1
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Moura JJG. The History of Desulfovibrio gigas Aldehyde Oxidoreductase-A Personal View. Molecules 2023; 28:4229. [PMID: 37241969 PMCID: PMC10223205 DOI: 10.3390/molecules28104229] [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: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to and target a wide-ranging audience. When preparing the manuscript and collecting references on the subject of this paper-aldehyde oxidoreductase from Desulfovibrio gigas-I felt like I was travelling back in time (and space), bringing together the people that have contributed most to this area of research. I sincerely hope that I can give my collaborators the credit they deserve. This study is not presented as a chronologic narrative but as a grouping of topics, the development of which occurred over many years.
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Affiliation(s)
- José J G Moura
- LAQV, NOVA School of Science and Technology|FCT NOVA, 2829-516 Caparica, Portugal
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2
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Bessonova TA, Fando MS, Kostareva OS, Tutukina MN, Ozoline ON, Gelfand MS, Nikulin AD, Tishchenko SV. Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome. Int J Mol Sci 2022; 23:ijms23158379. [PMID: 35955512 PMCID: PMC9369180 DOI: 10.3390/ijms23158379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.
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Affiliation(s)
- Tatiana A. Bessonova
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Maria S. Fando
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Olga S. Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Maria N. Tutukina
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
- Correspondence:
| | - Olga N. Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
| | - Alexey D. Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Svetlana V. Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
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3
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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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4
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Nitric oxide stimulates type IV MSHA pilus retraction in Vibrio cholerae via activation of the phosphodiesterase CdpA. Proc Natl Acad Sci U S A 2022; 119:2108349119. [PMID: 35135874 PMCID: PMC8851539 DOI: 10.1073/pnas.2108349119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 01/30/2023] Open
Abstract
All organisms sense and respond to their environments. One way bacteria interact with their surroundings is by dynamically extending and retracting filamentous appendages from their surface called pili. While pili are critical for many functions, such as attachment, motility, and DNA uptake, the factors that regulate their dynamic activity are poorly understood. Here, we describe how an environmental signal induces a signaling pathway to promote the retraction of mannose-sensitive hemagglutinin pili in Vibrio cholerae. The retraction of these pili promotes the detachment of V. cholerae from a surface and may provide a means by which V. cholerae can respond to changes in its environment. Bacteria use surface appendages called type IV pili to perform diverse activities including DNA uptake, twitching motility, and attachment to surfaces. The dynamic extension and retraction of pili are often required for these activities, but the stimuli that regulate these dynamics remain poorly characterized. To address this question, we study the bacterial pathogen Vibrio cholerae, which uses mannose-sensitive hemagglutinin (MSHA) pili to attach to surfaces in aquatic environments as the first step in biofilm formation. Here, we use a combination of genetic and cell biological approaches to describe a regulatory pathway that allows V. cholerae to rapidly abort biofilm formation. Specifically, we show that V. cholerae cells retract MSHA pili and detach from a surface in a diffusion-limited, enclosed environment. This response is dependent on the phosphodiesterase CdpA, which decreases intracellular levels of cyclic-di-GMP to induce MSHA pilus retraction. CdpA contains a putative nitric oxide (NO)–sensing NosP domain, and we demonstrate that NO is necessary and sufficient to stimulate CdpA-dependent detachment. Thus, we hypothesize that the endogenous production of NO (or an NO-like molecule) in V. cholerae stimulates the retraction of MSHA pili. These results extend our understanding of how environmental cues can be integrated into the complex regulatory pathways that control pilus dynamic activity and attachment in bacterial species.
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5
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Metcalfe GD, Smith TW, Hippler M. Advanced spectroscopic analysis and 15N-isotopic labelling study of nitrate and nitrite reduction to ammonia and nitrous oxide by E. coli. Analyst 2021; 146:7021-7033. [PMID: 34693414 DOI: 10.1039/d1an01261d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitrate and nitrite reduction to ammonia and nitrous oxide by anaerobic E. coli batch cultures is investigated by advanced spectroscopic analytical techniques with 15N-isotopic labelling. Non-invasive, in situ analysis of the headspace is achieved using White cell FTIR and cavity-enhanced Raman (CERS) spectroscopies alongside liquid-phase Raman spectroscopy. For gas-phase analysis, White cell FTIR measures CO2, ethanol and N2O while CERS allows H2, N2 and O2 monitoring. The 6 m pathlength White cell affords trace gas detection of N2O with a noise equivalent detection limit of 60 nbar or 60 ppbv in 1 atm. Quantitative analysis is discussed for all four 14N/15N-isotopomers of N2O. Monobasic and dibasic phosphates, acetate, formate, glucose and NO3- concentrations are obtained by liquid-phase Raman spectroscopy, with a noise equivalent detection limit of 0.6 mM for NO3- at 300 s integration time. Concentrations of the phosphate anions are used to calculate the pH in situ using a modified Henderson-Hasselbalch equation. NO2- concentrations are determined by sampling for colorimetric analysis and NH4+ by basifying samples to release 14N/15N-isotopomers of NH3 for measurement in a second FTIR White cell. The reductions of 15NO3-, 15NO2-, and mixed 15NO3- and 14NO2- by anaerobic E. coli batch cultures are discussed. In a major pathway, NO3- is reduced to NH4+via NO2-, with the bulk of NO2- reduction occurring after NO3- depletion. Using isotopically labelled 15NO3-, 15NH4+ production is distinguished from background 14NH4+ in the growth medium. In a minor pathway, NO2- is reduced to N2O via the toxic radical NO. With excellent detection sensitivities, N2O serves as a monitor for trace NO2- reduction, even when cells are predominantly reducing NO3-. The analysis of N2O isotopomers reveals that for cultures supplemented with mixed 15NO3- and 14NO2- enzymatic activity to reduce 14NO2- occurs immediately, even before 15NO3- reduction begins. Optical density and pH measurements are discussed in the context of acetate, formate and CO2 production. H2 production is repressed by NO3-; but in experiments with NO2- supplementation only, CERS detects H2 produced by formate disproportionation after NO2- depletion.
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Affiliation(s)
- George D Metcalfe
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
| | - Thomas W Smith
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK. .,School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, UK
| | - Michael Hippler
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
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6
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Lifshitz A, Shemer B, Hazan C, Shpigel E, Belkin S. A bacterial bioreporter for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX). Anal Bioanal Chem 2021; 414:5329-5336. [PMID: 34622323 DOI: 10.1007/s00216-021-03685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
We report the design, construction, and testing of Escherichia coli-based bioluminescent bioreporters for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX), one of the most prevalent military-grade explosives in use today. These sensor strains are based on a fusion between the promoter of either the hmp (nitric oxide dioxygenase) or the hcp (a high-affinity nitric oxide reductase) E. coli gene, to the microbial bioluminescence luxCDABEG gene cassette. Signal intensity was enhanced in ∆hmp and ∆hcp mutants, and detection sensitivity was improved when the two gene promoters were cloned in tandem. The Photobacterium leiognathi luxCDABEG reporter genes were superior to those of Aliivibrio fischeri in terms of signal intensity, but in most cases inferior in terms of detection sensitivity, due to a higher background signal. Both sensor strains were also induced by additional nitro-organic explosives, as well as by nitrate salts. Sensitive detection of RDX in a solid matrix (either LB agar or sand) was also demonstrated, with the bioreporters encapsulated in 1.5-mm calcium alginate beads. Lowest RDX concentration detected in sand was 1.67 mg/kg sand. The bioreporter strains described herein may serve as a basis for a standoff detection technology of RDX-based explosive devices, including buried landmines.
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Affiliation(s)
- Amir Lifshitz
- Department of Plant & Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Benjamin Shemer
- Department of Plant & Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Carina Hazan
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Etai Shpigel
- Department of Plant & Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Shimshon Belkin
- Department of Plant & Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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7
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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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8
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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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9
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Vargas-Maya NI, Padilla-Vaca F, Romero-González OE, Rosales-Castillo EAS, Rangel-Serrano Á, Arias-Negrete S, Franco B. Refinement of the Griess method for measuring nitrite in biological samples. J Microbiol Methods 2021; 187:106260. [PMID: 34090997 DOI: 10.1016/j.mimet.2021.106260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 12/19/2022]
Abstract
Nitric oxide (NO) is a reactive gas that participates in many physiological as well as pathogenic processes in higher eukaryotic organisms. Inflammatory responses elicit higher levels of this molecule. Nevertheless, there are many technical challenges to accurately measure the amount of NO produced. Previously, a method using whole-cell extracts from Escherichia coli was able to generate the conversion of nitrate into nitrite to measure the amount of nitrate or indirectly the NO present in a sample using the Griess reaction. Here we present an improvement to this method, by using E. coli whole-cell extracts lacking one of the two nitrite reductases, rendered a more precise measurement when coupled with the Griess reaction than our previous report. Alternatively, osmotic stress showed to downregulate the expression of both nitrate reductases, which can be an alternative for indirect nitrate and NO reduction. The results presented here show an easy method for nitrate and NO reduction to nitrite and avoid the reconversion to nitrate, also as an alternative for other analytical methods that are based on cadmium, purified nitrate reductase enzyme, or salicylic methods to reduce NO. This method can be widely used for measuring NO production in living organisms, soil, and other relevant microbiological samples.
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Affiliation(s)
- Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico
| | - Oscar E Romero-González
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico
| | | | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico
| | - Sergio Arias-Negrete
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico.
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N 36050, Guanajuato, Gto, Mexico.
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10
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Cole JA. Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses. Mol Microbiol 2021; 116:29-40. [PMID: 33706420 DOI: 10.1111/mmi.14713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.
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Affiliation(s)
- J A Cole
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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11
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Coulson TJD, Malenfant RM, Patten CL. Characterization of the TyrR Regulon in the Rhizobacterium Enterobacter ludwigii UW5 Reveals Overlap with the CpxR Envelope Stress Response. J Bacteriol 2020; 203:e00313-20. [PMID: 33046562 PMCID: PMC7723952 DOI: 10.1128/jb.00313-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/03/2020] [Indexed: 01/06/2023] Open
Abstract
The TyrR transcription factor controls the expression of genes for the uptake and biosynthesis of aromatic amino acids in Escherichia coli In the plant-associated and clinically significant proteobacterium Enterobacter ludwigii UW5, the TyrR orthologue was previously shown to regulate genes that encode enzymes for synthesis of the plant hormone indole-3-acetic acid and for gluconeogenesis, indicating a broader function for the transcription factor. This study aimed to delineate the TyrR regulon of E. ludwigii by comparing the transcriptomes of the wild type and a tyrR deletion strain. In E. ludwigii, TyrR positively or negatively regulates the expression of over 150 genes. TyrR downregulated expression of envelope stress response regulators CpxR and CpxP through interaction with a DNA binding site in the intergenic region between divergently transcribed cpxP and cpxR Repression of cpxP was alleviated by tyrosine. Methyltransferase gene dmpM, which is possibly involved in antibiotic synthesis, was strongly activated in the presence of tyrosine and phenylalanine by TyrR binding to its promoter region. TyrR also regulated expression of genes for aromatic catabolism and anaerobic respiration. Our findings suggest that the E. ludwigii TyrR regulon has diverged from that of E. coli to include genes for survival in the diverse environments that this bacterium inhabits and illustrate the expansion and plasticity of transcription factor regulons.IMPORTANCE Genome-wide RNA sequencing revealed a broader regulatory role for the TyrR transcription factor in the ecologically versatile bacterium Enterobacter ludwigii beyond that of aromatic amino acid synthesis and transport that constitute the role of the TyrR regulon of E. coli In E. ludwigii, a plant symbiont and human gut commensal, the TyrR regulon is expanded to include genes that are beneficial for plant interactions and response to stresses. Identification of the genes regulated by TyrR provides insight into the mechanisms by which the bacterium adapts to its environment.
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Affiliation(s)
- Thomas J D Coulson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - René M Malenfant
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Cheryl L Patten
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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12
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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13
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Abstract
Most bacteria rely on the redox activity of respiratory complexes embedded in the cytoplasmic membrane to gain energy in the form of ATP and of an electrochemical gradient established across the membrane. Nevertheless, production of harmful and toxic nitric oxide by actively growing bacteria as either an intermediate or side-product of nitrate respiration challenges how homeostasis control is exerted. Here, we show that components of the nitrate electron transport chain are clustered, likely influencing the kinetics of the process. Nitric oxide production from this respiratory chain is controlled and handled through a multiprotein complex, including detoxifying systems. These findings point to an essential role of compartmentalization of respiratory components in bacterial cell growth. Respiration is a fundamental process that has to optimally respond to metabolic demand and environmental changes. We previously showed that nitrate respiration, crucial for gut colonization by enterobacteria, is controlled by polar clustering of the nitrate reductase increasing the electron flux through the complex. Here, we show that the formate dehydrogenase electron-donating complex, FdnGHI, also clusters at the cell poles under nitrate-respiring conditions. Its proximity to the nitrate reductase complex was confirmed by its identification in the interactome of the latter, which appears to be specific to the nitrate-respiring condition. Interestingly, we have identified a multiprotein complex dedicated to handle nitric oxide resulting from the enhanced activity of the electron transport chain terminated by nitrate reductase. We demonstrated that the cytoplasmic NADH-dependent nitrite reductase NirBD and the hybrid cluster protein Hcp are key contributors to regulation of the nitric oxide level during nitrate respiration. Thus, gathering of actors involved in respiration and NO homeostasis seems to be critical to balancing maximization of electron flux and the resulting toxicity.
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Ras G, Leroy S, Talon R. Nitric oxide synthase: What is its potential role in the physiology of staphylococci in meat products? Int J Food Microbiol 2018; 282:28-34. [PMID: 29890305 DOI: 10.1016/j.ijfoodmicro.2018.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/23/2018] [Accepted: 06/06/2018] [Indexed: 12/17/2022]
Abstract
Coagulase-negative staphylococci are frequently isolated from meat products and two species are used as starter cultures in dry fermented sausages. In these products, they face various environmental conditions such as variation of redox potential and oxygen levels that can lead to oxidative stress. Furthermore, when nitrate and nitrite are added as curing salts, staphylococci also experience nitrosative stress. A nos gene encoding a nitric oxide synthase (NOS) is present in the genome of all staphylococci. NOS produces nitric oxide (NO) and citrulline from arginine, but its activity is still poorly characterized, particularly in coagulase-negative staphylococci. NO is highly reactive with a broad spectrum of activity resulting from targeting metal centres (heme and non-heme) and protein thiols. At low concentration, NO acts as a signalling molecule, while at higher concentration it generates stress. Thus, it was initially suggested that staphylococcal NOS counteract oxidative stress in relation to PerR and Fur regulators. In the physiology of staphylococci, it has recently been highlighted that NO controls the rate of aerobic respiration and regulates the transition from aerobic to nitrate respiration and also helps maintain the membrane potential in relation to the two-component systems SrrAB and AirRS. As NO interacts with heme centres, it binds the heme iron atom of myoglobin to form nitrosomyglobin, which is the typical red pigment of cured meat. However, the contribution of NOS to this reaction in meat products has yet to be evaluated.
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Affiliation(s)
- Geoffrey Ras
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France; CHR. HANSEN SAS, Saint-Germain-les-Arpajon, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France.
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15
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Balasiny B, Rolfe MD, Vine C, Bradley C, Green J, Cole J. Release of nitric oxide by the Escherichia coli YtfE (RIC) protein and its reduction by the hybrid cluster protein in an integrated pathway to minimize cytoplasmic nitrosative stress. Microbiology (Reading) 2018; 164:563-575. [DOI: 10.1099/mic.0.000629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Basema Balasiny
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthew D. Rolfe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Claire Vine
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Charlene Bradley
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jeff Cole
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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16
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Abstract
This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products. Second, the physiological significance of reports based upon experiments under extreme conditions that bacteria do not encounter in their natural environment requires reassessment. Third, responses to the primary source of stress need to be distinguished from secondary consequences of chemical damage due to failure of repair mechanisms to cope with extreme conditions. NO is generated by many mechanisms, some of which remain undefined. An example is the recent demonstration that the hybrid cluster protein combines with YtfE (or RIC protein, for repair of iron centres damaged by nitrosative stress) in a new pathway to repair key iron-sulphur proteins damaged by nitrosative stress. The functions of many genes expressed in response to nitrosative stress remain either controversial or are completely unknown. The concentration of NO that accumulates in the bacterial cytoplasm is essentially unknown, so dogmatic statements cannot be made that damage to transcription factors (Fur, FNR, SoxRS, MelR, OxyR) occurs naturally as part of a physiologically relevant signalling mechanism. Such doubts can be resolved by simple experiments to meet six proposed criteria.
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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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18
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Ferrari E, Walter MC, Huptas C, Scherer S, Müller-Herbst S. Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698. Front Microbiol 2017; 8:1672. [PMID: 28919887 PMCID: PMC5585140 DOI: 10.3389/fmicb.2017.01672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to analyze the adaptation of the environmental Listeria weihenstephanensis DSM 24698 to anaerobiosis. The complete circular genome sequence of this species is reported and the adaptation of L. weihenstephanensis DSM 24698 to oxygen availability was investigated by global transcriptional analyses via RNAseq at 18 and 34°C. A list of operons was created based on the transcriptional data. Forty-two genes were upregulated anaerobically and 62 genes were downregulated anaerobically. The oxygen dependent gene expression of selected genes was further validated via qPCR. Many of the differentially regulated genes encode metabolic enzymes indicating broad metabolic adaptations with respect to oxygen availability. Genes showing the strongest oxygen-dependent adaption encoded nitrate (narGHJI) and nitrite (nirBD) reductases. Together with the observation that nitrate supported anaerobic growth, these data indicate that L. weihenstephanensis DSM 24698 performs anaerobic nitrate respiration. The wide overlap between the oxygen-dependent transcriptional regulation at 18 and 34°C suggest that temperature does not play a key role in the oxygen-dependent transcriptional regulation of L. weihenstephanensis DSM 24698.
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Affiliation(s)
- Elena Ferrari
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Mathias C. Walter
- Department of Genome-Oriented Bioinformatics, Technische Universität MünchenFreising, Germany
| | - Christopher Huptas
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Siegfried Scherer
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Stefanie Müller-Herbst
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
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19
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Tutukina MN, Potapova AV, Cole JA, Ozoline ON. Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation. Microbiology (Reading) 2016; 162:1220-1231. [DOI: 10.1099/mic.0.000297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Maria N. Tutukina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
| | - Anna V. Potapova
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
| | - Jeffrey A. Cole
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Olga N. Ozoline
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Russia
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20
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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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21
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Roco CA, Bergaust LL, Bakken LR, Yavitt JB, Shapleigh JP. Modularity of nitrogen-oxide reducing soil bacteria: linking phenotype to genotype. Environ Microbiol 2016; 19:2507-2519. [PMID: 26914200 DOI: 10.1111/1462-2920.13250] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 01/25/2016] [Indexed: 12/26/2022]
Abstract
Model denitrifiers convert NO3- to N2 , but it appears that a significant fraction of natural populations are truncated, conducting only one or two steps of the pathway. To better understand the diversity of partial denitrifiers in soil and whether discrepancies arise between the presence of known N-oxide reductase genes and phenotypic features, bacteria able to reduce NO3- to NO2- were isolated from soil, N-oxide gas products were measured for eight isolates, and six were genome sequenced. Gas phase analyses revealed that two were complete denitrifiers, which genome sequencing corroborated. The remaining six accumulated NO and N2 O to varying degrees and genome sequencing of four indicated that two isolates held genes encoding nitrate reductase as the only dissimilatory N-oxide reductase, one contained genes for both nitrate and nitric oxide reductase, and one had nitrate and nitrite reductase. The results demonstrated that N-oxide production was not always predicted by the genetic potential and suggested that partial denitrifiers could be readily isolated among soil bacteria. This supported the hypothesis that each N-oxide reductase could provide a selectable benefit on its own, and therefore, reduction of nitrate to dinitrogen may not be obligatorily linked to complete denitrifiers but instead a consequence of a functionally diverse community.
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Affiliation(s)
| | - Linda L Bergaust
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ǻs, Norway
| | - Lars R Bakken
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ǻs, Norway
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
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22
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An integrated biochemical system for nitrate assimilation and nitric oxide detoxification in Bradyrhizobium japonicum. Biochem J 2015; 473:297-309. [PMID: 26564204 PMCID: PMC4724949 DOI: 10.1042/bj20150880] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022]
Abstract
Rhizobia are recognized to establish N2-fixing symbiotic interactions with legume plants. Bradyrhizobium japonicum, the symbiont of soybeans, can denitrify and grow under free-living conditions with nitrate (NO3 (-)) or nitrite (NO2 (-)) as sole nitrogen source. Unlike related bacteria that assimilate NO3 (-), genes encoding the assimilatory NO3 (-) reductase (nasC) and NO2 (-) reductase (nirA) in B. japonicum are located at distinct chromosomal loci. The nasC gene is located with genes encoding an ABC-type NO3 (-) transporter, a major facilitator family NO3 (-)/NO2 (-) transporter (NarK), flavoprotein (Flp) and single-domain haemoglobin (termed Bjgb). However, nirA clusters with genes for a NO3 (-)/NO2 (-)-responsive regulator (NasS-NasT). In the present study, we demonstrate NasC and NirA are both key for NO3 (-) assimilation and that growth with NO3 (-), but not NO2 (-) requires flp, implying Flp may function as electron donor to NasC. In addition, bjgb and flp encode a nitric oxide (NO) detoxification system that functions to mitigate cytotoxic NO formed as a by-product of NO3 (-) assimilation. Additional experiments reveal NasT is required for NO3 (-)-responsive expression of the narK-bjgb-flp-nasC transcriptional unit and the nirA gene and that NasS is also involved in the regulatory control of this novel bipartite assimilatory NO3 (-)/NO2 (-) reductase pathway.
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23
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Hesketh A, Deery MJ, Hong HJ. High-Resolution Mass Spectrometry Based Proteomic Analysis of the Response to Vancomycin-Induced Cell Wall Stress in Streptomyces coelicolor A3(2). J Proteome Res 2015; 14:2915-28. [PMID: 25965010 DOI: 10.1021/acs.jproteome.5b00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how bacteria survive periods of cell wall stress is of fundamental interest and can help generate ideas for improved antibacterial treatments. In this study we use tandem mass tagging to characterize the proteomic response of vancomycin resistant Streptomyces coelicolor to the exposure to sublethal levels of the antibiotic. A common set of 804 proteins were identified in triplicate experiments. Contrasting changes in the abundance of proteins closely associated with the cytoplasmic membrane with those taking place in the cytosol identified aspects of protein spatial localization that are associated with the response to vancomycin. Enzymes for peptidoglycan precursor, mycothiol, ectoine and menaquinone biosynthesis together with a multisubunit nitrate reductase were recruited to the membrane following vancomycin treatment. Many proteins with regulatory functions (including sensor protein kinases) also exhibited significant changes in abundance exclusively in the membrane-associated protein fraction. Several enzymes predicted to be involved in extracellular peptidoglycan crossbridge formation became significantly depleted from the membrane. A comparison with data previously acquired on the changes in gene transcription following vancomycin treatment identified a common high-confidence set of changes in gene expression. Generalized changes in protein abundance indicate roles for proteolysis, the pentose phosphate pathway and a reorganization of amino acid biosynthesis in the stress response.
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Affiliation(s)
- Andy Hesketh
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Michael J Deery
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Hee-Jeon Hong
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K
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24
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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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25
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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26
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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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27
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Crack JC, Stapleton MR, Green J, Thomson AJ, Le Brun NE. Mechanism of [4Fe-4S](Cys)4 cluster nitrosylation is conserved among NO-responsive regulators. J Biol Chem 2013; 288:11492-502. [PMID: 23471974 DOI: 10.1074/jbc.m112.439901] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Fumarate nitrate reduction (FNR) regulator from Escherichia coli controls expression of >300 genes in response to O2 through reaction with its [4Fe-4S] cluster cofactor. FNR is the master switch for the transition between anaerobic and aerobic respiration. In response to physiological concentrations of nitric oxide (NO), FNR also regulates genes, including the nitrate reductase (nar) operon, a major source of endogenous cellular NO, and hmp, which encodes an NO-detoxifying enzyme. Here we show that the [4Fe-4S] cluster of FNR reacts rapidly in a multiphasic reaction with eight NO molecules. Oxidation of cluster sulfide ions (S(2-)) to sulfane (S(0)) occurs, some of which remains associated with the protein as Cys persulfide. The nitrosylation products are similar to a pair of dinuclear dinitrosyl iron complexes, [Fe(I)2(NO)4(Cys)2](0), known as Roussin's red ester. A similar reactivity with NO was reported for the Wbl family of [4Fe-4S]-containing proteins found only in actinomycetes, such as Streptomyces and Mycobacteria. These results show that NO reacts via a common mechanism with [4Fe-4S] clusters in phylogenetically unrelated regulatory proteins that, although coordinated by four Cys residues, have different cluster environments. The reactivity of E. coli FNR toward NO, in addition to its sensitivity toward O2, is part of a hierarchal network that monitors, and responds to, NO, both endogenously generated and exogenously derived.
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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, United Kingdom
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28
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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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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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Vine CE, Cole JA. Unresolved sources, sinks, and pathways for the recovery of enteric bacteria from nitrosative stress. FEMS Microbiol Lett 2011; 325:99-107. [DOI: 10.1111/j.1574-6968.2011.02425.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Claire E. Vine
- School of Biosciences; University of Birmingham; Birmingham; UK
| | - Jeffrey A. Cole
- School of Biosciences; University of Birmingham; Birmingham; UK
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