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Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Global patterns in gene content of soil microbiomes emerge from microbial interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542950. [PMID: 38014336 PMCID: PMC10680560 DOI: 10.1101/2023.05.31.542950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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Genomic structure predicts metabolite dynamics in microbial communities. Cell 2022; 185:530-546.e25. [PMID: 35085485 DOI: 10.1016/j.cell.2021.12.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/16/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
Abstract
The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.
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Kobayashi S, Hira D, Yoshida K, Toyofuku M, Shida Y, Ogasawara W, Yamaguchi T, Araki N, Oshiki M. Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, Nitrososphaera viennensis. Microbes Environ 2018; 33:428-434. [PMID: 30318500 PMCID: PMC6308003 DOI: 10.1264/jsme2.me18058] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15NO2− to 15NO, the oxidation of hydroxylamine (15NH2OH) to 15NO, and the production of 14–15N2O from 15NH2OH and 14NO2−. To the best of our knowledge, the present study is the first to document the enzymatic properties of AOA NirK.
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Affiliation(s)
- Shun Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Daisuke Hira
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University
| | - Keitaro Yoshida
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology
| | | | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
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Affiliation(s)
- M. K. Firestone
- Department of Plant and Soil Biology University of California; Berkeley
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Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 2006; 188:1473-88. [PMID: 16452431 PMCID: PMC1367237 DOI: 10.1128/jb.188.4.1473-1488.2006] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 11/30/2005] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.
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Affiliation(s)
- Harry R Beller
- Lawrence Livermore National Laboratory, P.O. Box 808, L-542, Livermore, California 94551-0808, USA.
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Mancinelli RL, Cronin S, Hochstein LI. The purification and properties of a cd-cytochrome nitrite reductase from Paracoccus halodenitrificans. Arch Microbiol 2001; 145:202-8. [PMID: 11540874 DOI: 10.1007/bf00446781] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Paracoccus halodenitrificans, grown anaerobically in the presence of nitrite, contained membrane and cytoplasmic nitrite reductases. When assayed in the presence of phenazine methosulfate and ascorbate, the membrane-bound enzyme produced nitrous oxide whereas the cytoplasmic enzyme produced nitric oxide. When both enzymes were assayed in the presence of methyl viologen and dithionite, the cytoplasmic enzyme produced ammonia. Following solubilization, the membrane-bound enzyme behaved like the cytoplasmic enzyme, producing nitric oxide in the presence of phenazine methosulfate and ascorbate, and ammonia when assayed in the presence of methyl viologen and dithionite. The cytoplasmic and membrane-bound enzymes were purified to essentially the same specific activity. Only a single nitrite-reductase activity was detected on electrophoretic gels and the electrophoretic behavior of both enzymes suggested they were identical. The spectral properties of both enzymes suggested they were cd-type cytochromes. These data suggest that the products of nitrite reduction by the cd-cytochrome nitrite reductase are determined by the location of the enzyme and the redox potential of the electron donor.
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Affiliation(s)
- R L Mancinelli
- Planetary Biology Division, Ames Research Center, Moffett Field, CA 94035, USA
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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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Ozawa S, Sakamoto E, Watanabe Y, Morishima I. Formation of nitrosyl-iron(II)β-oxoporphyrin π-cation radical complexes. Models for a reaction intermediate of dissimilatory nitrite reductases. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/c39940000935] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Silvestrini MC, Falcinelli S, Ciabatti I, Cutruzzolà F, Brunori M. Pseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview. Biochimie 1994; 76:641-54. [PMID: 7893816 DOI: 10.1016/0300-9084(94)90141-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The biochemistry and molecular biology of nitrite reductase, a key enzyme in the dissimilatory denitrification pathway of Ps aeruginosa which reduces nitrite to NO, is reviewed in this paper. The enzyme is a non-covalent homodimer, each subunit containing one heme c and one heme d1. The reaction mechanisms of nitrite and oxygen reduction are discussed in detail, as well as the interaction of the enzyme with its macromolecular substrates, azurin and cytochrome c551. Special attention is paid to new structural information, such as the chemistry of the d1 prosthetic group and the primary sequence of the gene and the protein. Finally, results on the expression both in Ps aeruginosa and in heterologous systems are presented.
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Affiliation(s)
- M C Silvestrini
- Dipartimento di Scienze Biochimiche, Università di Roma La Sapienza, Italy
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Moir JW, Baratta D, Richardson DJ, Ferguson SJ. The purification of a cd1-type nitrite reductase from, and the absence of a copper-type nitrite reductase from, the aerobic denitrifier Thiosphaera pantotropha; the role of pseudoazurin as an electron donor. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:377-85. [PMID: 8383046 DOI: 10.1111/j.1432-1033.1993.tb17672.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Thiosphaera pantotropha has been reported to contain a copper-type nitrite reductase on the basis that the copper chelator diethyldithiocarbamate inhibited the overall process of denitrification. It is now shown that nitrous oxide reduction is 100% inhibited by 10 mM diethyldithiocarbamate or 100 microM azide. We also found that both these inhibitors partially inhibited nitrite reduction in this organism. We purified the nitrite reductase of T. pantotropha and found that it was of the cytochrome cd1 type, contrary to the published report of it being a copper-type nitrite reductase. This is of importance since T. pantotropha is capable of aerobic nitrite reduction. The only detectable nitrite reductase in anaerobically or aerobically grown cells is the cd1 type. We also purified a small copper-containing protein, pseudoazurin. Pseudoazurin was found to be capable of donating electrons to the cd1-type nitrite reductase in vitro, and its copper centre was chelated by diethyldithiocarbamate. Since nitrite reduction is partially inhibited by diethyldithiocarbamate, it is thought that pseudoazurin is an electron donor to nitrite reductase in vivo.
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Affiliation(s)
- J W Moir
- Department of Biochemistry, University of Oxford, England
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13
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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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14
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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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15
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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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Liu MC, Huynh BH, Payne WJ, Peck HD, Dervartanian DV, Legall J. Optical, EPR and Mössbauer spectroscopic studies on the NO derivatives of cytochrome cd1 from Thiobacillus denitrificans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 169:253-8. [PMID: 2826139 DOI: 10.1111/j.1432-1033.1987.tb13605.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have used optical, EPR and Mössbauer spectroscopies to study the formation of heme-NO complex upon the addition of nitrite to reduced cytochrome cd1 from Thiobacillus denitrificans. The reduced d1 heme binds NO under both alkaline and acidic conditions, but the binding of NO to the reduced c heme was strongly pH-dependent. The Mössbauer data showed unambiguously that at pH 7.6 the c heme does not complex NO, whereas at pH 5.8 approximately half of the reduced c heme binds NO. This observation was confirmed by EPR studies, which showed that the spin concentration of the heme-NO EPR signal increased from 2 spins/molecule at pH 8.0 to approximately 3 spins/molecule at pH 5.8. Optical absorption study also showed strong pH dependence in the binding of NO to the reduced c heme. We have also analyzed the Mössbauer spectra of the ferrous d1 heme-NO complex using a spin-Hamiltonian formalism. The magnetic hyperfine coupling tensor was found to be consistent with the unpaired electron residing on a sigma orbital.
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Affiliation(s)
- M C Liu
- Department of Microbiology, University of Georgia, Athens
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17
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Sublette KL, Sylvester ND. Oxidation of hydrogen sulfide byThiobacillus denitrificans: Desulfurization of natural gas. Biotechnol Bioeng 1987; 29:249-57. [DOI: 10.1002/bit.260290216] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Liu MY, Liu MC, Payne WJ, Legall J. Properties and electron transfer specificity of copper proteins from the denitrifier "Achromobacter cycloclastes". J Bacteriol 1986; 166:604-8. [PMID: 3700338 PMCID: PMC214647 DOI: 10.1128/jb.166.2.604-608.1986] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A blue copper protein (Mr 12,000) was purified from cells of "Achromobacter cycloclastes" grown as a denitrifier. When reduced, the blue copper protein transferred electrons to the copper protein nitrite reductase purified from the same cells, whereas a variety of cytochromes from denitrifiers failed to do so. Inclusion of a protease inhibitor, phenylmethylsulfonyl fluoride, in the buffers employed during preparation yielded purified blue copper protein with 18 more amino acid residues and two times more specific enzyme activity than other researchers have found.
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Trudinger PA, Meyer TE, Bartsch RG, Kamen MD. The major soluble cytochromes of the obligately aerobic sulfur bacterium, Thiobacillus neapolitanus. Arch Microbiol 1985; 141:273-8. [PMID: 2990367 DOI: 10.1007/bf00428836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Four cytochromes were isolated from soluble extracts of the aerobic sulfur bacterium, Thiobacillus neapolitanus. The two most abundant proteins were purified to homogeneity and thoroughly characterized. Cytochrome c-554 (547) is a monomeric, small molecular weight protein which is unusual in having two well-resolved alpha peaks in UV-visible absorption spectra. The redox potential is 208 mV. Native cytochrome c-549 is oligomeric, but has a subunit size of about 26,000. The yield of this protein could be improved dramatically by washing membranes with 30% ammonium sulfate, but the material solubilized by this method had a larger native molecular weight than that in the initial 0.1 M Tris-Cl extract and behaved differently on chromatography. The properties of cytochrome c-549 including subunit size and UV-visible absorption spectra are similar to mitochondrial cytochrome c1 and chloroplast cytochrome f, which suggests that it may be a modified form of the predominant membrane cytochrome. Based on cytochrome content, it is suggested that T. neapolitanus is not closely related to other thiobacilli.
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Solubilization and resolution of the membrane-bound nitrite reductase from Paracoccus halodenitrificans into nitrite and nitric oxide reductases. Arch Microbiol 1984. [DOI: 10.1007/bf00454923] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
Present knowledge of the different enzymatic steps of the denitrification chains in various bacteria, particularly Paracoccus denitrificans and Pseudomonas aeruginosa has been briefly reviewed. The question whether nitric oxide (NO), nitrous oxide (N2O) and other nitrogen derivatives are obligatory intermediates has been discussed. The second part is an extensive review of the structure and the function of a key enzyme in denitrification, cytochrome c551-nitrite-oxidoreductase from P. aeruginosa. Recent results on the stoichiometry of nitrite reduction have been discussed.
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Timkovich R, Cork MS, Taylor PV. Proposed structure for the noncovalently associated heme prosthetic group of dissimilatory nitrite reductases. Identification of substituents. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43448-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Grant MA, Hochstein LI. A dissimilatory nitrite reductase in Paracoccus halodenitrificans. Arch Microbiol 1984; 137:79-84. [PMID: 6712419 DOI: 10.1007/bf00425812] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Paracoccus halodenitrificans produced a membrane-associated nitrite reductase. Spectrophotometric analysis showed it to be associated with a cd-cytochrome and located on the inner side of the cytoplasmic membrane. When supplied with nitrite, membrane preparations produced nitrous oxide and nitric oxide in different ratios depending on the electron donor employed. The nitrite reductase was maximally active at relatively low concentrations of sodium chloride and remained attached to the membranes at 100 mM sodium chloride.
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Poole RK. Bacterial cytochrome oxidases. A structurally and functionally diverse group of electron-transfer proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 726:205-43. [PMID: 6311261 DOI: 10.1016/0304-4173(83)90006-x] [Citation(s) in RCA: 225] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15N tracer studies on the reduction of nitrite by the purified dissimilatory nitrite reductase of Pseudomonas aeruginosa. Evidence for direct production of N2O without free NO as an intermediate. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32505-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Liu MC, Payne WJ, Peck HD, LeGall J. Comparison of cytochromes from anaerobically and aerobically grown cells of Pseudomonas perfectomarinus. J Bacteriol 1983; 154:278-86. [PMID: 6833178 PMCID: PMC217457 DOI: 10.1128/jb.154.1.278-286.1983] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas perfectomarinus (ATCC 14405) is a facultative anaerobe capable of either oxygen respiration or anaerobic nitrate respiration, i.e., denitrification. A comparative study of the electron transfer components of cells revealed five c-type cytochromes and cytochrome cd in the soluble fraction from anaerobically grown cells and four c-type cytochromes in the soluble fraction from aerobically grown cells. Purification procedures yielded three c-type cytochromes (designated c-551, c-554, and acidic c-type) from both kinds of cells as indicated by similarities in absorption spectra, molecular weight, and electrophoretic mobility. Cytochrome cd, a diheme c-type cytochrome (cytochrome c-552), and a split-alpha c-type cytochrome were recovered only from anaerobically grown cells. A c-type cytochrome with a low ratio of alpha to beta absorption peak heights was uniquely present in the aerobically grown cells. Liquid N2 temperature absorption spectroscopy on the membrane fraction from anaerobically grown cells revealed residual cytochrome cd as well as differences in the relative amounts of c-type and b-type cytochromes in membranes prepared from cells grown under the two different conditions.
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Abstract
Little is known about the role of nitrate in evolution of bacterial energy-generating mechanisms. Denitrifying bacteria are commonly regarded to have evolved from nitrate-respiring bacteria. Some researchers regard denitrification to be the precursor of aerobic respiration; others feel the opposite is true. Currently recognized denitrifying bacteria such as Hyphomicrobium, Paracoccus, Pseudomonas and Thiobacillus form a very diverse group. However, inadequate testing procedures and uncertain taxonomic identification of many isolates may have overstated the number of genera with species capable of denitrification. Nitrate reductases are structurally similar among denitrifying bacteria, but distinct from the enzymes in other nitrate-reducing organisms. Denitryfying bacteria have one of two types of nitrite reductase, either a copper-containing enzyme or an enzyme containing a cytochrome cd moiety. Both types are distinct from other nitrate reductases. Organisms capable of dissimilatory nitrate reduction are widely distributed among eubacterial groups defined by 16S ribosomal RNA phylogeny. Indeed, nitrate reduction is an almost universal property of actinomycetes and enteric organisms. However, denitrification is restricted to genera within the purple photosynthetic group. Denitrification within the genus Pseudomonas is distributed in accordance with DNA and RNA homology complexes. Denitrifiers seem to have evolved from a common ancestor within the purple photosynthetic bacterial group, but not from a nitrate-reducing organism such as those found today. Although denitrification seems to have arisen at the same time as aerobic respiration, the evolutionary relationship between the two cannot be determined at this time.
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Zumft WG, Frunzke K. Discrimination of ascorbate-dependent nonenzymatic and enzymatic, membrane-bound reduction of nitric oxide in denitrifying Pseudomonas perfectomarinus. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 681:459-68. [PMID: 7126558 DOI: 10.1016/0005-2728(82)90188-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The marine nitrite-respiring (denitrifying) bacterium, Pseudomonas perfectomarinus, catalyzes by a membrane-bound enzyme the reduction of nitric oxide to nitrous oxide with ascorbic-reduced phenazine methosulfate as electron donor. The entire nitric oxide-reducing capability of a cell-free system was membrane bound and this process was studied with respect to pH and substrate dependency. The enzymatic process was perturbed by an identical nonenzymatic reduction by iron(II) ascorbate in neutral to alkaline aqueous solution. 2 mol nitric oxide and 1 mol ascorbate were consumed per mol nitrous oxide formed. Enzymatic and nonenzymatic processes were discriminated by their differential behavior towards pH and metal-chelating agents. The pH optimum for the enzymatic and nonenzymatic reaction was 5.2 and greater than 7.0, respectively. EDTA (10 mM) inhibited the nonenzymatic reduction completely without interfering with the membrane-bound activity. The nonenzymatic system mimics the reaction of nitric oxide reductase and could serve as a model to study the formation of the N-N bond in denitrification. Enzymatic generation of nitric oxide by cytochrome cd and subsequent nonenzymatic reduction to nitrous oxide simulate an overall quasi-enzymatic nitrous oxide formation by cytochrome cd. The nonenzymatic reduction of nitric oxide might have occurred in previous work due to the ubiquitous use of ascorbate in studies on nitrite respiration and the likelihood of adventitious iron in biological samples.
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Timkovich R, Dhesi R, Martinkus KJ, Robinson MK, Rea TM. Isolation of Paracoccus denitrificans cytochrome cd1: comparative kinetics with other nitrite reductases. Arch Biochem Biophys 1982; 215:47-58. [PMID: 6284044 DOI: 10.1016/0003-9861(82)90277-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Boogerd FC, Van Verseveld HW, Stouthamer AH. Respiration-driven proton translocation with nitrite and nitrous oxide in Paracoccus denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 638:181-91. [PMID: 7317386 DOI: 10.1016/0005-2728(81)90226-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
(1)H+ leads to/electron acceptor ratios have been determined with the oxidant pulse method for cells of denitrifying Paracoccus denitrificans oxidizing endogenous substrates during reduction of O2, NO2- or N2O. Under optimal H+-translocation conditions, the ratios leads to H+/O, H+ leads to/N2O, H+ leads to/NO2- for reduction to N2 and H+ leads to/NO2- for reduction to N2O were 6.0-6.3, 4.02, 5.79 and 3.37, respectively. (2) With ascorbate/N,N,N,'N'-tetramethyl-p-phenylene-diamine as exogenous substrate, addition of NO2- or N2O to an anaerobic cell suspension resulted in rapid alkalinization of the outer bulk medium. H+/N2O, H+/NO2- for reduction to N2 and H+/NO2- for reduction to N2O were -0.84, -2.33 and -1.90, respectively. (3) The H+/oxidant ratios, mentioned in item 2, were not altered in the presence of valinomycin/K+ and the triphenylmethylphosphonium cation. (4) A simplified scheme of electron transport to O2, NO2- and N2O is presented which shows a periplasmic orientation of the nitrite reductase as well as the nitrous oxide reductase. Electrons destined for NO2-, N2O or O2 pass two H+-trans-locating sites. The H+ leads to/electron acceptor ratios predicted by this scheme are in good agreement with the experimental values.
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Liu M, Peck HD. The isolation of a hexaheme cytochrome from Desulfovibrio desulfuricans and its identification as a new type of nitrite reductase. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(18)43021-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Cotton TM, Timkovich R, Cork MS. Resonance Raman and surface-enhanced resonance Raman studies of cytochrome cd1. FEBS Lett 1981; 133:39-44. [PMID: 6273217 DOI: 10.1016/0014-5793(81)80466-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Van den Eijnden D, Schiphorst W. Detection of beta-galactosyl(1 leads to 4)N-acetylglucosaminide alpha(2 leads to 3)-sialyltransferase activity in fetal calf liver and other tissues. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69581-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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The Electron Transport System and Hydrogenase of Paracoccus denitrificans. CURRENT TOPICS IN BIOENERGETICS 1981. [DOI: 10.1016/b978-0-12-152512-5.50009-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Wharton DC, Weintraub ST. Identification of nitric oxide and nitrous oxide as products of nitrite reduction by Pseudomonas cytochrome oxidase (nitrate reductase). Biochem Biophys Res Commun 1980; 97:236-42. [PMID: 6257240 DOI: 10.1016/s0006-291x(80)80159-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Aminuddin M. Substrate level versus oxidative phosphorylation in the generation of ATP in Thiobacillus denitrificans. Arch Microbiol 1980; 128:19-25. [PMID: 7458535 DOI: 10.1007/bf00422300] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Particulate fractions of Thiobacillus denitrificans catalyse that the phosphorylation of ADP to ATP during the oxidation of various inorganic sulphur compounds or NADH via an electron transport chain. On the other hand, a "soluble" cell-free fraction synthesized ATP from APS and inorganic phosphate. The production of ATP was verified either by the firefly luciferin-luciferase enzyme system or by the incorporation of 32Pi into ATP. During the oxidation of sulphide, sulphite and NADH the production of ATP from ADP by particulate fractions is inhibited by compounds that inhibit electron transfer and by uncouplers of oxidative phosphorylation. However, these compounds had little effect on the production of ATP from AMP during the oxidation of sulphite by the soluble fraction. NADH was the most effective electron donor for oxidative phosphorylation. The soluble fraction contained high activities of ATP sulphurylase, inorganic pyrophosphatase and adenylate kinase but ADP sulphurylase activity was relatively low. The effects of inhibitors on ATP production from APS and Pi are compared with those on adenylate kinase and ATP sulphurylase.
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Zumft WG, Vega JM. Reduction of nitrite to nitrous oxide by a cytoplasmic membrane fraction from the marine denitrifier Pseudomonas perfectomarinus. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 548:484-99. [PMID: 228713 DOI: 10.1016/0005-2728(79)90060-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A cytoplasmic membrane fraction from the marine denitrifier Pseudomonas perfectomarinus reduced nitrite to nitrous oxide in a stoichiometric reaction without nitric oxide as free intermediate. The membrane system had a specific requirement for FMN with NAD(P)H as electron donors. Other electron donors were ascorbate-reduced cytochrome c-551 or phenazine methosulfate. The membrane fraction contained tightly bound cytochrome cd which represented only a small portion of the total cytochrome cd of the cell. As further terminal oxidase cytochrome o was identified. The membrane fraction produced also nitrous oxide from nitric oxide, however, at a substantially lower rate than from nitrite when using ascorbate-reduced phenazine methosulfate as electron donor.
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LeGall J, Payne WJ, Morgan TV, DerVartanian D. On the purification of nitrite reductase from Thiobacillus denitrificans and its reaction with nitrite under reducing conditions. Biochem Biophys Res Commun 1979; 87:355-62. [PMID: 220969 DOI: 10.1016/0006-291x(79)91804-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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