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Weibel N, Curcio M, Schreiber A, Arriaga G, Mausy M, Mehdy J, Brüllmann L, Meyer A, Roth L, Flury T, Pecina V, Starlinger K, Dernič J, Jungfer K, Ackle F, Earp J, Hausmann M, Jinek M, Rogler G, Antunes Westmann C. Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases. ACS Synth Biol 2024; 13:2376-2390. [PMID: 39115381 DOI: 10.1021/acssynbio.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation with no cure and limited treatment options that often have systemic side effects. In this study, we developed a target-specific system to potentially treat IBD by engineering the probiotic bacterium Escherichia coli Nissle 1917 (EcN). Our modular system comprises three components: a transcription factor-based sensor (NorR) capable of detecting the inflammation biomarker nitric oxide (NO), a type 1 hemolysin secretion system, and a therapeutic cargo consisting of a library of humanized anti-TNFα nanobodies. Despite a reduction in sensitivity, our system demonstrated a concentration-dependent response to NO, successfully secreting functional nanobodies with binding affinities comparable to the commonly used drug Adalimumab, as confirmed by enzyme-linked immunosorbent assay and in vitro assays. This newly validated nanobody library expands EcN therapeutic capabilities. The adopted secretion system, also characterized for the first time in EcN, can be further adapted as a platform for screening and purifying proteins of interest. Additionally, we provided a mathematical framework to assess critical parameters in engineering probiotic systems, including the production and diffusion of relevant molecules, bacterial colonization rates, and particle interactions. This integrated approach expands the synthetic biology toolbox for EcN-based therapies, providing novel parts, circuits, and a model for tunable responses at inflammatory hotspots.
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Affiliation(s)
- Nathalie Weibel
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Martina Curcio
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Atilla Schreiber
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Gabriel Arriaga
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marine Mausy
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jana Mehdy
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lea Brüllmann
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Meyer
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Len Roth
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tamara Flury
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Valerie Pecina
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Kim Starlinger
- University of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jan Dernič
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Kenny Jungfer
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Ackle
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, CH-8006 Zürich, Switzerland
| | - Jennifer Earp
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, CH-8006 Zürich, Switzerland
| | - Martin Hausmann
- Department of Gastroenterology and Hepatology, University Hospital Zürich and Zürich University, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zürich and Zürich University, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Cauã Antunes Westmann
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
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2
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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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3
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Skoog EJ, Bosak T. Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13228. [PMID: 38192240 PMCID: PMC10866078 DOI: 10.1111/1758-2229.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Integrative Oceanography DivisionScripps Institution of Oceanography, UC San DiegoLa JollaCaliforniaUSA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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4
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Chua KJ, Ling H, Hwang IY, Lee HL, March JC, Lee YS, Chang MW. An Engineered Probiotic Produces a Type III Interferon IFNL1 and Reduces Inflammations in in vitro Inflammatory Bowel Disease Models. ACS Biomater Sci Eng 2023; 9:5123-5135. [PMID: 36399014 PMCID: PMC10498420 DOI: 10.1021/acsbiomaterials.2c00202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 11/01/2022] [Indexed: 11/21/2022]
Abstract
The etiology of inflammatory bowel diseases (IBDs) frequently results in the uncontrolled inflammation of intestinal epithelial linings and the local environment. Here, we hypothesized that interferon-driven immunomodulation could promote anti-inflammatory effects. To test this hypothesis, we engineered probiotic Escherichia coli Nissle 1917 (EcN) to produce and secrete a type III interferon, interferon lambda 1 (IFNL1), in response to nitric oxide (NO), a well-known colorectal inflammation marker. We then validated the anti-inflammatory effects of the engineered EcN strains in two in vitro models: a Caco-2/Jurkat T cell coculture model and a scaffold-based 3D coculture IBD model that comprises intestinal epithelial cells, myofibroblasts, and T cells. The IFNL1-expressing EcN strains upregulated Foxp3 expression in T cells and thereafter reduced the production of pro-inflammatory cytokines such as IL-13 and -33, significantly ameliorating inflammation. The engineered strains also rescued the integrity of the inflamed epithelial cell monolayer, protecting epithelial barrier integrity even under inflammation. In the 3D coculture model, IFNL1-expressing EcN treatment enhanced the population of regulatory T cells and increased anti-inflammatory cytokine IL-10. Taken together, our study showed the anti-inflammatory effects of IFNL1-expressing probiotics in two in vitro IBD models, demonstrating their potential as live biotherapeutics for IBD immunotherapy.
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Affiliation(s)
- Koon Jiew Chua
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,117596, Singapore
- Wilmar-NUS
Corporate Laboratory, National University
of Singapore, 117599, Singapore
| | - Hua Ling
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,117596, Singapore
- Wilmar-NUS
Corporate Laboratory, National University
of Singapore, 117599, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,117596, Singapore
- Wilmar-NUS
Corporate Laboratory, National University
of Singapore, 117599, Singapore
| | - Hui Ling Lee
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,117596, Singapore
- Wilmar-NUS
Corporate Laboratory, National University
of Singapore, 117599, Singapore
| | - John C. March
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Yung Seng Lee
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore,117596, Singapore
- Wilmar-NUS
Corporate Laboratory, National University
of Singapore, 117599, Singapore
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5
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Huang H, Feng G, Wang M, Liu C, Wu Y, Dong L, Feng L, Zheng X, Chen Y. Nitric Oxide: A Neglected Driver for the Conjugative Transfer of Antibiotic Resistance Genes among Wastewater Microbiota. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6466-6478. [PMID: 35512279 DOI: 10.1021/acs.est.2c01889] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dissemination of plasmid-borne antibiotic resistance genes (ARGs) in wastewater is becoming an urgent concern. Previous studies mainly focused on the effects of coexisting contaminants on plasmid conjugation, but ignored the potential contribution of some byproducts inevitably released from wastewater treatment processes. Herein, we demonstrate for the first time that nitric oxide (NO), an intermediate of the wastewater nitrogen cycle, can significantly boost the conjugative transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella typhimurium, and wastewater microbiota). Phenotypic and genotypic tests confirmed that NO-induced promotion was not attributed to the SOS response, a well-recognized driver for horizontal gene transfer. Instead, NO exposure increased the outer membrane permeability of both the donor and recipient by inhibiting the expression of key genes involved in lipopolysaccharide biosynthesis (such as waaJ), thereby lowering the membrane barrier for conjugation. On the other hand, NO exposure not only resulted in the accumulation of intracellular tryptophan but also triggered the deficiency of intracellular methionine, both of which were validated to play key roles in regulating the global regulatory genes (korA, korB, and trbA) of plasmid RP4, activating its encoding transfer apparatus (represented by trfAp and trbBp). Overall, our findings highlighted the risks of NO in spreading ARGs among wastewater microbiota and updated the regulation mechanism of plasmid conjugation.
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Affiliation(s)
- Haining Huang
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Guanqun Feng
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meng Wang
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chao Liu
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yang Wu
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lei Dong
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Municipal Engn Design Inst Grp Co. Ltd., 901 Zhongshan North Second Road, Shanghai 200092, P. R. China
| | - Leiyu Feng
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Xiong Zheng
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yinguang Chen
- State key laboratory of pollution control and Resource reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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6
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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7
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The Amino Acids Motif -32GSSYN36- in the Catalytic Domain of E. coli Flavorubredoxin NO Reductase Is Essential for Its Activity. Catalysts 2021. [DOI: 10.3390/catal11080926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif, -G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release.
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8
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Cole JA. Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses. Mol Microbiol 2021; 116:29-40. [PMID: 33706420 DOI: 10.1111/mmi.14713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.
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Affiliation(s)
- J A Cole
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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9
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Chou WK, Vaikunthan M, Schröder HV, Link AJ, Kim H, Brynildsen MP. Synergy Screening Identifies a Compound That Selectively Enhances the Antibacterial Activity of Nitric Oxide. Front Bioeng Biotechnol 2020; 8:1001. [PMID: 32984281 PMCID: PMC7477088 DOI: 10.3389/fbioe.2020.01001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
Antibiotic resistance poses a serious threat to global health. To reinforce the anti-infective arsenal, many novel therapeutic strategies to fight bacterial infections are being explored. Among them, anti-virulence therapies, which target pathways important for virulence, have attracted much attention. Nitric oxide (NO) defense systems have been identified as critical for the pathogenesis of various bacteria, making them an appealing therapeutic target. In this study, we performed chemical screens to identify inhibitors of NO detoxification in Escherichia coli. We found that 2-mercaptobenzothiazole (2-MBT) can potently inhibit cellular detoxification of NO, achieving a level of inhibition that resembled the effect of genetically removing Hmp, the dominant detoxification enzyme under oxygenated conditions. Further analysis revealed that in the presence of NO, 2-MBT impaired the catalysis of Hmp and synthesis of Hmp and other proteins, whereas in its absence there were minimal perturbations to growth and protein synthesis. In addition, by studying the structure-activity relationship of 2-MBT, we found that both sulfur atoms in 2-MBT were vital for its inhibition of NO detoxification. Interestingly, when 2-mercaptothiazole (2-MT), which lacked the benzene ring, was used, differing biological activities were observed, although they too were NO dependent. Specifically, 2-MT could still prohibit NO detoxification, though it did not interfere with Hmp catalysis; rather, it was a stronger inhibitor of protein synthesis and it reduced the transcript levels of hmp, which was not observed with 2-MBT. Overall, these results provide a strong foundation for further exploration of 2-MBT and 2-MT for therapeutic applications.
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Affiliation(s)
- Wen Kang Chou
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Mathini Vaikunthan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Hendrik V. Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, NJ, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Hahn Kim
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, NJ, United States
- Small Molecule Screening Center, Princeton University, Princeton, NJ, United States
| | - Mark P. Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States
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10
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Role of the Nitric Oxide Reductase NorVW in the Survival and Virulence of Enterohaemorrhagic Escherichia coli during Infection. Pathogens 2020; 9:pathogens9090683. [PMID: 32825770 PMCID: PMC7558590 DOI: 10.3390/pathogens9090683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 01/20/2023] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) are bacterial pathogens responsible for life-threatening diseases in humans, such as hemolytic and uremic syndrome. It has been previously demonstrated that the interplay between EHEC and nitric oxide (NO), a mediator of the host immune innate response, is critical for infection outcome, since NO affects both Shiga toxin (Stx) production and adhesion to enterocytes. In this study, we investigated the role of the NO reductase NorVW in the virulence and fitness of two EHEC strains in a murine model of infection. We determined that the deletion of norVW in the strain O91:H21 B2F1 has no impact on its virulence, whereas it reduces the ability of the strain O157:H7 620 to persist in the mouse gut and to produce Stx. We also revealed that the fitness defect of strain 620 ΔnorVW is strongly attenuated when mice are treated with an NO synthase inhibitor. Altogether, these results demonstrate that the NO reductase NorVW participates in EHEC resistance against NO produced by the host and promotes virulence through the modulation of Stx synthesis. The contribution of NorVW in the EHEC infectious process is, however, strain-dependent and suggests that the EHEC response to nitrosative stress is complex and multifactorial.
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11
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Gardette M, Le Hello S, Mariani-Kurkdjian P, Fabre L, Gravey F, Garrivier A, Loukiadis E, Jubelin G. Identification and prevalence of in vivo-induced genes in enterohaemorrhagic Escherichia coli. Virulence 2019; 10:180-193. [PMID: 30806162 PMCID: PMC6550539 DOI: 10.1080/21505594.2019.1582976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 02/06/2019] [Indexed: 12/14/2022] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) are food-borne pathogens responsible for bloody diarrhoea and renal failure in humans. While Shiga toxin (Stx) is the cardinal virulence factor of EHEC, its production by E. coli is not sufficient to cause disease and many Shiga-toxin producing E. coli (STEC) strains have never been implicated in human infection. So far, the pathophysiology of EHEC infection is not fully understood and more knowledge is needed to characterize the "auxiliary" factors that enable a STEC strain to cause disease in humans. In this study, we applied a recombinase-based in vivo expression technology (RIVET) to the EHEC reference strain EDL933 in order to identify genes specifically induced during the infectious process, using mouse as an infection model. We identified 31 in vivo-induced (ivi) genes having functions related to metabolism, stress adaptive response and bacterial virulence or fitness. Eight of the 31 ivi genes were found to be heterogeneously distributed in EHEC strains circulating in France these last years. In addition, they are more prevalent in strains from the TOP seven priority serotypes and particularly strains carrying significant virulence determinants such as Stx2 and intimin adhesin. This work sheds further light on bacterial determinants over-expressed in vivo during infection that may contribute to the potential of STEC strains to cause disease in humans.
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Affiliation(s)
- Marion Gardette
- UCA, INRA, UMR454 MEDIS, Clermont-Ferrand, France
- Laboratoire d’écologie microbienne de Lyon, Université de Lyon, CNRS, INRA, UCBL, VetAgro Sup, Marcy l’Etoile, France
| | - Simon Le Hello
- Centre de Référence National des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
- Université de Normandie, EA 2656 GRAM 2.0, UNICAEN, Caen, France
| | - Patricia Mariani-Kurkdjian
- Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Laetitia Fabre
- Centre de Référence National des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - François Gravey
- Centre de Référence National des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
- Université de Normandie, EA 2656 GRAM 2.0, UNICAEN, Caen, France
| | | | - Estelle Loukiadis
- Laboratoire d’écologie microbienne de Lyon, Université de Lyon, CNRS, INRA, UCBL, VetAgro Sup, Marcy l’Etoile, France
- Laboratoire national de référence des E. coli, Université de Lyon, VetAgro Sup, Marcy l’Etoile, France
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12
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Liu J, Dong Y, Wang N, Ma S, Lu C, Liu Y. Diverse effects of nitric oxide reductase NorV on Aeromonas hydrophila virulence-associated traits under aerobic and anaerobic conditions. Vet Res 2019; 50:67. [PMID: 31547881 PMCID: PMC6755692 DOI: 10.1186/s13567-019-0683-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/23/2019] [Indexed: 11/10/2022] Open
Abstract
NorV has been known to be an anaerobic nitric oxide reductase associated with nitric oxide (NO) detoxification. Recently, we showed that the norV gene of Aeromonas hydrophila was highly upregulated after co-culturing with Tetrahymena thermophila. Here, we demonstrated that the transcription and expression levels of norV were upregulated in a dose-dependent manner after exposure to NO under aerobic and anaerobic conditions. To investigate the roles of norV in resisting predatory protists and virulence of A. hydrophila, we constructed the norV gene-deletion mutant (ΔnorV). Compared to the wild type, the ΔnorV mutant showed no significant difference in growth at various NO concentrations under aerobic conditions but significantly stronger NO-mediated growth inhibition under anaerobic conditions. The deletion of norV exhibited markedly decreased cytotoxicity, hemolytic and protease activities under aerobic and anaerobic conditions. Also, the hemolysin co-regulated protein (Hcp) in the ΔnorV mutant showed increased secretion under aerobic conditions but decreased secretion under anaerobic conditions as compared to the wild-type. Moreover, the inactivation of norV led to reduced resistance to predation by T. thermophila, decreased survival within macrophages and highly attenuated virulence in zebrafish. Our data indicate a diverse role for norV in the expression of A. hydrophila virulence-associated traits that is not completely dependent on its function as a nitric oxide reductase. This study provides insights into an unexplored area of NorV, which will contribute to our understanding of bacterial pathogenesis and the development of new control strategies for A. hydrophila infection.
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Affiliation(s)
- Jin Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuhao Dong
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nannan Wang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing, 211169, China
| | - Shuiyan Ma
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengping Lu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongjie Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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13
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Shimizu T, Matsumoto A, Noda M. Cooperative Roles of Nitric Oxide-Metabolizing Enzymes To Counteract Nitrosative Stress in Enterohemorrhagic Escherichia coli. Infect Immun 2019; 87:e00334-19. [PMID: 31209149 PMCID: PMC6704613 DOI: 10.1128/iai.00334-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 06/08/2019] [Indexed: 11/20/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) has at least three enzymes, NorV, Hmp, and Hcp, that act independently to lower the toxicity of nitric oxide (NO), a potent antimicrobial molecule. This study aimed to reveal the cooperative roles of these defensive enzymes in EHEC against nitrosative stress. Under anaerobic conditions, combined deletion of all three enzymes significantly increased the NO sensitivity of EHEC determined by the growth at late stationary phase; however, the expression of norV restored the NO resistance of EHEC. On the other hand, the growth of Δhmp mutant EHEC was inhibited after early stationary phase, indicating that NorV and Hmp play a cooperative role in anaerobic growth. Under microaerobic conditions, the growth of Δhmp mutant EHEC was inhibited by NO, indicating that Hmp is the enzyme that protects cells from NO stress under microaerobic conditions. When EHEC cells were exposed to a lower concentration of NO, the NO level in bacterial cells of Δhcp mutant EHEC was higher than those of the other EHEC mutants, suggesting that Hcp is effective at regulating NO levels only at a low concentration. These findings of a low level of NO in bacterial cells with hcp indicate that the NO consumption activity of Hcp was suppressed by Hmp at a low range of NO concentrations. Taken together, these results show that the cooperative effects of NO-metabolizing enzymes are regulated by the range of NO concentrations to which the EHEC cells are exposed.
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Affiliation(s)
- Takeshi Shimizu
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akio Matsumoto
- Department of Aging Pharmacology, School of Medicine, Toho University, Tokyo, Japan
| | - Masatoshi Noda
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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14
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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15
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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16
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Do nitric oxide, carbon monoxide and hydrogen sulfide really qualify as 'gasotransmitters' in bacteria? Biochem Soc Trans 2018; 46:1107-1118. [PMID: 30190328 PMCID: PMC6195638 DOI: 10.1042/bst20170311] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 01/04/2023]
Abstract
A gasotransmitter is defined as a small, generally reactive, gaseous molecule that, in solution, is generated endogenously in an organism and exerts important signalling roles. It is noteworthy that these molecules are also toxic and antimicrobial. We ask: is this definition of a gasotransmitter appropriate in the cases of nitric oxide, carbon monoxide and hydrogen sulfide (H2S) in microbes? Recent advances show that, not only do bacteria synthesise each of these gases, but the molecules also have important signalling or messenger roles in addition to their toxic effects. However, strict application of the criteria proposed for a gasotransmitter leads us to conclude that the term ‘small molecule signalling agent’, as proposed by Fukuto and others, is preferable terminology.
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17
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Nitric Oxide-Mediated Induction of Dispersal in Pseudomonas aeruginosa Biofilms Is Inhibited by Flavohemoglobin Production and Is Enhanced by Imidazole. Antimicrob Agents Chemother 2018; 62:AAC.01832-17. [PMID: 29263060 DOI: 10.1128/aac.01832-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023] Open
Abstract
The biological signal molecule nitric oxide (NO) was found to induce biofilm dispersal across a range of bacterial species, which led to its consideration for therapeutic strategies to treat biofilms and biofilm-related infections. However, biofilms are often not completely dispersed after exposure to NO. To better understand this phenomenon, we investigated the response of Pseudomonas aeruginosa biofilm cells to successive NO treatments. When biofilms were first pretreated with a low, noneffective dose of NO, a second dose of the signal molecule at a concentration usually capable of inducing dispersal did not have any effect. Amperometric analysis revealed that pretreated P. aeruginosa cells had enhanced NO-scavenging activity, and this effect was associated with the production of the flavohemoglobin Fhp. Further, quantitative real-time reverse transcription-PCR (qRT-PCR) analysis showed that fhp expression increased by over 100-fold in NO-pretreated biofilms compared to untreated biofilms. Biofilms of mutant strains harboring mutations in fhp or fhpR, encoding a NO-responsive regulator of fhp, were not affected in their dispersal response after the initial pretreatment with NO. Overall, these results suggest that FhpR can sense NO to trigger production of the flavohemoglobin Fhp and inhibit subsequent dispersal responses to NO. Finally, the addition of imidazole, which can inhibit the NO dioxygenase activity of flavohemoglobin, attenuated the prevention of dispersal after NO pretreatment and improved the dispersal response in older, starved biofilms. This study clarifies the underlying mechanisms of impaired dispersal induced by repeated NO treatments and offers a new perspective for improving the use of NO in biofilm control strategies.
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López G, Diaz-Cárdenas C, Shapiro N, Woyke T, Kyrpides NC, David Alzate J, González LN, Restrepo S, Baena S. Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes. Stand Genomic Sci 2017; 12:78. [PMID: 29255573 PMCID: PMC5731063 DOI: 10.1186/s40793-017-0292-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022] Open
Abstract
Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3.0 μm × 0.5–1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14–3T. The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14–3T. We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.
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Affiliation(s)
- Gina López
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Carolina Diaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - J David Alzate
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Laura N González
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Silvia Restrepo
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
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Tharmalingam S, Alhasawi A, Appanna VP, Lemire J, Appanna VD. Reactive nitrogen species (RNS)-resistant microbes: adaptation and medical implications. Biol Chem 2017. [PMID: 28622140 DOI: 10.1515/hsz-2017-0152] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nitrosative stress results from an increase in reactive nitrogen species (RNS) within the cell. Though the RNS - nitric oxide (·NO) and peroxynitrite (ONOO-) - play pivotal physiological roles, at elevated concentrations, these moieties can be poisonous to both prokaryotic and eukaryotic cells alike due to their capacity to disrupt a variety of essential biological processes. Numerous microbes are known to adapt to nitrosative stress by elaborating intricate strategies aimed at neutralizing RNS. In this review, we will discuss both the enzymatic systems dedicated to the elimination of RNS as well as the metabolic networks that are tailored to generate RNS-detoxifying metabolites - α-keto-acids. The latter has been demonstrated to nullify RNS via non-enzymatic decarboxylation resulting in the production of a carboxylic acid, many of which are potent signaling molecules. Furthermore, as aerobic energy production is severely impeded during nitrosative stress, alternative ATP-generating modules will be explored. To that end, a holistic understanding of the molecular adaptation to nitrosative stress, reinforces the notion that neutralization of toxicants necessitates significant metabolic reconfiguration to facilitate cell survival. As the alarming rise in antimicrobial resistant pathogens continues unabated, this review will also discuss the potential for developing therapies that target the alternative ATP-generating machinery of bacteria.
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Galia W, Leriche F, Cruveiller S, Garnier C, Navratil V, Dubost A, Blanquet-Diot S, Thevenot-Sergentet D. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. BMC Genomics 2017; 18:574. [PMID: 28774270 PMCID: PMC5543532 DOI: 10.1186/s12864-017-3957-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. RESULTS Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. CONCLUSION In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.
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Affiliation(s)
- Wessam Galia
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France.
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France.
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France.
| | - Francoise Leriche
- Université Clermont Auvergne, INRA, UMRF, F-15000, Aurillac, France
- VetAgro Sup, Campus Agronomique de Lempdes, Lempdes, France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute Genoscope & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, Evry, France
| | - Cindy Garnier
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Audrey Dubost
- UMR 5557 Ecologie Microbienne, CNRS, Université de Lyon, Lyon, France
| | - Stéphanie Blanquet-Diot
- UMR UCA INRA 454 MEDIS Microbiota Digestive environment and Health, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Thevenot-Sergentet
- UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France
- Reference Laboratory for Escherichia coli including Shiga Toxin-Producing E. coli, VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, Marcy l'Etoile, Lyon, France
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Stress Responses, Adaptation, and Virulence of Bacterial Pathogens During Host Gastrointestinal Colonization. Microbiol Spectr 2017; 4. [PMID: 27227312 DOI: 10.1128/microbiolspec.vmbf-0007-2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Invading pathogens are exposed to a multitude of harmful conditions imposed by the host gastrointestinal tract and immune system. Bacterial defenses against these physical and chemical stresses are pivotal for successful host colonization and pathogenesis. Enteric pathogens, which are encountered due to the ingestion of or contact with contaminated foods or materials, are highly successful at surviving harsh conditions to colonize and cause the onset of host illness and disease. Pathogens such as Campylobacter, Helicobacter, Salmonella, Listeria, and virulent strains of Escherichia have evolved elaborate defense mechanisms to adapt to the diverse range of stresses present along the gastrointestinal tract. Furthermore, these pathogens contain a multitude of defenses to help survive and escape from immune cells such as neutrophils and macrophages. This chapter focuses on characterized bacterial defenses against pH, osmotic, oxidative, and nitrosative stresses with emphasis on both the direct and indirect mechanisms that contribute to the survival of each respective stress response.
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Hartman CE, Samuels DJ, Karls AC. Modulating Salmonella Typhimurium's Response to a Changing Environment through Bacterial Enhancer-Binding Proteins and the RpoN Regulon. Front Mol Biosci 2016; 3:41. [PMID: 27583250 PMCID: PMC4987338 DOI: 10.3389/fmolb.2016.00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/28/2016] [Indexed: 12/25/2022] Open
Abstract
Transcription sigma factors direct the selective binding of RNA polymerase holoenzyme (Eσ) to specific promoters. Two families of sigma factors determine promoter specificity, the σ(70) (RpoD) family and the σ(54) (RpoN) family. In transcription controlled by σ(54), the Eσ(54)-promoter closed complex requires ATP hydrolysis by an associated bacterial enhancer-binding protein (bEBP) for the transition to open complex and transcription initiation. Given the wide host range of Salmonella enterica serovar Typhimurium, it is an excellent model system for investigating the roles of RpoN and its bEBPs in modulating the lifestyle of bacteria. The genome of S. Typhimurium encodes 13 known or predicted bEBPs, each responding to a unique intracellular or extracellular signal. While the regulons of most alternative sigma factors respond to a specific environmental or developmental signal, the RpoN regulon is very diverse, controlling genes for response to nitrogen limitation, nitric oxide stress, availability of alternative carbon sources, phage shock/envelope stress, toxic levels of zinc, nucleic acid damage, and other stressors. This review explores how bEBPs respond to environmental changes encountered by S. Typhimurium during transmission/infection and influence adaptation through control of transcription of different components of the S. Typhimurium RpoN regulon.
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Affiliation(s)
| | - David J Samuels
- Department of Microbiology, University of Georgia Athens, GA, USA
| | - Anna C Karls
- Department of Microbiology, University of Georgia Athens, GA, USA
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Runkel S, Wells HC, Rowley G. Living with Stress: A Lesson from the Enteric Pathogen Salmonella enterica. ADVANCES IN APPLIED MICROBIOLOGY 2016; 83:87-144. [PMID: 23651595 DOI: 10.1016/b978-0-12-407678-5.00003-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability to sense and respond to the environment is essential for the survival of all living organisms. Bacterial pathogens such as Salmonella enterica are of particular interest due to their ability to sense and adapt to the diverse range of conditions they encounter, both in vivo and in environmental reservoirs. During this cycling from host to non-host environments, Salmonella encounter a variety of environmental insults ranging from temperature fluctuations, nutrient availability and changes in osmolarity, to the presence of antimicrobial peptides and reactive oxygen/nitrogen species. Such fluctuating conditions impact on various areas of bacterial physiology including virulence, growth and antimicrobial resistance. A key component of the success of any bacterial pathogen is the ability to recognize and mount a suitable response to the discrete chemical and physical stresses elicited by the host. Such responses occur through a coordinated and complex programme of gene expression and protein activity, involving a range of transcriptional regulators, sigma factors and two component regulatory systems. This review briefly outlines the various stresses encountered throughout the Salmonella life cycle and the repertoire of regulatory responses with which Salmonella counters. In particular, how these Gram-negative bacteria are able to alleviate disruption in periplasmic envelope homeostasis through a group of stress responses, known collectively as the Envelope Stress Responses, alongside the mechanisms used to overcome nitrosative stress, will be examined in more detail.
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Affiliation(s)
- Sebastian Runkel
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. J Biol Inorg Chem 2016; 21:39-52. [PMID: 26767750 DOI: 10.1007/s00775-015-1329-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/28/2015] [Indexed: 12/27/2022]
Abstract
Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal.
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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Abstract
Nitrate reduction to ammonia via nitrite occurs widely as an anabolic process through which bacteria, archaea, and plants can assimilate nitrate into cellular biomass. Escherichia coli and related enteric bacteria can couple the eight-electron reduction of nitrate to ammonium to growth by coupling the nitrate and nitrite reductases involved to energy-conserving respiratory electron transport systems. In global terms, the respiratory reduction of nitrate to ammonium dominates nitrate and nitrite reduction in many electron-rich environments such as anoxic marine sediments and sulfide-rich thermal vents, the human gastrointestinal tract, and the bodies of warm-blooded animals. This review reviews the regulation and enzymology of this process in E. coli and, where relevant detail is available, also in Salmonella and draws comparisons with and implications for the process in other bacteria where it is pertinent to do so. Fatty acids may be present in high levels in many of the natural environments of E. coli and Salmonella in which oxygen is limited but nitrate is available to support respiration. In E. coli, nitrate reduction in the periplasm involves the products of two seven-gene operons, napFDAGHBC, encoding the periplasmic nitrate reductase, and nrfABCDEFG, encoding the periplasmic nitrite reductase. No bacterium has yet been shown to couple a periplasmic nitrate reductase solely to the cytoplasmic nitrite reductase NirB. The cytoplasmic pathway for nitrate reduction to ammonia is restricted almost exclusively to a few groups of facultative anaerobic bacteria that encounter high concentrations of environmental nitrate.
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Mehta HH, Liu Y, Zhang MQ, Spiro S. Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microb Genom 2015; 1:e000031. [PMID: 28348816 PMCID: PMC5320621 DOI: 10.1099/mgen.0.000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022] Open
Abstract
Uropathogenic Escherchia coli (UPEC) is the causative agent of urinary tract infections. Nitric oxide (NO) is a toxic water-soluble gas that is encountered by UPEC in the urinary tract. Therefore, UPEC probably requires mechanisms to detoxify NO in the host environment. Thus far, flavohaemoglobin (Hmp), an NO denitrosylase, is the only demonstrated NO detoxification system in UPEC. Here we show that, in E. coli strain CFT073, the NADH-dependent NO reductase flavorubredoxin (FlRd) also plays a major role in NO scavenging. We generated a mutant that lacks all known and candidate NO detoxification pathways (Hmp, FlRd and the respiratory nitrite reductase, NrfA). When grown and assayed anaerobically, this mutant expresses an NO-inducible NO scavenging activity, pointing to the existence of a novel detoxification mechanism. Expression of this activity is inducible by both NO and nitrate, and the enzyme is membrane-associated. Genome-wide transcriptional profiling of UPEC grown under anaerobic conditions in the presence of nitrate (as a source of NO) highlighted various aspects of the response of the pathogen to nitrate and NO. Several virulence-associated genes are upregulated, suggesting that host-derived NO is a potential regulator of UPEC virulence. Chromatin immunoprecipitation and sequencing was used to evaluate the NsrR regulon in CFT073. We identified 49 NsrR binding sites in promoter regions in the CFT073 genome, 29 of which were not previously identified in E. coli K-12. NsrR may regulate some CFT073 genes that do not have homologues in E. coli K-12.
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Affiliation(s)
- Heer H. Mehta
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Yuxuan Liu
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Michael Q. Zhang
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
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Chhabra S, Spiro S. Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli. Microbiology (Reading) 2015; 161:2029-2038. [DOI: 10.1099/mic.0.000151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Shivani Chhabra
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
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Complete Genome Sequence of Marinobacter sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01103-15. [PMID: 26404584 PMCID: PMC4582590 DOI: 10.1128/genomea.01103-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Marinobacter sp. CP1 was isolated from a self-regenerating and self-sustaining biocathode biofilm that can fix CO2 and generate electric current. We present the complete genome sequence of this strain, which consists of a circular 4.8-Mbp chromosome, to understand the mechanism of extracellular electron transfer in a microbial consortium.
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Crack JC, Munnoch J, Dodd EL, Knowles F, Al Bassam MM, Kamali S, Holland AA, Cramer SP, Hamilton CJ, Johnson MK, Thomson AJ, Hutchings MI, Le Brun NE. NsrR from Streptomyces coelicolor is a nitric oxide-sensing [4Fe-4S] cluster protein with a specialized regulatory function. J Biol Chem 2015; 290:12689-704. [PMID: 25771538 PMCID: PMC4432287 DOI: 10.1074/jbc.m115.643072] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 12/31/2022] Open
Abstract
The Rrf2 family transcription factor NsrR controls expression of genes in a wide range of bacteria in response to nitric oxide (NO). The precise form of the NO-sensing module of NsrR is the subject of controversy because NsrR proteins containing either [2Fe-2S] or [4Fe-4S] clusters have been observed previously. Optical, Mössbauer, resonance Raman spectroscopies and native mass spectrometry demonstrate that Streptomyces coelicolor NsrR (ScNsrR), previously reported to contain a [2Fe-2S] cluster, can be isolated containing a [4Fe-4S] cluster. ChIP-seq experiments indicated that the ScNsrR regulon is small, consisting of only hmpA1, hmpA2, and nsrR itself. The hmpA genes encode NO-detoxifying flavohemoglobins, indicating that ScNsrR has a specialized regulatory function focused on NO detoxification and is not a global regulator like some NsrR orthologues. EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR binds specifically and tightly to an 11-bp inverted repeat sequence in the promoter regions of the identified target genes and that DNA binding is abolished following reaction with NO. Resonance Raman data were consistent with cluster coordination by three Cys residues and one oxygen-containing residue, and analysis of ScNsrR variants suggested that highly conserved Glu-85 may be the fourth ligand. Finally, we demonstrate that some low molecular weight thiols, but importantly not physiologically relevant thiols, such as cysteine and an analogue of mycothiol, bind weakly to the [4Fe-4S] cluster, and exposure of this bound form to O2 results in cluster conversion to the [2Fe-2S] form, which does not bind to DNA. These data help to account for the observation of [2Fe-2S] forms of NsrR.
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Affiliation(s)
- Jason C Crack
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry
| | | | - Erin L Dodd
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry
| | | | | | - Saeed Kamali
- the Department of Chemistry, University of California, Davis, California 95616, and
| | - Ashley A Holland
- the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Stephen P Cramer
- the Department of Chemistry, University of California, Davis, California 95616, and
| | - Chris J Hamilton
- the School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Michael K Johnson
- the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Andrew J Thomson
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry
| | | | - Nick E Le Brun
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry,
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Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X. The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR. Mol Microbiol 2015; 95:17-30. [PMID: 25354037 DOI: 10.1111/mmi.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2014] [Indexed: 11/28/2022]
Abstract
σ(54)-dependent transcription controls a wide range of stress-related genes in bacteria and is tightly regulated. In contrast to σ(70), the σ(54)-RNA polymerase holoenzyme forms a stable closed complex at the promoter site that rarely isomerises into transcriptionally competent open complexes. The conversion into open complexes requires the ATPase activity of activator proteins that bind remotely upstream of the transcriptional start site. These activators belong to the large AAA protein family and the majority of them consist of an N-terminal regulatory domain, a central AAA domain and a C-terminal DNA binding domain. Here we use a functional variant of the NorR activator, a dedicated NO sensor, to provide the first structural and functional characterisation of a full length AAA activator in complex with its enhancer DNA. Our data suggest an inter-dependent and synergistic relationship of all three functional domains and provide an explanation for the dependence of NorR on enhancer DNA. Our results show that NorR readily assembles into higher order oligomers upon enhancer binding, independent of activating signals. Upon inducing signals, the N-terminal regulatory domain relocates to the periphery of the AAA ring. Together our data provide an assembly and activation mechanism for NorR.
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Affiliation(s)
- Matt Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
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Miura Y, Yoshimitsu K, Takatani N, Watanabe Y, Nakajima H. Effect of nitric oxide on VnfA, a transcriptional activator of VFe-nitrogenase in Azotobacter vinelandii. J Biochem 2014; 157:365-75. [PMID: 25500211 DOI: 10.1093/jb/mvu083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/09/2014] [Indexed: 11/13/2022] Open
Abstract
The transcriptional activator, VnfA, is necessary for the expression of the structural genes encoding vanadium-dependent nitrogenase in Azotobacter vinelandii. We have previously reported that VnfA harbours a Fe-S cluster as a prosthetic group, presumably a 3Fe-4S type, which is vital for the transcriptionally active VnfA. A plausible effector molecule is a reactive oxygen species (ROS), which disassembles the Fe-S cluster switching the active VnfA to become fully inactive. This finding prompted us to investigate the effect of nitric oxide (NO), another physiologically important radical species on the VnfA activity. Unlike ROS, the VnfA activity was moderately inhibited and converged to 70% of the maximum by NO irrespective of its concentration. The Fe-S cluster of VnfA was found to react with NO to form a dinitrosyl-iron complex, either in the dimeric or monomeric form, dependent on the relative stoichiometry of NO to the Fe-S cluster. The VnfA species harbouring the dinitrosyl-iron complexes in each form exhibited 50% ATPase activity compared to the active VnfA. The findings of this study would open an argument about a biological effect of NO on nitrogenase in light of its transcriptional regulatory system.
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Affiliation(s)
- Yukio Miura
- Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Kyohei Yoshimitsu
- Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Nobuyuki Takatani
- Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
| | - Hiroshi Nakajima
- Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan Department of Chemistry, Graduate School of Science; Graduate School of Bioagricultural Science; and Research Center of Materials Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan
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Nitric oxide reactivities of the two globins of the foodborne pathogen Campylobacter jejuni: roles in protection from nitrosative stress and analysis of potential reductants. Nitric Oxide 2013; 34:65-75. [PMID: 23764490 DOI: 10.1016/j.niox.2013.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 12/29/2022]
Abstract
BACKGROUND During infection and pathogenesis, Campylobacter, the leading cause of gastroenteritis, encounters NO and reactive nitrogen species (RNS) derived from the host. To combat these species, Campylobacter jejuni expresses two haemoglobins: the single domain haemoglobin (Cgb) detoxifies NO but the role of the truncated globin (Ctb) is unclear. Confirmation of Cgb activity and more extensive exploration of Ctb function(s) in vivo are restricted due to difficulties in expressing proteins in Campylobacter and our lack of understanding of how the globin haems are re-reduced after ligand reactions. METHODS The cgb and ctb genes were cloned under the control of arabinose-inducible promoters and the globins expressed in an Escherichia coli mutant lacking the main NO detoxification mechanisms (Hmp and the Nor system comprising the transcription regulator NorR, the flavorubredoxin and its reductase (NorVW)); cellular responses under oxidative and nitrosative stress conditions were assessed. Spectroscopic changes of the Cgb and Ctb haems in soluble fractions after oxidation by NO were evaluated. Construction of E. coli nor mutants and a ubiquinone-defective strain allowed the exploration of the flavorubredoxin reductase and the aerobic respiratory chain as candidates for Cgb electron donors in E. coli mutants. RESULTS Cgb, but not Ctb, complements the NO- and RNS-sensitive phenotype of an E. coli hmp mutant in aerobic conditions; however, Cgb fails to protect an hmp norR mutant in the absence of oxygen. Reduction of Cgb and Ctb in E. coli and C. jejuni soluble extracts and turnover after NO oxidation is demonstrated. Finally, we report a minor role for NorW as a Cgb reductase partner in E. coli but no role for respiratory electron flux in globin redox cycling. CONCLUSIONS The NO detoxification capacity of Cgb is confirmed by heterologous expression in E. coli. The reducibility of Cgb and Ctb in E. coli and C. jejuni extracts and the lack of dependence of reduction upon flavorubredoxin reductase and the respiratory chain in E. coli argue in favor of a non-specific reductase system. GENERAL SIGNIFICANCE We present the most persuasive evidence to date that Cgb, but not Ctb, confers tolerance to NO and RNS by reaction with NO. Since certain hypotheses for the mechanism of haem re-reduction in E. coli following the reaction with NO are not proven, the mechanisms of reduction in C. jejuni now require challenging experimental evaluation.
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The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. Microbiol Mol Biol Rev 2013; 76:497-529. [PMID: 22933558 DOI: 10.1128/mmbr.00006-12] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial enhancer binding proteins (bEBPs) are transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ(54). We present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. The review is structured by introducing each of the three domains in turn: the central catalytic domain, the N-terminal regulatory domain, and the C-terminal DNA binding domain. The role of the central catalytic domain is presented with particular reference to (i) oligomerization, (ii) ATP hydrolysis, and (iii) the key GAFTGA motif that contacts σ(54) for remodeling. Each of these functions forms a potential target of the signal-sensing N-terminal regulatory domain, which can act either positively or negatively to control the activation of σ(54)-dependent transcription. Finally, we focus on the DNA binding function of the C-terminal domain and the enhancer sites to which it binds. Particular attention is paid to the importance of σ(54) to the bacterial cell and its unique role in regulating transcription.
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Abstract
Campylobacter jejuni is a zoonotic Gram-negative bacterial pathogen that is exposed to reactive nitrogen species, such as nitric oxide, from a variety of sources. To combat the toxic effects of this nitrosative stress, C. jejuni upregulates a small regulon under the control of the transcriptional activator NssR, which positively regulates the expression of a single-domain globin protein (Cgb) and a truncated globin protein (Ctb). Cgb has previously been shown to detoxify nitric oxide, but the role of Ctb remains contentious. As C. jejuni is amenable to genetic manipulation, and its globin proteins are easily expressed and purified, a combination of mutagenesis, complementation, transcriptomics, spectroscopic characterisation and structural analyses has been used to probe the regulation, function and structure of Cgb and Ctb. This ability to study Cgb and Ctb with such a multi-pronged approach is a valuable asset, especially since only a small fraction of known globin proteins have been functionally characterised.
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Gardner PR. Hemoglobin: a nitric-oxide dioxygenase. SCIENTIFICA 2012; 2012:683729. [PMID: 24278729 PMCID: PMC3820574 DOI: 10.6064/2012/683729] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/04/2012] [Indexed: 05/09/2023]
Abstract
Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as NO dioxygenases (NODs). Indeed, the NOD function has emerged as a more common and ancient function than the well-known role in O2 transport-storage. Novel hemoglobins possessing a NOD function continue to be discovered in diverse life forms. Unique hemoglobin structures evolved, in part, for catalysis with different electron donors. The mechanism of NOD catalysis by representative single domain hemoglobins and multidomain flavohemoglobin occurs through a multistep mechanism involving O2 migration to the heme pocket, O2 binding-reduction, NO migration, radical-radical coupling, O-atom rearrangement, nitrate release, and heme iron re-reduction. Unraveling the physiological functions of multiple NODs with varying expression in organisms and the complexity of NO as both a poison and signaling molecule remain grand challenges for the NO field. NOD knockout organisms and cells expressing recombinant NODs are helping to advance our understanding of NO actions in microbial infection, plant senescence, cancer, mitochondrial function, iron metabolism, and tissue O2 homeostasis. NOD inhibitors are being pursued for therapeutic applications as antibiotics and antitumor agents. Transgenic NOD-expressing plants, fish, algae, and microbes are being developed for agriculture, aquaculture, and industry.
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Affiliation(s)
- Paul R. Gardner
- Miami Valley Biotech, 1001 E. 2nd Street, Suite 2445, Dayton, OH 45402, USA
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Abstract
SIGNIFICANCE In bacteria, transcriptional responses to reactive oxygen and nitrogen species (ROS and RNS, respectively) are typically coordinated by regulatory proteins that employ metal centers or reactive thiols to detect the presence of those species. This review is focused on the structure, function and mechanism of three regulatory proteins (Fur, PerR, and NorR) that contain non-heme iron and regulate the transcription of target genes in response to ROS and/or RNS. The targets for regulation include genes encoding detoxification activities, and genes encoding proteins involved in the repair of the damage caused by ROS and RNS. RECENT ADVANCES Three-dimensional structures of several Fur proteins and of PerR are revealing important details of the metal binding sites of these proteins, showing a surprising degree of structural diversity in the Fur family. CRITICAL ISSUES Discussion of the interaction of Fur with ROS and RNS will illustrate the difficulty that sometimes exists in distinguishing between true physiological responses and adventitious reactions of a regulatory protein with a reactive ligand. FUTURE DIRECTIONS Consideration of these three sensor proteins illuminates some of the key questions that remain unanswered, for example, the nature of the biochemical determinants that dictate the sensitivity and specificity of the interaction of the sensor proteins with their cognate signals.
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Affiliation(s)
- Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA.
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Archer EJ, Robinson AB, Süel GM. Engineered E. coli that detect and respond to gut inflammation through nitric oxide sensing. ACS Synth Biol 2012; 1:451-7. [PMID: 23656184 DOI: 10.1021/sb3000595] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Advances in synthetic biology now allow for the reprogramming of microorganisms to execute specific tasks. Here, we describe the development of an engineered strain of E. coli capable of sensing and responding to the presence of a mammalian inflammatory signal. The synthetic gene regulatory circuit is designed to permanently alter gene expression in response to the well characterized inflammatory signal nitric oxide. The detection of nitric oxide initiates the expression of a DNA recombinase, causing the permanent activation of a DNA switch. We demonstrate that E. coli containing this synthetic circuit respond to nitric oxide from both chemical and biological sources, with permanent DNA recombination occurring in the presence of nitric oxide donor compounds or inflamed mouse ileum explants. In the future, this synthetic genetic circuit will be optimized to allow E. coli to reliably detect and respond to inflammation in vivo.
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Spiro S. Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors. Philos Trans R Soc Lond B Biol Sci 2012; 367:1213-25. [PMID: 22451107 DOI: 10.1098/rstb.2011.0309] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several biochemical mechanisms contribute to the biological generation of nitrous oxide (N(2)O). N(2)O generating enzymes include the respiratory nitric oxide (NO) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. On the other hand, there is only one enzyme that is known to use N(2)O as a substrate, which is the respiratory N(2)O reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). This article will briefly review the properties of the enzymes that make and consume N(2)O, together with the accessory proteins that have roles in the assembly and maturation of those enzymes. The expression of the genes encoding the enzymes that produce and consume N(2)O is regulated by environmental signals (typically oxygen and NO) acting through regulatory proteins, which, either directly or indirectly, control the frequency of transcription initiation. The roles and mechanisms of these proteins, and the structures of the regulatory networks in which they participate will also be reviewed.
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Affiliation(s)
- Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
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Shimizu T, Tsutsuki H, Matsumoto A, Nakaya H, Noda M. The nitric oxide reductase of enterohaemorrhagic Escherichia coli plays an important role for the survival within macrophages. Mol Microbiol 2012; 85:492-512. [DOI: 10.1111/j.1365-2958.2012.08122.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Bowman LAH, McLean S, Poole RK, Fukuto JM. The diversity of microbial responses to nitric oxide and agents of nitrosative stress close cousins but not identical twins. Adv Microb Physiol 2012; 59:135-219. [PMID: 22114842 DOI: 10.1016/b978-0-12-387661-4.00006-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nitric oxide and related nitrogen species (reactive nitrogen species) now occupy a central position in contemporary medicine, physiology, biochemistry, and microbiology. In particular, NO plays important antimicrobial defenses in innate immunity but microbes have evolved intricate NO-sensing and defense mechanisms that are the subjects of a vast literature. Unfortunately, the burgeoning NO literature has not always been accompanied by an understanding of the intricacies and complexities of this radical and other reactive nitrogen species so that there exists confusion and vagueness about which one or more species exert the reported biological effects. The biological chemistry of NO and derived/related molecules is complex, due to multiple species that can be generated from NO in biological milieu and numerous possible reaction targets. Moreover, the fate and disposition of NO is always a function of its biological environment, which can vary significantly even within a single cell. In this review, we consider newer aspects of the literature but, most importantly, consider the underlying chemistry and draw attention to the distinctiveness of NO and its chemical cousins, nitrosonium (NO(+)), nitroxyl (NO(-), HNO), peroxynitrite (ONOO(-)), nitrite (NO(2)(-)), and nitrogen dioxide (NO(2)). All these species are reported to be generated in biological systems from initial formation of NO (from nitrite, NO synthases, or other sources) or its provision in biological experiments (typically from NO gas, S-nitrosothiols, or NO donor compounds). The major targets of NO and nitrosative damage (metal centers, thiols, and others) are reviewed and emphasis is given to newer "-omic" methods of unraveling the complex repercussions of NO and nitrogen oxide assaults. Microbial defense mechanisms, many of which are critical for pathogenicity, include the activities of hemoglobins that enzymically detoxify NO (to nitrate) and NO reductases and repair mechanisms (e.g., those that reverse S-nitrosothiol formation). Microbial resistance to these stresses is generally inducible and many diverse transcriptional regulators are involved-some that are secondary sensors (such as Fnr) and those that are "dedicated" (such as NorR, NsrR, NssR) in that their physiological function appears to be detecting primarily NO and then regulating expression of genes that encode enzymes with NO as a substrate. Although generally harmful, evidence is accumulating that NO may have beneficial effects, as in the case of the squid-Vibrio light-organ symbiosis, where NO serves as a signal, antioxidant, and specificity determinant. Progress in this area will require a thorough understanding not only of the biology but also of the underlying chemical principles.
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Affiliation(s)
- Lesley A H Bowman
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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42
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Vine CE, Cole JA. Unresolved sources, sinks, and pathways for the recovery of enteric bacteria from nitrosative stress. FEMS Microbiol Lett 2011; 325:99-107. [DOI: 10.1111/j.1574-6968.2011.02425.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Claire E. Vine
- School of Biosciences; University of Birmingham; Birmingham; UK
| | - Jeffrey A. Cole
- School of Biosciences; University of Birmingham; Birmingham; UK
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Abstract
The toxic free radical NO (nitric oxide) has diverse biological roles in eukaryotes and bacteria, being involved in signalling, vasodilation, blood clotting and immunity, and as an intermediate in microbial denitrification. The predominant biological mechanism of detecting NO is through the formation of iron nitrosyl complexes, although this is a deleterious process for other iron-containing enzymes. We have previously applied techniques such as UV–visible and EPR spectroscopy to the analysis of protein Fe–NO complex formation in order to study how NO controls the activity of the bacterial transcriptional regulators NorR and NsrR. These studies have analysed NO-dependent biological activity both in vitro and in vivo using diverse biochemical, molecular and spectroscopic methods. Recently, we have applied ultrafast 2D-IR (two-dimensional IR) spectroscopy to the analysis of NO–protein interactions using Mb (myoglobin) and Cc (cytochrome c) as model haem proteins. The ultrafast fluctuations of Cc and Mb show marked differences, indicating altered flexibility of the haem pockets. We have extended this analysis to bacterial catalase enzymes that are known to play a role in the nitrosative stress response by detoxifying peroxynitrite. The first 2D-IR analysis of haem nitrosylation and perspectives for the future are discussed.
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Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification. Biochem Soc Trans 2011; 39:289-93. [PMID: 21265790 DOI: 10.1042/bst0390289] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A flavorubredoxin and its associated oxidoreductase (encoded by norV and norW respectively) detoxify NO (nitric oxide) to form N2O (nitrous oxide) under anaerobic conditions in Escherichia coli. Transcription of the norVW genes is activated in response to NO by the σ54-dependent regulator and dedicated NO sensor, NorR, a member of the bacterial enhancer-binding protein family. In the absence of NO, the catalytic activity of the central ATPase domain of NorR is repressed by the N-terminal regulatory domain that contains a non-haem iron centre. Binding of NO to this centre results in the formation of a mononitrosyl iron species, enabling the activation of ATPase activity. Our studies suggest that the highly conserved GAFTGA loop in the ATPase domain, which engages with the alternative σ factor σ54 to activate transcription, is a target for intramolecular repression by the regulatory domain. Binding of NorR to three conserved enhancer sites upstream of the norVW promoter is essential for transcriptional activation and promotes the formation of a stable higher-order NorR nucleoprotein complex. We propose that enhancer-driven assembly of this oligomeric complex, in which NorR apparently forms a DNA-bound hexamer in the absence of NO, provides a 'poised' system for transcriptional activation that can respond rapidly to nitrosative stress.
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Bush M, Ghosh T, Tucker N, Zhang X, Dixon R. Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR. Mol Microbiol 2011; 77:1278-88. [PMID: 20624215 PMCID: PMC2941729 DOI: 10.1111/j.1365-2958.2010.07290.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial enhancer binding proteins (bEBPs) are specialized transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ54. Transcriptional activation by the NorR bEBP is controlled by a regulatory GAF domain that represses the ATPase activity of the central AAA+ domain in the absence of nitric oxide. Here, we investigate the mechanism of interdomain repression in NorR by characterizing substitutions in the AAA+ domain that bypass repression by the regulatory domain. Most of these substitutions are located in the vicinity of the surface-exposed loops that engage σ54 during the ATP hydrolysis cycle or in the highly conserved GAFTGA motif that directly contacts σ54. Biochemical studies suggest that the bypass mutations in the GAFTGA loop do not influence the DNA binding properties of NorR or the assembly of higher order oligomers in the presence of enhancer DNA, and as expected these variants retain the ability to activate open complex formation in vitro. We identify a crucial arginine residue in the GAF domain that is essential for interdomain repression and demonstrate that hydrophobic substitutions at this position suppress the bypass phenotype of the GAFTGA substitutions. These observations suggest a novel mechanism for negative regulation in bEBPs in which the GAF domain targets the σ54-interaction surface to prevent access of the AAA+ domain to the sigma factor.
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Affiliation(s)
- Matthew Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney NR4 7UH, UK
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46
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Wang Y, Dunn AK, Wilneff J, McFall-Ngai MJ, Spiro S, Ruby EG. Vibrio fischeri flavohaemoglobin protects against nitric oxide during initiation of the squid-Vibrio symbiosis. Mol Microbiol 2010; 78:903-15. [PMID: 20815823 PMCID: PMC2978254 DOI: 10.1111/j.1365-2958.2010.07376.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nitric oxide (NO) is implicated in a wide range of biological processes, including innate immunity against pathogens, signal transduction and protection against oxidative stress. However, its possible roles in beneficial host-microbe associations are less well recognized. During the early stages of the squid-vibrio symbiosis, the bacterial symbiont Vibrio fischeri encounters host-derived NO, which has been hypothesized to serve as a specificity determinant. We demonstrate here that the flavohaemoglobin, Hmp, of V. fischeri protects against NO, both in culture and during colonization of the squid host. Transcriptional analyses indicate that hmp expression is highly responsive to NO, principally through the repressor, NsrR. Hmp protects V. fischeri from NO inhibition of aerobic respiration, and removes NO under both oxic and anoxic conditions. A Δhmp mutant of V. fischeri initiates squid colonization less effectively than wild type, but is rescued by the presence of an NO synthase inhibitor. The hmp promoter is activated during the initial stage of colonization, during which the Δhmp strain fails to form normal-sized aggregates of colonizing cells. Taken together, these results suggest that the sensing of host-derived NO by NsrR, and the subsequent removal of NO by Hmp, influence aggregate size and, thereby, V. fischeri colonization efficiency.
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Affiliation(s)
- Yanling Wang
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison
| | - Anne K. Dunn
- Department of Botany and Microbiology, University of Oklahoma
| | - Jacqueline Wilneff
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison
| | | | - Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas
| | - Edward G. Ruby
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison
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47
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Tucker NP, Le Brun NE, Dixon R, Hutchings MI. There's NO stopping NsrR, a global regulator of the bacterial NO stress response. Trends Microbiol 2010; 18:149-56. [PMID: 20167493 DOI: 10.1016/j.tim.2009.12.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 11/24/2009] [Accepted: 12/10/2009] [Indexed: 12/20/2022]
Abstract
Nitric oxide (NO) is a toxic, free radical gas with diverse biological roles in eukaryotes and bacteria, being involved in signalling, vasodilation, blood clotting and immunity and as an intermediate in microbial denitrification. Several bacterial transcriptional regulators sense this molecule and regulate the expression of genes involved in both NO detoxification and NO damage repair. However, a recently discovered NO sensing repressor, named NsrR, has gained attention because of its suggested role as a global regulator of the bacterial NO stress response. Recent advances in biochemical and transcriptomic studies of NsrR make it timely to review the current evidence for NsrR as a global regulator and to speculate on the recent controversy over its NO sensing mechanism.
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Affiliation(s)
- Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Royal College, 204 George Street, University of Strathclyde, Glasgow, Scotland GR1 1XW, UK.
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48
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Tucker NP, Ghosh T, Bush M, Zhang X, Dixon R. Essential roles of three enhancer sites in sigma54-dependent transcription by the nitric oxide sensing regulatory protein NorR. Nucleic Acids Res 2009; 38:1182-94. [PMID: 19955233 PMCID: PMC2831303 DOI: 10.1093/nar/gkp1065] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The bacterial activator protein NorR binds to enhancer-like elements, upstream of the promoter site, and activates σ54-dependent transcription of genes that encode nitric oxide detoxifying enzymes (NorVW), in response to NO stress. Unique to the norVW promoter in Escherichia coli is the presence of three enhancer sites associated with a binding site for σ54-RNA polymerase. Here we show that all three sites are required for NorR-dependent catalysis of open complex formation by σ54-RNAP holoenzyme (Eσ54). We demonstrate that this is essentially due to the need for all three enhancers for maximal ATPase activity of NorR, energy from which is used to remodel the closed Eσ54 complex and allow melting of the promoter DNA. We also find that site-specific DNA binding per se promotes oligomerisation but the DNA flanking the three sites is needed to further stabilise the functional higher order oligomer of NorR at the enhancers.
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Affiliation(s)
- Nicholas P Tucker
- Department of Molecular Microbiology, John Innes Center, Colney, Norwich, NR4 7UH, UK
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49
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Abstract
Bacterial pathogens must overcome a range of challenges during the process of infecting their host. The ability of a pathogen to sense and respond appropriately to changes in host environment is vital if the pathogen is to succeed. Mammalian defense strategies include the use of barriers like skin and epithelial surfaces, the production of a chemical arsenal, such as stomach acid and reactive oxygen and nitrogen species, and a highly coordinated cellular and humoral immune response. Salmonella serovars are significant human and animal pathogens which have evolved several mechanisms to overcome mammalian host defense. Here we focus on the interplay which occurs between Salmonella and the host during the infection process, with particular emphasis on the complex bacterial response to reactive nitrogen species produced by the host. We discuss recent advances in our understanding of the key mechanisms which confer bacterial resistance to nitrogen species, which in response to nitric oxide include the flavohemoglobin, HmpA, the flavorubredoxin, NorV, and the cytochrome c nitrite reductase, NrfA, whilst in response to nitrate include a repertoire of nitrate reductases. Elucidating the precise role of different aspects of microbial physiology, nitrogen metabolism, and detoxification during infection will provide valuable insight into novel opportunities and potential targets for the development of therapeutic approaches.
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50
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Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S. NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility. Mol Microbiol 2009; 73:680-94. [PMID: 19656291 DOI: 10.1111/j.1365-2958.2009.06799.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Escherichia coli NsrR protein is a nitric oxide-sensitive repressor of transcription. The NsrR-binding site is predicted to comprise two copies of an 11 bp motif arranged as an inverted repeat with 1 bp spacing. By mutagenesis we confirmed that both 11 bp motifs are required for maximal NsrR repression of the ytfE promoter. We used chromatin immunoprecipitation and microarray analysis (ChIP-chip) to show that NsrR binds to 62 sites close to the 5' ends of genes. Analysis of the ChIP-chip data suggested that a single 11 bp motif (with the consensus sequence AANATGCATTT) can function as an NsrR-binding site in vivo. NsrR binds to sites in the promoter regions of the fliAZY, fliLMNOPQR and mqsR-ygiT transcription units, which encode proteins involved in motility and biofilm development. Reporter fusion assays confirmed that NsrR negatively regulates the fliA and fliL promoters. A mutation in the predicted 11 bp NsrR-binding site in the fliA promoter impaired repression by NsrR and prevented detectable binding in vivo. Assays on soft-agar confirmed that NsrR is a negative regulator of motility in E. coli K12 and in a uropathogenic strain; surface attachment assays revealed decreased levels of attached growth in the absence of NsrR.
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Affiliation(s)
- Jonathan D Partridge
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
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