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Krzyżanowska DM, Jabłońska M, Kaczyński Z, Czerwicka-Pach M, Macur K, Jafra S. Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize. Sci Rep 2023; 13:9445. [PMID: 37296159 PMCID: PMC10256816 DOI: 10.1038/s41598-023-36494-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.
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Affiliation(s)
- Dorota M Krzyżanowska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Magdalena Jabłońska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Zbigniew Kaczyński
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Małgorzata Czerwicka-Pach
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland.
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2
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Crack JC, Balasiny BK, Bennett SP, Rolfe MD, Froes A, MacMillan F, Green J, Cole JA, Le Brun NE. The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress. J Am Chem Soc 2022; 144:7129-7145. [PMID: 35416044 PMCID: PMC9052748 DOI: 10.1021/jacs.1c12407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Previously characterized
nitrite reductases fall into three classes:
siroheme-containing enzymes (NirBD), cytochrome c hemoproteins (NrfA and NirS), and copper-containing enzymes (NirK).
We show here that the di-iron protein YtfE represents a physiologically
relevant new class of nitrite reductases. Several functions have been
previously proposed for YtfE, including donating iron for the repair
of iron–sulfur clusters that have been damaged by nitrosative
stress, releasing nitric oxide (NO) from nitrosylated iron, and reducing
NO to nitrous oxide (N2O). Here, in vivo reporter assays confirmed that Escherichia coli YtfE increased cytoplasmic NO production from nitrite. Spectroscopic
and mass spectrometric investigations revealed that the di-iron site
of YtfE exists in a mixture of forms, including nitrosylated and nitrite-bound,
when isolated from nitrite-supplemented, but not nitrate-supplemented,
cultures. Addition of nitrite to di-ferrous YtfE resulted in nitrosylated
YtfE and the release of NO. Kinetics of nitrite reduction were dependent
on the nature of the reductant; the lowest Km, measured for the di-ferrous form, was ∼90 μM,
well within the intracellular nitrite concentration range. The vicinal
di-cysteine motif, located in the N-terminal domain of YtfE, was shown
to function in the delivery of electrons to the di-iron center. Notably,
YtfE exhibited very low NO reductase activity and was only able to
act as an iron donor for reconstitution of apo-ferredoxin under conditions
that damaged its di-iron center. Thus, YtfE is a high-affinity, low-capacity
nitrite reductase that we propose functions to relieve nitrosative
stress by acting in combination with the co-regulated NO-consuming
enzymes Hmp and Hcp.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Basema K Balasiny
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Sophie P Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew D Rolfe
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Afonso Froes
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Fraser MacMillan
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Jeffrey Green
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jeffrey A Cole
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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3
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Chen J, Xie P, Huang Y, Gao H. Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide. Int J Mol Sci 2022; 23:979. [PMID: 35055165 PMCID: PMC8780969 DOI: 10.3390/ijms23020979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Affiliation(s)
| | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (J.C.); (P.X.); (Y.H.)
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4
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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: 92] [Impact Index Per Article: 30.7] [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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5
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Pal N, Jana M, Majumdar A. Reduction of NO by diiron complexes in relation to flavodiiron nitric oxide reductases. Chem Commun (Camb) 2021; 57:8682-8698. [PMID: 34373873 DOI: 10.1039/d1cc03149j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reduction of nitric oxide (NO) to nitrous oxide (N2O) is associated with immense biological and health implications. Flavodiiron nitric oxide reductases (FNORs) are diiron containing enzymes that catalyze the two electron reduction of NO to N2O and help certain pathogenic bacteria to survive under "nitrosative stress" in anaerobic growth conditions. Consequently, invading bacteria can proliferate inside the body of mammals by bypassing the immune defense mechanism involving NO and may thus lead to harmful infections. Various mechanisms, namely the direct reduction, semireduction, superreduction and hyponitrite mechanisms, have been proposed over time for catalytic NO reduction by FNORs. Model studies in relation to the diiron active site of FNORs have immensely helped to replicate the minimal structure-reactivity relationship and to understand the mechanism of NO reduction. A brief overview of the FNOR activity and the proposed reaction mechanisms followed by a systematic description and detailed analysis of the model studies is presented, which describes the development in the area of NO reduction by diiron complexes and its implications. A great deal of successful modeling chemistry as well as the shortcomings related to the synthesis and reactivity studies is discussed in detail. Finally, future prospects in this particular area of research are proposed, which in due course may bring more clarity in the understanding of this important redox reaction.
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Affiliation(s)
- Nabhendu Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India.
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6
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Guo K, Gao H. Physiological Roles of Nitrite and Nitric Oxide in Bacteria: Similar Consequences from Distinct Cell Targets, Protection, and Sensing Systems. Adv Biol (Weinh) 2021; 5:e2100773. [PMID: 34310085 DOI: 10.1002/adbi.202100773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/19/2021] [Indexed: 12/22/2022]
Abstract
Nitrite and nitric oxide (NO) are two active nitrogen oxides that display similar biochemical properties, especially when interacting with redox-sensitive proteins (i.e., hemoproteins), an observation serving as the foundation of the notion that the antibacterial effect of nitrite is largely attributed to NO formation. However, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. Although both nitrite and NO are formed and decomposed by enzymes participating in the transformation of these nitrogen species, NO can also be generated via amino acid metabolism by bacterial NO synthetase and scavenged by flavohemoglobin. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to heme-copper oxidases. Consequently, the homeostasis of redox-sensitive proteins may be responsible for the substantial difference in NO-targets identified to date among different bacteria. In addition, most protective systems against NO damage have no significant role in alleviating inhibitory effects of nitrite. Furthermore, when functioning as signal molecules, nitrite and NO are perceived by completely different sensing systems, through which they are linked to different biological processes.
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Affiliation(s)
- Kailun Guo
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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7
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Iwadate Y, Ramezanifard R, Golubeva YA, Fenlon LA, Slauch JM. PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Mol Microbiol 2021; 115:1379-1394. [PMID: 33481283 PMCID: PMC10923242 DOI: 10.1111/mmi.14686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Salmonella and E. coli synthesize, import, and export cadaverine, putrescine, and spermidine to maintain physiological levels and provide pH homeostasis. Both low and high intracellular levels of polyamines confer pleiotropic phenotypes or lethality. Here, we demonstrate that the previously uncharacterized inner membrane protein PaeA (YtfL) is required for reducing cytoplasmic cadaverine and putrescine concentrations. We identified paeA as a gene involved in stationary phase survival when cells were initially grown in acidic medium, in which they produce cadaverine. The paeA mutant is also sensitive to putrescine, but not to spermidine or spermine. Sensitivity to external cadaverine in stationary phase is only observed at pH > 8, suggesting that the polyamines need to be deprotonated to passively diffuse into the cell cytoplasm. In the absence of PaeA, intracellular polyamine levels increase and the cells lose viability. Degradation or modification of the polyamines is not relevant. Ectopic expression of the known cadaverine exporter, CadB, in stationary phase partially suppresses the paeA phenotype, and overexpression of PaeA in exponential phase partially complements a cadB mutant grown in acidic medium. These data support the hypothesis that PaeA is a cadaverine/putrescine exporter, reducing potentially toxic levels under certain stress conditions.
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Affiliation(s)
- Yumi Iwadate
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Luke A. Fenlon
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
- Current address: Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, Utah 84132
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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8
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Jana M, White CJ, Pal N, Demeshko S, Cordes (née Kupper) C, Meyer F, Lehnert N, Majumdar A. Functional Models for the Mono- and Dinitrosyl Intermediates of FNORs: Semireduction versus Superreduction of NO. J Am Chem Soc 2020; 142:6600-6616. [DOI: 10.1021/jacs.9b13795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Corey J. White
- Department of Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor 48109, Michigan, United States
| | - Nabhendu Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Serhiy Demeshko
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen 37077, Germany
| | | | - Franc Meyer
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen 37077, Germany
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor 48109, Michigan, United States
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
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9
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
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10
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Cytochromes c Constitute a Layer of Protection against Nitric Oxide but Not Nitrite. Appl Environ Microbiol 2018; 84:AEM.01255-18. [PMID: 29934335 DOI: 10.1128/aem.01255-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/20/2018] [Indexed: 11/20/2022] Open
Abstract
Nitric oxide (NO) is a radical gas that reacts with various biological molecules in complex ways to inhibit growth as a bacteriostatic agent. NO is nearly ubiquitous because it can be generated both biotically and abiotically. To protect the cell from NO damage, bacteria have evolved many strategies, with the production of detoxifying enzymatic systems being the most efficient. Here, we report that c-type cytochromes (cytochromes c) constitute a primary NO protection system in Shewanella oneidensis, a Gram-negative environmental bacterium renowned for respiratory versatility due to its high cytochrome c content. By using mutants producing cytochromes c at varying levels, we found that the content of these proteins is inversely correlated with the growth inhibition imposed by NO, whereas the effect of each individual cytochrome c is negligible. This NO-protecting system has no effect on nitrite inhibition. In the absence of cytochromes c, other NO targets and protective proteins, such as NnrS, emerge to show physiological influences during the NO stress. We further demonstrate that cytochromes c also play a similar role in Escherichia coli, albeit only modestly. Our data thus identify the in vivo function of an important group of proteins in alleviating NO stress.IMPORTANCE It is widely accepted that the antibacterial effects of nitrite are attributable to nitric oxide (NO) formation, suggesting a correlation of bacterial susceptibilities to these two chemicals. However, compared to E. coli, S. oneidensis is highly sensitive to nitrite but resistant to NO, implying the presence of robust NO-protective systems. Here, we show that c-type cytochromes (cytochromes c) play a main role in protecting S. oneidensis against damages from NO but not from nitrite. In their absence, impacts of proteins that promote NO tolerance and that are targets of NO inhibition become evident. Our data thus reveal the specific activity of cytochromes c in alleviating the stress caused by NO but not nitrite.
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11
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Distinct Nitrite and Nitric Oxide Physiologies in Escherichia coli and Shewanella oneidensis. Appl Environ Microbiol 2018; 84:AEM.00559-18. [PMID: 29654177 DOI: 10.1128/aem.00559-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/06/2018] [Indexed: 11/20/2022] Open
Abstract
Nitrite has been used as a bacteriostatic agent for centuries in food preservation. It is widely accepted that this biologically inert molecule functions indirectly, serving as a stable reservoir of bioactive nitric oxide (NO) and other reactive nitrogen species to impact physiology. As a result, to date, we know surprisingly little about in vivo targets of nitrite. Here, we carry out comparative analyses of nitrite and NO physiology in Escherichia coli and in Shewanella oneidensis, a Gram-negative environmental bacterium renowned for respiratory versatility. These two bacteria differ from each other in many aspects of nitrite and NO physiology, including NO generation, NO degradation, and unexpectedly, their contrary susceptibility to nitrite and NO. In cell extracts of both bacteria, most of the NO targets are also susceptible to nitrite, and vice versa. However, with respect to growth inhibition caused by NO, the targets are impacted distinctly; NO targets are responsible for the inhibition of growth of E. coli but not of S. oneidensis More surprisingly, all proteins identified to be implicated in NO tolerance in other bacteria appear to play a dispensable role in protecting S. oneidensis against NO. These data suggest that S. oneidensis is equipped with a robust but yet unknown NO protecting system. In the case of nitrite, it is clear that the target of physiological significance in both bacteria is cytochrome heme-copper oxidase.IMPORTANCE Nitrite is toxic to living organisms at high levels, but such antibacterial effects of nitrite are attributable to the formation of nitric oxide (NO), a highly reactive radical gas molecule. Here, we report that Shewanella oneidensis is highly resistant to NO but sensitive to nitrite compared to Escherichia coli by approximately 4-fold. In both bacteria, nitrite inhibits bacterial growth by targeting cytochrome heme-copper oxidase. In contrast, the targets of NO are diverse. Although these targets are similar in E. coli and S. oneidensis, they are responsible for growth inhibition caused by NO in the former but not in the latter. Overall, the presented data, along with the previous data, solidify a proposal that the in vivo targets of NO and nitrite in bacteria are largely different.
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12
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances. Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high resolution structural data. Though this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- School of Chemistry , University of East Anglia , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry , University plain , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
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13
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Iwadate Y, Kato JI. Involvement of the ytfK gene from the PhoB regulon in stationary-phase H 2 O 2 stress tolerance in Escherichia coli. Microbiology (Reading) 2017; 163:1912-1923. [DOI: 10.1099/mic.0.000534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yumi Iwadate
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Jun-ichi Kato
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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14
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Mauffrey F, Cucaita A, Constant P, Villemur R. Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1. PeerJ 2017; 5:e4098. [PMID: 29201569 PMCID: PMC5710167 DOI: 10.7717/peerj.4098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. METHODS Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, [Formula: see text] or sodium nitroprusside, and growth and N2O, [Formula: see text], [Formula: see text] and N2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N2O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators. RESULTS Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N2O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of cnorB1, cnorB2, nnrS and norR during the growth and the N2O accumulation phases suggests NO production in strain JAM1 cultures. DISCUSSION By showing that all the three denitrification reductases are active, this demonstrates that M. nitratireducenticrescens JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such an incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of the denitrification reactor from which it originates. The production of N2O in strain JAM1 did not involve Nar, contrary to what was demonstrated in Escherichia coli. M. nitratireducenticrescens JAM1 is the only reported Methylophaga species that has the capacity to grow under anoxic conditions by using [Formula: see text] and N2O as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities.
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Affiliation(s)
- Florian Mauffrey
- INRS–Institut Armand-Frappier, Laval, Québec, Canada
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
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McIlroy SJ, Kirkegaard RH, Dueholm MS, Fernando E, Karst SM, Albertsen M, Nielsen PH. Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. Front Microbiol 2017; 8:1134. [PMID: 28690595 PMCID: PMC5481317 DOI: 10.3389/fmicb.2017.01134] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.
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Affiliation(s)
- Simon J McIlroy
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Rasmus H Kirkegaard
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Morten S Dueholm
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Eustace Fernando
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Søren M Karst
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Mads Albertsen
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Per H Nielsen
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
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16
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Mandel MJ, Dunn AK. Impact and Influence of the Natural Vibrio-Squid Symbiosis in Understanding Bacterial-Animal Interactions. Front Microbiol 2016; 7:1982. [PMID: 28018314 PMCID: PMC5156696 DOI: 10.3389/fmicb.2016.01982] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Animals are colonized by bacteria, and in many cases partners have co-evolved to perform mutually beneficial functions. An exciting and ongoing legacy of the past decade has been an expansion of technology to enable study of natural associations in situ/in vivo. As a result, more symbioses are being examined, and additional details are being revealed for well-studied systems with a focus on the interactions between partners in the native context. With this framing, we review recent literature from the Vibrio fischeri-Euprymna scolopes symbiosis and focus on key studies that have had an impact on understanding bacteria-animal interactions broadly. This is not intended to be a comprehensive review of the system, but rather to focus on particular studies that have excelled at moving from pattern to process in facilitating an understanding of the molecular basis to intriguing observations in the field of host-microbe interactions. In this review we discuss the following topics: processes regulating strain and species specificity; bacterial signaling to host morphogenesis; multiple roles for nitric oxide; flagellar motility and chemotaxis; and efforts to understand unannotated and poorly annotated genes. Overall these studies demonstrate how functional approaches in vivo in a tractable system have provided valuable insight into general principles of microbe-host interactions.
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Affiliation(s)
- Mark J Mandel
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine Chicago, IL, USA
| | - Anne K Dunn
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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17
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Cadby IT, Ibrahim SA, Faulkner M, Lee DJ, Browning D, Busby SJ, Lovering AL, Stapleton MR, Green J, Cole JA. Regulation, sensory domains and roles of twoDesulfovibrio desulfuricansATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress. Mol Microbiol 2016; 102:1120-1137. [DOI: 10.1111/mmi.13540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Ian T. Cadby
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Susan A. Ibrahim
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Matthew Faulkner
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - David J. Lee
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Douglas Browning
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Stephen J. Busby
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Andrew L. Lovering
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
| | - Melanie R. Stapleton
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Jeffrey Green
- Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Jeffrey A. Cole
- Institute of Microbiology & Infection, School of Biosciences; University of Birmingham; Birmingham B15 2TT UK
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18
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Romão CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Frazão C. Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. J Mol Biol 2016; 428:4686-4707. [PMID: 27725182 DOI: 10.1016/j.jmb.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd), is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as a substrate in vitro, exhibiting a very low reactivity toward O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-β-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor. The metal center in the oxidized state has a μ-hydroxo bridge coordinating the two irons, while in the reduced state, this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through molecular dynamics simulations, no differences for O2 or NO permeation were found. The present data represent the first structure for a NO-selective FDP.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Bruno L Victor
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Elísio Silva
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal; Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria A Carrondo
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - David Turner
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal.
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal.
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19
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Bonato P, Batista MB, Camilios-Neto D, Pankievicz VCS, Tadra-Sfeir MZ, Monteiro RA, Pedrosa FO, Souza EM, Chubatsu LS, Wassem R, Rigo LU. RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae. Environ Microbiol 2016; 18:2677-88. [DOI: 10.1111/1462-2920.13422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Marcelo B. Batista
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Biotechnology; Universidade Estadual de Londrina; Londrina PR Brazil
| | - Vânia C. S. Pankievicz
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Michelle Z. Tadra-Sfeir
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Fabio O. Pedrosa
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Leda S. Chubatsu
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Roseli Wassem
- Department of Genetics; Universidade Federal do Paraná; Curitiba PR Brazil
| | - Liu Un Rigo
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba PR Brazil
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20
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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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21
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Wang J, Vine CE, Balasiny BK, Rizk J, Bradley CL, Tinajero-Trejo M, Poole RK, Bergaust LL, Bakken LR, Cole JA. The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures ofEscherichia coliagainst nitrosative stress. Mol Microbiol 2016; 100:877-92. [DOI: 10.1111/mmi.13356] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Wang
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Claire E. Vine
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Basema K. Balasiny
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - John Rizk
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Charlene L. Bradley
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
| | - Mariana Tinajero-Trejo
- Department of Molecular Biology & Biotechnology; University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | - Robert K. Poole
- Department of Molecular Biology & Biotechnology; University of Sheffield, Firth Court, Western Bank; Sheffield S10 2TN UK
| | | | - Lars R. Bakken
- Norwegian University of Life Science; PO box 5003 N-1432 Ås Norway
| | - Jeffrey A. Cole
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham; Birmingham B15 2TT UK
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22
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Crack JC, Svistunenko DA, Munnoch J, Thomson AJ, Hutchings MI, Le Brun NE. Differentiated, Promoter-specific Response of [4Fe-4S] NsrR DNA Binding to Reaction with Nitric Oxide. J Biol Chem 2016; 291:8663-72. [PMID: 26887943 PMCID: PMC4861436 DOI: 10.1074/jbc.m115.693192] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 12/19/2022] Open
Abstract
NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ∼2 NO per cluster, although for the hmpA1 and nsrR promoters, ∼4 and ∼8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8–10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ∼2 NO per cluster, along with two further intermediates at ∼4 and ∼6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes.
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Affiliation(s)
- Jason C Crack
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry, and
| | - Dimitri A Svistunenko
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - John Munnoch
- the School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ and
| | - Andrew J Thomson
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry, and
| | - Matthew I Hutchings
- the School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ and
| | - Nick E Le Brun
- From the Centre for Molecular and Structural Biochemistry, School of Chemistry, and
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23
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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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24
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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] [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
- Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, 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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25
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Frederick RE, Caranto JD, Masitas CA, Gebhardt LL, MacGowan CE, Limberger RJ, Kurtz DM. Dioxygen and nitric oxide scavenging by Treponema denticola flavodiiron protein: a mechanistic paradigm for catalysis. J Biol Inorg Chem 2015; 20:603-13. [PMID: 25700637 PMCID: PMC4768905 DOI: 10.1007/s00775-015-1248-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/13/2015] [Indexed: 10/24/2022]
Abstract
Flavodiiron proteins (FDPs) contain a unique active site consisting of a non-heme diiron carboxylate site proximal to a flavin mononucleotide (FMN). FDPs serve as the terminal components for reductive scavenging of dioxygen (to water) or nitric oxide (to nitrous oxide), which combats oxidative or nitrosative stress in many bacteria. Characterizations of FDPs from spirochetes or from any oral microbes have not been previously reported. Here, we report characterization of an FDP from the anaerobic spirochete, Treponema (T.) denticola, which is associated with chronic periodontitis. The isolated T. denticola FDP exhibited efficient four-electron dioxygen reductase activity and lower but significant anaerobic nitric oxide reductase activity. A mutant T. denticola strain containing the inactivated FDP-encoding gene was significantly more air-sensitive than the wild-type strain. Single turnover reactions of the four-electron-reduced FDP (FMNH2-Fe(II)Fe(II)) (FDPred) with O2 monitored on the milliseconds to seconds time scale indicated initial rapid formation of a spectral feature consistent with a cis-μ-1,2-peroxo-diferric intermediate, which triggered two-electron oxidation of FMNH2. Reaction of FDPred with NO showed apparent cooperativity between binding of the first and second NO to the diferrous site. The resulting diferrous dinitrosyl complex triggered two-electron oxidation of the FMNH2. Our cumulative results on this and other FDPs indicate that smooth two-electron FMNH2 oxidation triggered by the FDPred/substrate complex and overall four-electron oxidation of FDPred to FDPox constitutes a mechanistic paradigm for both dioxygen and nitric oxide reductase activities of FDPs. Four-electron reductive O2 scavenging by FDPs could contribute to oxidative stress protection in many other oral bacteria.
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Affiliation(s)
- Rosanne E. Frederick
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Cesar A. Masitas
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Linda L. Gebhardt
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Charles E. MacGowan
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Ronald J. Limberger
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
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26
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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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27
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Nitrite reduction by molybdoenzymes: a new class of nitric oxide-forming nitrite reductases. J Biol Inorg Chem 2015; 20:403-33. [DOI: 10.1007/s00775-014-1234-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/14/2014] [Indexed: 02/07/2023]
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28
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Khatua S, Majumdar A. Flavodiiron nitric oxide reductases: Recent developments in the mechanistic study and model chemistry for the catalytic reduction of NO. J Inorg Biochem 2015; 142:145-53. [DOI: 10.1016/j.jinorgbio.2014.09.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 11/24/2022]
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29
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Mettert EL, Kiley PJ. Fe-S proteins that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1284-93. [PMID: 25450978 DOI: 10.1016/j.bbamcr.2014.11.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023]
Abstract
Iron-sulfur (Fe-S) cluster containing proteins that regulate gene expression are present in most organisms. The innate chemistry of their Fe-S cofactors makes these regulatory proteins ideal for sensing environmental signals, such as gases (e.g. O2 and NO), levels of Fe and Fe-S clusters, reactive oxygen species, and redox cycling compounds, to subsequently mediate an adaptive response. Here we review the recent findings that have provided invaluable insight into the mechanism and function of these highly significant Fe-S regulatory proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Erin L Mettert
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
| | - Patricia J Kiley
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
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30
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Green J, Rolfe MD, Smith LJ. Transcriptional regulation of bacterial virulence gene expression by molecular oxygen and nitric oxide. Virulence 2014; 5:794-809. [PMID: 25603427 PMCID: PMC4601167 DOI: 10.4161/viru.27794] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular oxygen (O2) and nitric oxide (NO) are diatomic gases that play major roles in infection. The host innate immune system generates reactive oxygen species and NO as bacteriocidal agents and both require O2 for their production. Furthermore, the ability to adapt to changes in O2 availability is crucial for many bacterial pathogens, as many niches within a host are hypoxic. Pathogenic bacteria have evolved transcriptional regulatory systems that perceive these gases and respond by reprogramming gene expression. Direct sensors possess iron-containing co-factors (iron–sulfur clusters, mononuclear iron, heme) or reactive cysteine thiols that react with O2 and/or NO. Indirect sensors perceive the physiological effects of O2 starvation. Thus, O2 and NO act as environmental cues that trigger the coordinated expression of virulence genes and metabolic adaptations necessary for survival within a host. Here, the mechanisms of signal perception by key O2- and NO-responsive bacterial transcription factors and the effects on virulence gene expression are reviewed, followed by consideration of these aspects of gene regulation in two major pathogens, Staphylococcus aureus and Mycobacterium tuberculosis.
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Key Words
- AIP, autoinducer peptide
- Arc, Aerobic respiratory control
- FNR
- FNR, fumarate nitrate reduction regulator
- GAF, cGMP-specific phosphodiesterase-adenylyl cyclase-FhlA domain
- Isc, iron–sulfur cluster biosynthesis machinery
- Mycobacterium tuberculosis
- NOX, NADPH oxidase
- PAS, Per-Amt-Sim domain
- RNS, reactive nitrogen species
- ROS, reactive oxygen species
- Staphylococcus aureus
- TB, tuberculosis
- WhiB-like proteins
- iNOS, inducible nitric oxide synthase
- iron–sulfur cluster
- nitric oxide sensors
- oxygen sensors
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Affiliation(s)
- Jeffrey Green
- a Krebs Institute; Molecular Biology & Biotechnology; University of Sheffield ; Western Bank , Sheffield , UK
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31
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Crack JC, Green J, Thomson AJ, Brun NEL. Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide. Acc Chem Res 2014; 47:3196-205. [PMID: 25262769 DOI: 10.1021/ar5002507] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Iron-sulfur cluster proteins exhibit a range of physicochemical properties that underpin their functional diversity in biology, which includes roles in electron transfer, catalysis, and gene regulation. Transcriptional regulators that utilize iron-sulfur clusters are a growing group that exploit the redox and coordination properties of the clusters to act as sensors of environmental conditions including O2, oxidative and nitrosative stress, and metabolic nutritional status. To understand the mechanism by which a cluster detects such analytes and then generates modulation of DNA-binding affinity, we have undertaken a combined strategy of in vivo and in vitro studies of a range of regulators. In vitro studies of iron-sulfur cluster proteins are particularly challenging because of the inherent reactivity and fragility of the cluster, often necessitating strict anaerobic conditions for all manipulations. Nevertheless, and as discussed in this Account, significant progress has been made over the past decade in studies of O2-sensing by the fumarate and nitrate reduction (FNR) regulator and, more recently, nitric oxide (NO)-sensing by WhiB-like (Wbl) and FNR proteins. Escherichia coli FNR binds a [4Fe-4S] cluster under anaerobic conditions leading to a DNA-binding dimeric form. Exposure to O2 converts the cluster to a [2Fe-2S] form, leading to protein monomerization and hence loss of DNA binding ability. Spectroscopic and kinetic studies have shown that the conversion proceeds via at least two steps and involves a [3Fe-4S](1+) intermediate. The second step involves the release of two bridging sulfide ions from the cluster that, unusually, are not released into solution but rather undergo oxidation to sulfane (S(0)) subsequently forming cysteine persulfides that then coordinate the [2Fe-2S] cluster. Studies of other [4Fe-4S] cluster proteins that undergo oxidative cluster conversion indicate that persulfide formation and coordination may be more common than previously recognized. This remarkable feature suggested that the original [4Fe-4S] cluster can be restored using persulfide as the source of sulfide ion. We have demonstrated that only iron and a source of electrons are required to promote efficient conversion back from the [2Fe-2S] to the [4Fe-4S] form. We propose this as a novel in vivo repair mechanism that does not require the intervention of an iron-sulfur cluster biogenesis pathway. A number of iron-sulfur regulators have evolved to function as sensors of NO. Although it has long been known that the iron-sulfur clusters of many phylogenetically unrelated proteins are vulnerable to attack by NO, our recent studies of Wbl proteins and FNR have provided new insights into the mechanism of cluster nitrosylation, which overturn the commonly accepted view that the product is solely a mononuclear iron dinitrosyl complex (known as a DNIC). The major reaction is a rapid, multiphase process involving stepwise addition of up to eight NO molecules per [4Fe-4S] cluster. The major iron nitrosyl product is EPR silent and has optical characteristics similar to Roussin's red ester, [Fe2(NO)4(RS)2] (RRE), although a species similar to Roussin's black salt, [Fe4(NO)7(S)3](-) (RBS) cannot be ruled out. A major future challenge will be to clarify the nature of these species.
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Affiliation(s)
- Jason C. Crack
- Centre
for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jeffrey Green
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Andrew J. Thomson
- Centre
for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Nick E. Le Brun
- Centre
for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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32
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Caranto JD, Weitz A, Giri N, Hendrich MP, Kurtz DM. A diferrous-dinitrosyl intermediate in the N2O-generating pathway of a deflavinated flavo-diiron protein. Biochemistry 2014; 53:5631-7. [PMID: 25144650 PMCID: PMC4159209 DOI: 10.1021/bi500836z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Flavo-diiron proteins (FDPs) function
as anaerobic nitric oxide
scavengers in some microorganisms, catalyzing reduction of nitric
to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site
(deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040–7049] reported that reaction of NO with reduced deflavo-FDP
produced substoichiometric N2O. Here we report a multispectroscopic
approach to identify the iron species in the reactions of deflavo-FDP
with NO. Mössbauer spectroscopy identified two distinct ferrous
species after reduction of the antiferromagnetically coupled diferric
site. Approximately 60% of the total ferrous iron was assigned to
a diferrous species associated with the N2O-generating
pathway. This pathway proceeds through successive diferrous-mononitrosyl
(S = 1/2 FeII{FeNO}7) and diferrous-dinitrosyl (S = 0 [{FeNO}7]2) species that form within ∼100 ms of
mixing of the reduced protein with NO. The diferrous-dinitrosyl intermediate
converted to an antiferromagnetically coupled diferric species that
was spectroscopically indistinguishable from that in the starting
deflavinated protein. These diiron species closely resembled those
reported for the flavinated FDP [Caranto et al. (2014) J.
Am. Chem. Soc. 136, 7981–7992], and
the time scales of their formation and decay were consistent with
the steady state turnover of the flavinated protein. The remaining
∼40% of ferrous iron was inactive in N2O generation
but reversibly bound NO to give an S = 3/2 {FeNO}7 species. The results demonstrate
that N2O formation in FDPs can occur via conversion of S = 0 [{FeNO}7]2 to a diferric form
without participation of the flavin cofactor.
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Affiliation(s)
- Jonathan D Caranto
- Department of Chemistry, University of Texas at San Antonio , San Antonio, Texas 78249, United States
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33
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Robinson JL, Adolfsen KJ, Brynildsen MP. Deciphering nitric oxide stress in bacteria with quantitative modeling. Curr Opin Microbiol 2014; 19:16-24. [PMID: 24983704 DOI: 10.1016/j.mib.2014.05.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/02/2014] [Accepted: 05/26/2014] [Indexed: 12/22/2022]
Abstract
Many pathogens depend on nitric oxide (NO•) detoxification and repair to establish an infection, and inhibitors of these systems are under investigation as next-generation antibiotics. Because of the broad reactivity of NO• and its derivatives with biomolecules, a deep understanding of how pathogens sense and respond to NO•, as an integrated system, has been elusive. Quantitative kinetic modeling has been proposed as a method to enhance analysis and understanding of NO• stress at the systems-level. Here we review the motivation for, current state of, and future prospects of quantitative modeling of NO• stress in bacteria, and suggest that such mathematical approaches would prove equally useful in the study of other broadly reactive antimicrobials, such as hydrogen peroxide (H2O2).
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Affiliation(s)
- Jonathan L Robinson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Kristin J Adolfsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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34
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Caranto J, Weitz A, Hendrich MP, Kurtz DM. The nitric oxide reductase mechanism of a flavo-diiron protein: identification of active-site intermediates and products. J Am Chem Soc 2014; 136:7981-92. [PMID: 24828196 PMCID: PMC4063189 DOI: 10.1021/ja5022443] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Indexed: 11/30/2022]
Abstract
The unique active site of flavo-diiron proteins (FDPs) consists of a nonheme diiron-carboxylate site proximal to a flavin mononucleotide (FMN) cofactor. FDPs serve as the terminal components for reductive scavenging of dioxygen or nitric oxide to combat oxidative or nitrosative stress in bacteria, archaea, and some protozoan parasites. Nitric oxide is reduced to nitrous oxide by the four-electron reduced (FMNH2-Fe(II)Fe(II)) active site. In order to clarify the nitric oxide reductase mechanism, we undertook a multispectroscopic presteady-state investigation, including the first Mössbauer spectroscopic characterization of diiron redox intermediates in FDPs. A new transient intermediate was detected and determined to be an antiferromagnetically coupled diferrous-dinitrosyl (S = 0, [{FeNO}(7)]2) species. This species has an exchange energy, J ≥ 40 cm(-1) (JS1 ° S2), which is consistent with a hydroxo or oxo bridge between the two irons. The results show that the nitric oxide reductase reaction proceeds through successive formation of diferrous-mononitrosyl (S = ½, Fe(II){FeNO}(7)) and the S = 0 diferrous-dinitrosyl species. In the rate-determining process, the diferrous-dinitrosyl converts to diferric (Fe(III)Fe(III)) and by inference N2O. The proximal FMNH2 then rapidly rereduces the diferric site to diferrous (Fe(II)Fe(II)), which can undergo a second 2NO → N2O turnover. This pathway is consistent with previous results on the same deflavinated and flavinated FDP, which detected N2O as a product (Hayashi Biochemistry 2010, 49, 7040). Our results do not support other proposed mechanisms, which proceed either via "super-reduction" of [{FeNO}(7)]2 by FMNH2 or through Fe(II){FeNO}(7) directly to a diferric-hyponitrite intermediate. The results indicate that an S = 0 [{FeNO}(7)}]2 complex is a proximal precursor to N-N bond formation and N-O bond cleavage to give N2O and that this conversion can occur without redox participation of the FMN cofactor.
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Affiliation(s)
- Jonathan
D. Caranto
- Department
of Chemistry, University of Texas at San
Antonio, San Antonio, Texas 78249, United
States
| | - Andrew Weitz
- Department
of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department
of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Donald M. Kurtz
- Department
of Chemistry, University of Texas at San
Antonio, San Antonio, Texas 78249, United
States
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35
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Mania D, Heylen K, van Spanning RJM, Frostegård Å. The nitrate-ammonifying andnosZ-carrying bacteriumBacillus viretiis a potent source and sink for nitric and nitrous oxide under high nitrate conditions. Environ Microbiol 2014; 16:3196-210. [DOI: 10.1111/1462-2920.12478] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/13/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Mania
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
| | - Kim Heylen
- Laboratory of Microbiology; Department of Biochemistry and Microbiology; University of Ghent; Gent Belgium
| | - Rob J. M. van Spanning
- Department of Molecular Cell Biology; Faculty of Earth and Life Science; VU University; Amsterdam The Netherlands
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Ås Norway
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36
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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37
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Mühlig A, Kabisch J, Pichner R, Scherer S, Müller-Herbst S. Contribution of the NO-detoxifying enzymes HmpA, NorV and NrfA to nitrosative stress protection of Salmonella Typhimurium in raw sausages. Food Microbiol 2014; 42:26-33. [PMID: 24929713 DOI: 10.1016/j.fm.2014.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/27/2014] [Accepted: 02/11/2014] [Indexed: 12/18/2022]
Abstract
The antimicrobial action of the curing agent sodium nitrite (NaNO2) in raw sausage fermentation is thought to mainly depend on the release of cytotoxic nitric oxide (NO) at acidic pH. Salmonella Typhimurium is capable of detoxifying NO via the flavohemoglobin HmpA, the flavorubredoxin NorV and the periplasmic cytochrome C nitrite reductase NrfA. In this study, the contribution of these systems to nitrosative stress tolerance in raw sausages was investigated. In vitro growth assays of the S. Typhimurium 14028 deletion mutants ΔhmpA, ΔnorV and ΔnrfA revealed a growth defect of ΔhmpA in the presence of acidified NaNO2. Transcriptional analysis of the genes hmpA, norV and nrfA in the wild-type showed a 41-fold increase in hmpA transcript levels in the presence of 150 mg/l acidified NaNO2, whereas transcription of norV and nrfA was not enhanced. However, challenge assays performed with short-ripened spreadable sausages produced with 0 or 150 mg/kg NaNO2 failed to reveal a phenotype for any of the mutants compared to the wild-type. Hence, none of the NO detoxification systems HmpA, NorV and NrfA is solely responsible for nitrosative stress tolerance of S. Typhimurium in raw sausages. Whether these systems act cooperatively, or if there are other yet undescribed mechanisms involved is currently unknown.
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Affiliation(s)
- Anna Mühlig
- Abteilung Mikrobiologie (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Jan Kabisch
- Institut für Mikrobiologie und Biotechnologie, MRI, Bundesforschungsinstitut für Ernährung und Lebensmittel, E.-C.-Baumann-Str. 20, D-95326 Kulmbach, Germany
| | - Rohtraud Pichner
- Institut für Mikrobiologie und Biotechnologie, MRI, Bundesforschungsinstitut für Ernährung und Lebensmittel, E.-C.-Baumann-Str. 20, D-95326 Kulmbach, Germany
| | - Siegfried Scherer
- Abteilung Mikrobiologie (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany; Lehrstuhl für Mikrobielle Ökologie, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Stefanie Müller-Herbst
- Abteilung Mikrobiologie (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany; Lehrstuhl für Mikrobielle Ökologie, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany.
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38
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Müller J, Schildknecht P, Müller N. Metabolism of nitro drugs metronidazole and nitazoxanide in Giardia lamblia: characterization of a novel nitroreductase (GlNR2). J Antimicrob Chemother 2013; 68:1781-9. [PMID: 23580565 DOI: 10.1093/jac/dkt106] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The protozoan parasite Giardia lamblia causes giardiasis, a persistent diarrhoea. Nitro drugs such as the nitroimidazole metronidazole and the nitrothiazolide nitazoxanide are used for the treatment of giardiasis. Nitroreductases may play a role in activating these drugs. G. lamblia contains two nitroreductases, GlNR1 and GlNR2. The aim of this work was to elucidate the role of GlNR2. METHODS Expression of GlNR2 was analysed by reverse transcription PCR. Recombinant GlNR2 was overexpressed in G. lamblia and drug susceptibility was analysed. Recombinant GlNR2 was subjected to functional assays. Escherichia coli expressing full-length or truncated GlNR1 and GlNR2 were grown in the presence of nitro compounds. Using E. coli reporter strains for nitric oxide and DNA damage responses, we analysed whether GlNR1 and GlNR2 elicited the respective responses in the presence, or absence, of the drugs. RESULTS G. lamblia trophozoites overexpressing GlNR2 were less susceptible to both nitro drugs as compared with control trophozoites. GlNR2 was a functional nitroreductase when expressed in E. coli. E. coli expressing GlNR1 was more susceptible to metronidazole under aerobic and semi-aerobic and to nitazoxanide under semi-aerobic growth conditions. E. coli expressing GlNR2 was not susceptible to either drug. In reporter strains, GlNR1, but not GlNR2, elicited nitric oxide and DNA repair responses, even in the absence of nitro drugs. CONCLUSIONS These findings suggest that GlNR2 is an active nitroreductase with a mode of action different from that of GlNR1. Thus, susceptibility to nitro drugs may depend not only on activation, but also on inactivation of the drugs by specific nitroreductases.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
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Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. J Bacteriol 2013; 195:2684-90. [PMID: 23564166 DOI: 10.1128/jb.00074-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in gastrointestinal diseases and shown to stimulate the epithelial immune response, leading to increased production of inflammatory cytokines by macrophages. Activated macrophages are key cells of the immune system that impose nitrosative stress during phagocytosis. Hence, we have analyzed the in vitro and in vivo responses of Desulfovibrio vulgaris Hildenborough to nitric oxide (NO) and the role of the hybrid cluster proteins (HCP1 and HCP2) and rubredoxin oxygen oxidoreductases (ROO1 and ROO2) in NO protection. Among the four genes, hcp2 was the gene most highly induced by NO, and the hcp2 transposon mutant exhibited the lowest viability under conditions of NO stress. Studies in murine macrophages revealed that D. vulgaris survives incubation with these phagocytes and triggers NO production at levels similar to those stimulated by the cytokine gamma interferon (IFN-γ). Furthermore, D. vulgaris hcp and roo mutants exhibited reduced viability when incubated with macrophages, revealing that these gene products contribute to the survival of D. vulgaris during macrophage infection.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Depkat-Jakob PS, Brown GG, Tsai SM, Horn MA, Drake HL. Emission of nitrous oxide and dinitrogen by diverse earthworm families from Brazil and resolution of associated denitrifying and nitrate-dissimilating taxa. FEMS Microbiol Ecol 2012; 83:375-91. [DOI: 10.1111/j.1574-6941.2012.01476.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/31/2012] [Accepted: 08/17/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | - Siu M. Tsai
- Center for Nuclear Energy in Agriculture; University of São Paulo; São Paulo; Brazil
| | - Marcus A. Horn
- Department of Ecological Microbiology; University of Bayreuth; Bayreuth; Germany
| | - Harold L. Drake
- Department of Ecological Microbiology; University of Bayreuth; Bayreuth; Germany
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The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen. PLoS One 2012; 7:e42645. [PMID: 22880065 PMCID: PMC3411805 DOI: 10.1371/journal.pone.0042645] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/11/2012] [Indexed: 01/01/2023] Open
Abstract
Background Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. Methods Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA) software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. Results B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function “receptor activity”, most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. Conclusions B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to the identification of novel microbial targets for IBD therapies.
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Oxidative stress modulates the nitric oxide defense promoted by Escherichia coli flavorubredoxin. J Bacteriol 2012; 194:3611-7. [PMID: 22563051 DOI: 10.1128/jb.00140-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mammalian cells of innate immunity respond to pathogen invasion by activating proteins that generate a burst of oxidative and nitrosative stress. Pathogens defend themselves from the toxic compounds by triggering a variety of detoxifying enzymes. Escherichia coli flavorubredoxin is a nitric oxide reductase that is expressed under nitrosative stress conditions. We report that in contrast to nitrosative stress alone, exposure to both nitrosative and oxidative stresses abolishes the expression of flavorubredoxin. Electron paramagnetic resonance (EPR) experiments showed that under these conditions, the iron center of the flavorubredoxin transcription activator NorR loses the ability to bind nitric oxide. Accordingly, triggering of the NorR ATPase activity, a requisite for flavorubredoxin activation, was impaired by treatment of the protein with the double stress. Studies of macrophages revealed that the contribution of flavorubredoxin to the survival of E. coli depends on the stage of macrophage infection and that the lack of protection observed at the early phase is related to inhibition of NorR activity by the oxidative burst. We propose that the time-dependent activation of flavorubredoxin contributes to the adaptation of E. coli to the different fluxes of hydrogen peroxide and nitric oxide to which the bacterium is subjected during the course of macrophage infection.
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Cole JA. Legless pathogens: how bacterial physiology provides the key to understanding pathogenicity. MICROBIOLOGY-SGM 2012; 158:1402-1413. [PMID: 22493300 DOI: 10.1099/mic.0.059048-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review argues that knowledge of microbial physiology and metabolism is a prerequisite to understanding mechanisms of pathogenicity. The ability of Neisseria gonorrhoeae to cope with stresses such as those found during infection requires a sialyltransferase to sialylate its lipopolysaccharide using host-derived CMP-NANA in the human bloodstream, the ability to oxidize lactate that is abundant in the human body, outer-membrane lipoproteins that provide the first line of protection against oxidative and nitrosative stress, regulation of NO reduction independently from the nitrite reductase that forms NO, an extra haem group on the C-terminal extension of a cytochrome oxidase subunit, and a respiratory capacity far in excess of metabolic requirements. These properties are all normal components of neisserial physiology; they would all fail rigid definitions of a pathogenicity determinant. In anaerobic cultures of enteric bacteria, duplicate pathways for nitrate reduction to ammonia provide a selective advantage when nitrate is either abundant or scarce. Selection of these alternative pathways is in part regulated by two parallel two-component regulatory systems. NarX-NarL primarily ensures that nitrate is reduced in preference to thermodynamically less favourable terminal electron acceptors, but NarQ-NarP facilitates reduction of limited quantities of nitrate or other, less favourable, terminal electron acceptors in preference to fermentative growth. How enteric bacteria repair damage caused by nitrosative and oxidative damage inflicted by host defences is less well understood. In both N. gonorrhoeae and Escherichia coli, parallel pathways that duplicate particular biochemical functions are far from redundant, but fulfil specific physiological roles.
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Affiliation(s)
- Jeffrey A Cole
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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