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Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans. Sci Rep 2019; 9:17234. [PMID: 31754148 PMCID: PMC6872814 DOI: 10.1038/s41598-019-53553-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/29/2019] [Indexed: 12/25/2022] Open
Abstract
Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd1 nitrite reductase (cd1NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd1NiR, presumably because cd1NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd1NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd1NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd1NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.
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2
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Liu DM, Wang P, Zhang XY, Xu XL, Wu H, Li L. Characterization of nitrite degradation by Lactobacillus casei subsp. rhamnosus LCR 6013. PLoS One 2014; 9:e93308. [PMID: 24755671 PMCID: PMC3995639 DOI: 10.1371/journal.pone.0093308] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/28/2014] [Indexed: 11/18/2022] Open
Abstract
Nitrites are potential carcinogens. Therefore, limiting nitrites in food is critically important for food safety. The nitrite degradation capacity of Lactobacillus casei subsp. rhamnosus LCR 6013 was investigated in pickle fermentation. After LCR 6013 fermentation for 120 h at 37°C, the nitrite concentration in the fermentation system was significantly lower than that in the control sample without the LCR 6013 strain. The effects of NaCl and Vc on nitrite degradation by LCR 6013 in the De Man, Rogosa and Sharpe (MRS) medium were also investigated. The highest nitrite degradations, 9.29 mg/L and 9.89 mg/L, were observed when NaCl and Vc concentrations were 0.75% and 0.02%, respectively in the MRS medium, which was significantly higher than the control group (p ≤ 0.01). Electron capture/gas chromatography and indophenol blue staining were used to study the nitrite degradation pathway of LCR 6013. The nitrite degradation products contained N2O, but no NH4(+). The LCR 6013 strain completely degraded all NaNO2 (50.00 mg/L) after 16 h of fermentation. The enzyme activity of NiR in the periplasmic space was 2.5 times of that in the cytoplasm. Our results demonstrated that L. casei subsp. rhamnosus LCR 6013 can effectively degrade nitrites in both the pickle fermentation system and in MRS medium by NiR. Nitrites are degraded by the LCR 6013 strain, likely via the nitrate respiration pathway (NO2(-)>NO->N2O->N2), rather than the aammonium formation pathway (dissimilatory nitrate reduction to ammonium, DNRA), because the degradation products contain N2O, but not NH4(+).
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Affiliation(s)
- Dong-mei Liu
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
- * E-mail:
| | - Pan Wang
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
| | - Xin-yue Zhang
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
| | - Xi-lin Xu
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
| | - Hui Wu
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
| | - Li Li
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, Guangdong, China
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3
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Abstract
The structure-function relationships in nitrite reductases, key enzymes in the dissimilatory denitrification pathway which reduce nitrite to nitric oxide (NO), are reviewed in this paper. The mechanisms of NO production are discussed in detail and special attention is paid to new structural information, such as the high resolution structure of the copper- and heme-containing enzymes from different sources. Finally, some implications relevant to regulation of the steady state levels of NO in denitrifiers are presented.
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Affiliation(s)
- F Cutruzzolà
- Dipartimento di Scienze Biochimiche, Università di Roma 'La Sapienza', P.le A. Moro, 5, 00185, Rome, Italy.
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4
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Abstract
The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms.
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Affiliation(s)
- A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain.
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5
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Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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6
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7
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Berks BC, Ferguson SJ, Moir JW, Richardson DJ. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1232:97-173. [PMID: 8534676 DOI: 10.1016/0005-2728(95)00092-5] [Citation(s) in RCA: 390] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- B C Berks
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, UK
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8
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Saraiva LM, Fauque G, Besson S, Moura I. Physico-chemical and spectroscopic properties of the monohemic cytochrome C552 from Pseudomonas nautica 617. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 224:1011-7. [PMID: 7925398 DOI: 10.1111/j.1432-1033.1994.01011.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A c-type monohemic ferricytochrome C552 (11 kDa) was isolated from the soluble extract of a marine denitrifier, Pseudomonas nautica strain 617, grown under anaerobic conditions with nitrate as final electron acceptor. The NH2-terminal sequence and the amino acid composition of the cytochrome were determined. The heme iron of the cytochrome C552 has histidine-methionine as axial ligands, and a pH-dependent mid-point redox potential, equal to 250 mV at pH 7.6. The presence of methionine was demonstrated by visible, EPR and NMR spectroscopies. The assignment of most of the hemic protons was performed applying two-dimensional NOE spectroscopy (NOESY), and the aromatic region was assigned through two-dimensional correlated spectroscopy (COSY) experiments. The EPR spectrum of the oxidised form of the cytochrome C552 is typical of a low-spin ferric heme.
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Affiliation(s)
- L M Saraiva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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9
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Jones AM, Hollocher TC. Nitric oxide reductase of Achromobacter cycloclastes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1993. [DOI: 10.1016/0005-2728(93)90121-u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Germany
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11
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12
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Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89474-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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13
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Goretski J, Hollocher TC. Catalysis of nitrosyl transfer by denitrifying bacteria is facilitated by nitric oxide. Biochem Biophys Res Commun 1991; 175:901-5. [PMID: 2025262 DOI: 10.1016/0006-291x(91)91650-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two denitrifying bacteria, Pseudomonas stutzeri and Achromobacter cycloclastes, were incubated with Na15NO2 and NaN3 under conditions that allowed catalysis of nitrosyl transfer from nitrite to azide. This transfer, which is presumed to be mediated by the heme- and copper-containing nitrite reductase of P. stutzeri and A. cycloclastes, respectively, leads to formation of isotopically mixed 14,15N2O, whereas denitrification leads to 15N2O. The conditions that emphasized nitrosyl transfer also partially inhibited the nitric oxide reductase system and led to accumulation of 15NO. Absorption of NO from the gas phase by acidic CrSO4 in a sidewell largely abolished nitrosyl transfer to azide. With these two organisms, which are thought to be representative of denitrifiers generally, catalysis of nitrosyl transfer seemed to depend on NO.
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Affiliation(s)
- J Goretski
- Department of Biochemistry, Brandeis University, Waltham, MA 02254
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The denitrifying nitrite reductase of Bacillus halodenitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1991. [DOI: 10.1016/s0005-2728(05)80053-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Andersson LA, Loehr TM, Wu WS, Chang CK, Timkovich R. Modelling heme d1. The spectral properties of copper(II) porphyrindiones. FEBS Lett 1990; 267:285-8. [PMID: 2116325 DOI: 10.1016/0014-5793(90)80946-g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The heme d1 macrocycle of Ps. aeruginosa dissimilatory nitrite reductase is an iron porphyrin-3,8-dione with a 17-acrylate substituent. We have compared the RR properties of Cu-d1, the copper(II) TME of extracted heme d1, with those of models that differ only with respect to the acrylate: Cu-17-acrylate mesoporphyrin-3,8-dione (2) and Cu-mesoporphyrin-3,8-dione (3). The RR spectrum of Cu-d1 is very similar to that of 2, including v(C = O) at approximately 1720 cm-1. Replacement of the acrylate with propionate changes the spectrum markedly. For example, the v(C = O) mode of 3 shifts to 1712 cm-1, and peaks of Cu-d1 and 2 at approximately 1400 and approximately 1535 cm-1 are shifted or absent from the spectrum of 3. FTIR spectra of 2 and 3 also differ in their voxo(C = O) frequencies. The acrylate thus has a surprisingly strong influence on the electronic structural and spectral properties of heme d1. These data provide a foundation for studies of the novel biological porphyrindione macrocycles.
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Affiliation(s)
- L A Andersson
- Department of Chemical and Biological Sciences, Oregon Graduate Institute, Beaverton 97006-1999
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16
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Coyne MS, Arunakumari A, Pankratz HS, Tiedje JM. Localization of the cytochrome cd1 and copper nitrite reductases in denitrifying bacteria. J Bacteriol 1990; 172:2558-62. [PMID: 2158973 PMCID: PMC208897 DOI: 10.1128/jb.172.5.2558-2562.1990] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The locations of cytochrome cd1 nitrite reductases in Pseudomonas aeruginosa and Pseudomonas fluorescens and copper nitrite reductases in Achromobacter cycloclastes and Achromobacter xylosoxidans were identified. Immunogold labeling with colloidal-gold probes showed that the nitrite reductases were synthesized exclusively in anaerobically grown (denitrifying) cells. Little immunogold label occurred in the cytoplasm of these four strains; most was found in the periplasmic space or was associated with cell membranes. Immunogold labeling of thin sections was superior to fractionation by osmotic shock for locating nitrite reductases. The results support models of dentrification energetics that require a periplasmic, not a cytoplasmic, location for nitrite reductases.
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Affiliation(s)
- M S Coyne
- Department of Crop and Soil Sciences, Michigan State University, East Lansing 48824
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17
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Goretski J, Hollocher TC. The kinetic and isotopic competence of nitric oxide as an intermediate in denitrification. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40133-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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18
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Jørgensen KS. Annual Pattern of Denitrification and Nitrate Ammonification in Estuarine Sediment. Appl Environ Microbiol 1989; 55:1841-7. [PMID: 16347979 PMCID: PMC202960 DOI: 10.1128/aem.55.7.1841-1847.1989] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The seasonal variation and depth distribution of the capacity for denitrification and dissimilatory NO
3
−
reduction to NH
4
+
(NO
3
−
ammonification) were studied in the upper 4 cm of the sediment of Norsminde Fjord estuary, Denmark. A combination of C
2
H
2
inhibition and
15
N isotope techniques was used in intact sediment cores in short-term incubations (maximum, 4 h). The denitrification capacity exhibited two maxima, one in the spring and one in the fall, whereas the capacity for NO
3
−
ammonification was maximal in the late summer, when sediments were progressively reduced. The denitrification capacity was always highest in the uppermost 1 cm of the sediment and declined with depth. The NO
3
−
ammonification was usually higher with depth, but the maximum activity in late summer was observed within the upper 1 cm. The capacity for NO
3
−
incorporation into organic material was investigated on two occasions in intact sediment cores and accounted for less than 5% of the total NO
3
−
reduction. Denitrification accounted for between 13 and 51% of the total NO
3
−
reduction, and NH
4
+
production accounted for between 4 and 21%, depending on initial rates during the time courses. Changes of the rates during the incubation were observed in the late summer, which reflected synthesis of denitrifying enzymes. This time lag was eliminated in experiments with mixed sediment because of preincubation with NO
3
−
and alterations of the near-environmental conditions. The initial rates obtained in intact sediment cores therefore reflect the preexisting enzyme content of the sediment.
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Affiliation(s)
- K S Jørgensen
- Department of Ecology and Genetics, University of Aarhus, Ny Munkegade, DK-8000 Aarhus C, Denmark
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Heiss B, Frunzke K, Zumft WG. Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate-respiring (denitrifying) Pseudomonas stutzeri. J Bacteriol 1989; 171:3288-97. [PMID: 2542222 PMCID: PMC210048 DOI: 10.1128/jb.171.6.3288-3297.1989] [Citation(s) in RCA: 154] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nitric oxide (NO) reductase was solubilized by Triton X-100 from the membrane fraction of Pseudomonas stutzeri ZoBell and purified 100-fold to apparent electrophoretic homogeneity. The enzyme consisted of two polypeptides of Mr 38,000 and 17,000 associated with heme b and heme c, respectively. Absorption maxima of the reduced complex were at 420.5, 522.5, and 552.5 nm, with a shoulder at 560 nm. The electron paramagnetic resonance spectrum was characteristic of high- and low-spin ferric heme proteins; no signals typical for iron-sulfur proteins were found. Nitric oxide reductase stoichiometrically transformed NO to nitrous oxide in an ascorbate-phenazine methosulfate-dependent reaction with a specific activity of 11.8 mumols/min per mg of protein. The activity increased to 40 mumols upon the addition of soybean phospholipids, n-octyl-beta-D-glucopyranoside, or its thio derivative to the assay system. Apparent Km values for NO and phenazine methosulfate were 60 and 2 microM, respectively. The pH optimum of the reaction was at 4.8. Cytochrome co was purified from P. stutzeri to permit its distinction from NO reductase. Spectrophotometric binding assays and other criteria also differentiated NO reductase from the respiratory cytochrome bc1 complex.
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Affiliation(s)
- B Heiss
- Lehrstuhl für Mikrobiologie, Universität Karlsruhe, Federal Republic of Germany
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Purification and some characteristics of nitric oxide reductase-containing vesicles from Paracoccus denitrificans. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83270-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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21
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Goretski J, Hollocher TC. Trapping of nitric oxide produced during denitrification by extracellular hemoglobin. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69208-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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