed Pi but were apparently able to liberate Pi from phosphorylated products, notably through the synthesis of UDP-glucose. Whereas expression of the ahpCF and katG genes is enhanced in an OxyR-dependent manner in response to H2O2 challenge, we found that the inactivation of oxyR and both oxyR and rpoS genes had little effect on the viability of Pi-starved cells. In stark contrast, the inactivation of both oxyR and rpoS genes dramatically decreased the viability of glucose-starved cells.
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Affiliation(s)
- P L Moreau
- CNRS-LCB, 31 chemin Joseph Aiguier, 13009 Marseille, France.
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Abstract
Gene regulation mechanisms have evolved allowing cells to finetune the level of "endogenous" oxidative stress and to cope with increased free radicals from external sources. Levels of H2O2 are tightly controlled in E. coli by OxyR, which is activated by H2O2 to increase scavenging activities and limit H2O2 generation by the respiratory chain. Sub-micromolar levels of H2O2 are maintained in mammalian tissues, though the regulatory systems that govern this control are unknown. Excess superoxide triggers the soxRS system in E. coli, which is controlled by the oxidant-sensitive iron-sulfur centers of the SoxR protein. Nitric oxide activates SoxR by a different modification of the iron-sulfur centers. The soxRS regulon mobilizes diverse functions to scavenge free radicals and repair oxidative damage in macromolecules, and other mechanisms that exclude many environmental agents from the cell. Mammalian cells also sense and respond to sub-toxic levels of nitric oxide, activating expression of heme oxygenase 1 through stabilization of its mRNA. These inductions give rise to adaptive resistance to nitric oxide in neuronal and other cell types.
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Affiliation(s)
- B González-Flecha
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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27
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Changes in the topological state of DNA duringEscherichia coli adaptation to oxidative stress under glucose starvation and after the transition to growth. Microbiology (Reading) 2000. [DOI: 10.1007/bf02757258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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28
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Michán C, Manchado M, Dorado G, Pueyo C. In vivo transcription of the Escherichia coli oxyR regulon as a function of growth phase and in response to oxidative stress. J Bacteriol 1999; 181:2759-64. [PMID: 10217765 PMCID: PMC93716 DOI: 10.1128/jb.181.9.2759-2764.1999] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simultaneous expression of seven genes in Escherichia coli was measured by a reverse transcription-multiplex PCR fluorescence procedure. Genes studied were (i) oxyR (transcriptional regulator); (ii) katG, dps, gorA, and ahpCF (controlled by OxyR); (iii) sodA (controlled by SoxRS); and (iv) trxA (not related to OxyR or SoxRS). Except for trxA, transcription of all genes was activated during the course of growth of wild-type bacteria, though notable variations were observed with respect to both the time and extent of activation. Whereas oxyR, katG, dps, and gorA were activated during exponential growth, ahpCF and sodA were stimulated in stationary phase. Maximal induction ranged from 4.6- to 86.5-fold, for gorA and dps, respectively. Treatment with H2O2 stimulated expression of the genes (katG, dps, ahpCF, and gorA) previously identified as members of the OxyR regulon, except for oxyR itself. Induction by H2O2 was a remarkably rapid and reversible process that took place in an OxyR-dependent and sigmaS-independent manner. NaCl induced expression of the genes controlled by OxyR, including the oxyR locus. This transcriptional up-regulation was preserved in a strain with the DeltaoxyR::kan mutation, but it was abolished (ahpCF) or significantly reduced (oxyR and dps) in a strain with the rpoS::Tn10 mutation, potentially reflecting positive transcriptional regulation of the oxyR regulon by sigmaS. Expression of trxA was not increased either by H2O2 stress or by a shift to high-osmolarity conditions.
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Affiliation(s)
- C Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071 Córdoba, Spain
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Boonstra B, French CE, Wainwright I, Bruce NC. The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J Bacteriol 1999; 181:1030-4. [PMID: 9922271 PMCID: PMC93474 DOI: 10.1128/jb.181.3.1030-1034.1999] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The udhA gene of Escherichia coli was cloned and expressed in E. coli and found to encode an enzyme with soluble pyridine nucleotide transhydrogenase activity. The N-terminal end of the enzyme contains the fingerprint motif of a dinucleotide binding domain, not present in published E. coli genome sequences due to a sequencing error. E. coli is hereby the first organism reported to possess both a soluble and a membrane-bound pyridine nucleotide transhydrogenase.
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Affiliation(s)
- B Boonstra
- Institute of Biotechnology, University of Cambridge, Cambridge CB2 1QT, United Kingdom
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30
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Abstract
1. Complex genetic systems counteract different types of 'oxidative stress' caused by reactive derivatives of oxygen. 2. The bacterial oxyR system responds to peroxide stress and is governed by OxyR, a transcription factor activated by the formation of an intramolecular disulphide bond in H2O2-treated cells. Activated OxyR switches on several genes encoding antioxidant functions, such as catalase. During aerobic growth, oxyR acts homeostatically to regulate cellular H2O2 levels. 3. The bacterial soxRS system responds to superoxide or nitric oxide (NO) stress and is activated in two transcriptional stages. The SoxR protein is activated by oxidation of its [2Fe-2S] centres in cells exposed to superoxide-generating agents, such as paraquat, or to No. Activated SoxR stimulates the soxS gene and SoxS protein then induces at least 15 genes encoding antioxidant functions, such as superoxide dismutase, metabolic functions, such as fumarase, and antibiotic resistance by activation of efflux pumps. The soxRS system may function in resistance to NO-generating immune cells and may contribute to clinical antibiotic resistance. 4. Human cells respond to subtoxic levels of NO by inducing 12 proteins and down-regulating others. A key induced activity is haem oxygenase 1, which is controlled post-transcriptionally. 5. Motor neurons exhibit adaptive resistance to NO, triggered by exposure to subtoxic NO levels, and providing resistance to usually cytotoxic levels of this agent or H2O2. Adaptive resistance to NO depends strongly on the inducible heam oxygenase activity.
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Affiliation(s)
- B Demple
- Department of Cancer Cell Biology, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
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31
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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Ferguson GP, Creighton RI, Nikolaev Y, Booth IR. Importance of RpoS and Dps in survival of exposure of both exponential- and stationary-phase Escherichia coli cells to the electrophile N-ethylmaleimide. J Bacteriol 1998; 180:1030-6. [PMID: 9495739 PMCID: PMC106988 DOI: 10.1128/jb.180.5.1030-1036.1998] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mechanisms by which Escherichia coli cells survive exposure to the toxic electrophile N-ethylmaleimide (NEM) have been investigated. Stationary-phase E. coli cells were more resistant to NEM than exponential-phase cells. The KefB and KefC systems were found to play an important role in protecting both exponential- and stationary-phase cells against NEM. Additionally, RpoS and the DNA-binding protein Dps aided the survival of both exponential- and stationary-phase cells against NEM. Double mutants lacking both RpoS and Dps and triple mutants deficient in KefB and KefC and either RpoS or Dps had an increased sensitivity to NEM in both exponential- and stationary-phase cells compared to mutants missing only one of these protective mechanisms. Stationary- and exponential-phase cells of a quadruple mutant lacking all four protective systems displayed even greater sensitivity to NEM. These results indicated that protection by the KefB and KefC systems, RpoS and Dps can each occur independently of the other systems. Alterations in the level of RpoS in exponentially growing cells correlated with the degree of NEM sensitivity. Decreasing the level of RpoS by enriching the growth medium enhanced sensitivity to NEM, whereas a mutant lacking the ClpP protease accumulated RpoS and gained high levels of resistance to NEM. A slower-growing E. coli strain was also found to accumulate RpoS and had enhanced resistance to NEM. These data emphasize the multiplicity of pathways involved in protecting E. coli cells against NEM.
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Affiliation(s)
- G P Ferguson
- Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, United Kingdom.
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Proctor RA, von Humboldt A. Bacterial energetics and antimicrobial resistance. Drug Resist Updat 1998; 1:227-35. [PMID: 16904405 DOI: 10.1016/s1368-7646(98)80003-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/1998] [Revised: 05/13/1998] [Accepted: 05/20/1998] [Indexed: 10/25/2022]
Abstract
Defining resistance to antimicrobics with specific terms is very useful as the precise mechanisms often lead to better susceptibility testing and improved treatment of bacterial infections. When one can characterize a class of phenotypic resistant organisms as electron transport variants, this has value in that it provides information about the basis for resistance and removes them from the non-specific categorization as phenotypically resistant. Studies of bacterial small colony variants (SCVs) has provided new insights into antimicrobial resistance as well as the connection between expression of virulence factors and energy metabolism. It also provides a framework for further studies which link antibiotic resistance to phase of growth, availability of nutrients, other environmental conditions, and adaptations to stress into a single model wherein the bacterial cell uses the products of energy metabolism to detect its sense of well being and to alter its response to antibiotics (Fig. I). Levels of NADH and ATP are able to act as signaling molecules in both gram positive an gram negative bacteria to activate stress sigma factors and two component systems. In the future, a full understanding of the signaling pathways in bacterial pathogens may provide new targets for the development of drugs to reduce bacterial virulence and to enhance the activity of existing antibiotics.
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Affiliation(s)
- R A Proctor
- Dept of Medical Microbiology and Immunology, University of Wisconsin Medical School, Madison, WI 53706, USA.
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