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Nguyen VH, Wemheuer B, Song W, Bennett H, Palladino G, Burgsdorf I, Sizikov S, Steindler L, Webster NS, Thomas T. Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges. Syst Appl Microbiol 2023; 46:126401. [PMID: 36774720 DOI: 10.1016/j.syapm.2023.126401] [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: 03/10/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Cawthron Institute, Nelson, New Zealand
| | - Giorgia Palladino
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | | | | | | | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia; Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Burgsdorf I, Sizikov S, Squatrito V, Britstein M, Slaby BM, Cerrano C, Handley KM, Steindler L. Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool. THE ISME JOURNAL 2021; 16:1163-1175. [PMID: 34876682 PMCID: PMC8941161 DOI: 10.1038/s41396-021-01165-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/30/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.
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Affiliation(s)
- I Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - S Sizikov
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - V Squatrito
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - M Britstein
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - C Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - K M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - L Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
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3
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Morris BEL, Crable BR, Suflita JM. On the contributions of David Cleaveland White, MD, PhD to microbial ecology: celebrating the life of a pioneer. ISME JOURNAL 2008; 2:797-804. [DOI: 10.1038/ismej.2008.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Stewart V, Bledsoe PJ. Fnr-, NarP- and NarL-dependent regulation of transcription initiation from the Haemophilus influenzae Rd napF (periplasmic nitrate reductase) promoter in Escherichia coli K-12. J Bacteriol 2005; 187:6928-35. [PMID: 16199562 PMCID: PMC1251606 DOI: 10.1128/jb.187.20.6928-6935.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Periplasmic nitrate reductase (napFDAGHBC operon product) functions in anaerobic respiration. Transcription initiation from the Escherichia coli napF operon control region is activated by the Fnr protein in response to anaerobiosis and by the NarQ-NarP two-component regulatory system in response to nitrate or nitrite. The binding sites for the Fnr and phospho-NarP proteins are centered at positions -64.5 and -44.5, respectively, with respect to the major transcription initiation point. The E. coli napF operon is a rare example of a class I Fnr-activated transcriptional control region, in which the Fnr protein binding site is located upstream of position -60. To broaden our understanding of napF operon transcriptional control, we studied the Haemophilus influenzae Rd napF operon control region, expressed as a napF-lacZ operon fusion in the surrogate host E. coli. Mutational analysis demonstrated that expression required binding sites for the Fnr and phospho-NarP proteins centered at positions -81.5 and -42.5, respectively. Transcription from the E. coli napF operon control region is activated by phospho-NarP but antagonized by the orthologous protein, phospho-NarL. By contrast, expression from the H. influenzae napF-lacZ operon fusion in E. coli was stimulated equally well by nitrate in both narP and narL null mutants, indicating that phospho-NarL and -NarP are equally effective regulators of this promoter. Overall, the H. influenzae napF operon control region provides a relatively simple model for studying synergistic transcription by the Fnr and phospho-NarP proteins acting from class I and class II locations, respectively.
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Affiliation(s)
- Valley Stewart
- Section of Microbiology, University of California, One Shields Avenue, Davis, CA 95616-8665, USA.
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5
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Hubmacher D, Matzanke BF, Anemüller S. Effects of iron limitation on the respiratory chain and the membrane cytochrome pattern of the Euryarchaeon Halobacterium salinarum. Biol Chem 2004; 384:1565-73. [PMID: 14719798 DOI: 10.1515/bc.2003.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The effects of iron limitation on the electron transport chain of the extremely halophilic Euryarchaeon Halobacterium salinarum were analyzed. When iron was growth-limiting, the respiratory rates as well as the inhibition pattern of the membranes were significantly different from membranes of iron replete cells. Changes in the availability of iron cause the formation of different respiratory pathways including different entry sites for electrons, different terminal oxidases of the respiratory chain, and drastic changes of the cytochrome composition and of the relative amounts of cytochromes. Under iron-limiting conditions, mainly low-potential cytochromes were measured. EPR spectroscopic studies revealed that the amount of proteins containing iron-sulfur clusters is reduced in membranes under iron-limiting growth conditions. Taken together, our results strongly suggest for the first time an important role of iron supply for the bioenergetics of an Archaeon.
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Affiliation(s)
- Dirk Hubmacher
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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6
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Haraguchi H, Tanimoto K, Tamura Y, Mizutani K, Kinoshita T. Mode of antibacterial action of retrochalcones from Glycyrrhiza inflata. PHYTOCHEMISTRY 1998; 48:125-9. [PMID: 9621457 DOI: 10.1016/s0031-9422(97)01105-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Licochalcone A-D and echinatin, retrochalcones isolated from the roots of Glycyrrhiza inflata, showed antimicrobial activity. Among them, licochalcone A and C had potent activity against some Gram-positive bacteria. These retrochalcones inhibited oxygen consumption in susceptible bacterial cells. The oxidation of NADH in bacterial membrane preparations was also inhibited by them. NADH-cytochrome c reductase was inhibited by licochalcones, while cytochrome c oxidase was not. NADH-CoQ reductase and NADH-FMN oxidoreductase were not inhibited. The site of respiratory inhibition of licochalcones was thought to be between CoQ and cytochrome c in the bacterial respiratory electron transport chain.
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Affiliation(s)
- H Haraguchi
- Faculty of Engineering, Fukuyama University, Japan
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7
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Riedel K, Liebs P, Reinneberg R, Scheller F. Characterization of the Physiological State of Microorganisms Using the Respiration Electrode. ANAL LETT 1988. [DOI: 10.1080/00032718808059865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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de Vrij W, van den Burg B, Konings WN. Spectral and potentiometric analysis of cytochromes from Bacillus subtilis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 166:589-95. [PMID: 3111850 DOI: 10.1111/j.1432-1033.1987.tb13554.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bacillus subtilis cytoplasmic membranes contain several cytochromes which are linked to the respiratory chain. At least six different cytochromes have been separated and identified by ammonium sulphate fractionation and ion-exchange chromatography. They include two terminal oxidases with CO-binding properties and cyanide sensitivity. One of these is an aa3-type cytochrome c oxidase which has characteristic absorption maxima in the reduced-oxidized difference spectrum at 601 nm in the alpha-band and at 443 nm in the Soret band regions. In the alpha-band two separate electron transitions with Em = +205 mV and Em = +335 mV can be discriminated by redox potentiometric titration. The other CO-binding cytochrome c oxidase contains two cytochrome b components with alpha-band maxima at 556 nm and 559 nm. Cytochrome b556 can be reduced by ascorbate and has an Em + +215 mV, whereas cytochrome b559 has an Em = +140 mV. Furthermore a complex consisting of a cytochrome b564 (Em = +140 mV) associated with a cytochrome c554 (Em = +250 mV) was found. This cytochrome c554, which can be reduced by ascorbate, appears to have an asymmetrical alpha-peak and stains for heme-catalyzed peroxidase activity on SDS-containing polyacrylamide gels. A protein with a molecular mass of about 30 kDa is responsible for this activity. A cytochrome b559 (Em = +65 mV) appears to be an essential part of succinate dehydrogenase. Finally a cytochrome c550 component with an apparent mid-point potential of Em = +195 mV has been detected.
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9
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Arnold RG, DiChristina TJ, Hoffmann MR. Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans"). Appl Environ Microbiol 1986; 52:281-9. [PMID: 2428308 PMCID: PMC203516 DOI: 10.1128/aem.52.2.281-289.1986] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans"). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (less than 0.01 atm [1 atm = 101.29 kPa]). Induced cells were capable of O2 utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells.
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10
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Patchett RA, Jones CW. The apparent oxidation of NADH by whole cells of the methylotrophic bacterium Methylophilus methylotrophus. A cautionary tale. Antonie Van Leeuwenhoek 1986; 52:387-92. [PMID: 3098164 DOI: 10.1007/bf00393466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Previous reports that whole cells of Methylophilus methylotrophus oxidase exogenous NADH have been investigated. Essentially identical rates of oxygen consumption were observed following the addition of methanol or NADH to whole cells. Both activities were inhibited by EDTA and hydroxylamine, but not by HQNO, and exhibited similar pH optima. Analyses of the reaction stoichiometry with NADH as substrate showed that the expected amount of oxygen was consumed, but also revealed acidification (instead of alkalinisation) and no oxidation of NADH. Further studies showed that commercial NADH is contaminated with ethanol which is oxidised to acetic acid by the low specificity methanol oxidase system present in this organism. The oxidation of exogenous NADH by whole cells of M. methylotrophus reported previously is therefore spurious.
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11
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10 The Analysis of Cytochromes. METHODS IN MICROBIOLOGY 1985. [DOI: 10.1016/s0580-9517(08)70479-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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12
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Abstract
The composition and organization of the Bacillus cereus respiratory system were studied. The abolition of NADH-dependent respiration in vegetative and sporulating cell membranes by near-UV light (360 nm) indicated that electrons reduce oxygen only through a quinone-cytochrome pathway. Difference spectroscopy demonstrated the presence of cytochromes b555, c548, aa3, b562, and a2. This composition and studies with respiratory inhibitors suggested that cytochromes are organized in at least two branches, one being highly sensitive to cyanide.
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13
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Akimenko VK, Trutko SM. On the absence of correlation between cyanide-resistant respiration and cytochrome d content in bacteria. Arch Microbiol 1984; 138:58-63. [PMID: 6331332 DOI: 10.1007/bf00425408] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The regularity of appearance of cyanide-resistant respiration and cytochrome d in various bacteria as well as the relationship between the degree of resistance of respiration to cyanide and cytochrome d content was studied. Bacteria able to synthesize cyanide-resistant respiration were shown to appear during transition of culture to the stationary phase of growth caused by the exhaustion of carbon source. No regulatory of appearance of cytochrome d was observed. There is no correlation between the degree of resistance to cyanide and cytochrome d content. It was concluded that the cyanide-resistant respiration of bacteria and eukaryotic microorganisms may be associated with the functioning of a non-cytochrome nature oxidase.
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14
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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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15
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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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16
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Miller MJ, Gennis RB. The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44645-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Hänel F, Gräfe U, Trutko SM, Akimenko VK. Cyanide-resistant respiration inStreptomyces citreofluorescens. J Basic Microbiol 1983. [DOI: 10.1002/jobm.3630230706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Distribution of cyanide-resistant respiration among yeasts and bacteria and its relation to oversynthesis of metabolites. Arch Microbiol 1983. [DOI: 10.1007/bf00409851] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Hellingwerf K, Lolkema J, Otto R, Neijssel O, Stouthamer A, Harder W, Dam K, Westerhoff H. Energetics of microbial growth: an analysis of the relationship between growth and its mechanistic basis by mosaic non-equilibrium thermodynamics. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb00028.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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20
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Yang T. Tetramethyl-p-phenylenediamine oxidase of Pseudomonas aeruginosa. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 121:335-41. [PMID: 6800785 DOI: 10.1111/j.1432-1033.1982.tb05791.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An oxidase complex has been solubilized and partially purified from the membrane particle of Pseudomonas aeruginosa grown under limited oxygen condition. The oxidase consists of two major cytochrome components, cytochrome c554 and cytochrome o (b561), with a molar ratio of about 9:1 in terms of c-heme to protoheme content. Ninety percent of the cytochrome c+o complex, corresponding to all of the cytochrome c554, is reducible by reduced N,N,N',N'-tetramethyl-p-phenylenediamine. This partially purified oxidase exhibited a maximal specific activity about 5 mumol O2 uptake x min-1 x mg protein-1, with a Km (of reduced N,N,N',N'-tetramethyl-p-phenylenediamine) = 7.2 x 10(-4) M at 30 degrees C. The oxidase is sensitive to KCN, NaN3 and NaNO2. Oxidation-reduction potentiometric titration shows that cytochrome c554 has a midpoint potential of 289 mV and cytochrome o of + 25 mV at pH 7.2 in the partially purified oxidase preparation. The purity of the preparation has been estimated to be about 85--90% by gel electrophoresis.
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21
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Sweet WJ, Peterson JA. The respiratory system of Pseudomonas putida: participation of cytochromes in electron transport. Arch Biochem Biophys 1981; 209:256-65. [PMID: 6269495 DOI: 10.1016/0003-9861(81)90279-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
Among the L-amino acids, only L-cysteine was oxidized by isolated washed membranes of group B Neisseria meningitidis SD1C. The cysteine oxidase in the membrane obeyed Michaelis-Menten kinetics and was heat labile. The pH optimum for the maximum velocity of the reaction was 9.8. Specific activity of the enzyme increased as cell growth progressed through the exponential phase toward the stationary phase of growth. The enzyme activity was markedly sensitive to inhibition by metal chelators, but was resistant to inhibitors of terminal oxidases with the exception of cyanide. All known cytochromes in the membrane, except b563, were reduced with L-cysteine. The additive nature of L-cysteine oxidase and succinate oxidase activities suggests that an unidentified oxidase is involved in the oxidation of cysteine.
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23
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Cross AB, Anthony C. The electron-transport chains of the obligate methylotroph Methylophilus methylotrophus. Biochem J 1980; 192:429-39. [PMID: 7236221 PMCID: PMC1162357 DOI: 10.1042/bj1920429] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cytochrome complement of Methylophilus methylotrophus and its respiratory properties were determined during batch culture and in continuous culture under conditions of methanol-, nitrogen- and O(2)-limitation. About 35% of the cytochrome c produced by the bacteria was released into the growth medium, and of the remaining cytochrome c about half was membrane-bound and half was soluble. Two cytochromes c were always present on membranes (redox potentials 375mV and 310mV), and these probably correspond to the soluble cytochromes c described previously [Cross & Anthony (1980) Biochem. J.192, 421-427]. A third minor component of cytochrome c (midpoint potential 356mV) was only detected on membranes of methanol-limited bacteria. M. methylotrophus always contained two membrane-bound cytochromes b with alpha-band absorption maxima of about 556 and 563nm (measured at room temperature) and midpoint potentials of 110 and 60mV respectively. There appeared to be relatively more of the cytochrome b(563) in methanol-limited bacteria. A third b-type cytochrome with an alpha-band absorption maximum at 558 (at 77K) reacted with CO and had a high midpoint redox potential (260mV); it is thus a potential oxidase and hence is called cytochrome o. The roles of these cytochromes in electron transport were confirmed by investigating the patterns of respiratory inhibition. It is proposed that two cytochromes are physiological oxidases: cytochrome a+a(3), which is present only in methanol-limited conditions, and the cytochrome o, which is induced 10-fold in conditions of methanol excess. Schemes for electron transport from methanol and NAD(P)H to O(2) in M. methylotrophus under various limitations are proposed. Spectra and potentiometric titrations of cytochromes in whole cells and membranes of M. methylotrophus grown under various nutrient limitations have been deposited as Supplementary Publication SUP 50111 (10 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1978) 169, 5.
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Yu EK, DeVoe IW. Terminal branching of the respiratory electron transport chain in Neisseria meningitidis. J Bacteriol 1980; 142:879-87. [PMID: 6769915 PMCID: PMC294113 DOI: 10.1128/jb.142.3.879-887.1980] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The respiratory components of the envelope membrane preparation of Neisseria meningitidis were investigated. Oxidase activities were demonstrated in this fraction in the presence of succinic acid, reduced nicotinamide adenine dinucleotide, and ascorbate-N,N,N',N'-tetramethyl-p-phenylene-diamine (TMPD). Differences in the kinetics of inhibition by terminal oxidase inhibitors on the three oxidase activities indicated that ascorbate-TMPD oxidation involved only an azide-sensitive oxidase, whereas oxidation of the physiological substrates involved two oxidases, one of which was relatively azide resistant. Spectrophotometric studies revealed that ascorbate-TMPD donated its electrons exclusively to cytochrome o, whereas the physiological substrates were oxidized via both cytochromes o and a. The effects of class II inhibitors on the oxidases suggest terminal branching of the electron transport chain at the cytochrome b level. A model of the respiratory system in N. meningitidis is proposed.
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25
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Ensley BD, Finnerty WR. Influences of growth substrates and oxygen on the electron transport system in Acinetobacter sp. HO1-N. J Bacteriol 1980; 142:859-68. [PMID: 7380810 PMCID: PMC294111 DOI: 10.1128/jb.142.3.859-868.1980] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The electron transport system of Acinetobacter sp. HO1-N was studied to determine the specific cytochromes and to measure changes in the composition of the respiratory system due to growth in various concentrations of oxygen or types of growth substrates. Spectrophotometric analysis revealed that the quantity and types of cytochromes changed in response to growth under various concentrations of oxygen. Growth on alkane and nonalkane substrates resulted in only minor differences in cytochrome composition or oxidase activities. Membranes prepared from cells grown under oxygen-limiting conditions contained at least one b-type cytochrome, cytochrome o, cytochrome d, and slight traces of cytochrome a1, whereas membranes prepared from cells grown in the presence of high oxygen concentrations contained only low levels of cytochromes b and o. Polarographic measurements, electron transport inhibitor studies, and photoaction spectrum analyses indicated that cytochromes o, a1, and d were potentially capable of functioning as terminal oxidases in this organism. These experiments also revealed that all three cytochromes may be involved in the oxidation of reduced nicotinamide adenine dinucleotide, succinate, or N,N,N',N'-tetramethyl-p-phenylenediamine.
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26
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Electron transport reactions in respiratory particles of hydrogenase-induced Anacystis nidulans. Arch Microbiol 1980. [DOI: 10.1007/bf00403208] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Peschek GA. Restoration of respiratory electron-transport reactions in quinone-depleted particle preparations from Anacystis nidulans. Biochem J 1980; 186:515-23. [PMID: 6769434 PMCID: PMC1161604 DOI: 10.1042/bj1860515] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Electron transport from H2, NADPH, NADH and succinate to O2 or ferricytochrome c in respiratory particles isolated from Anacystis nidulans in which hydrogenase had been induced was abolished after extraction of the membranes with n-pentane; oxidation of ascorbate plus NNN'N'-tetramethyl-p-phenylenediamine remained unaffected. Incorporation of authentic ubiquinone-10, plastoquinone-9, menaquinone-7 and phylloquinone (in order of increasing efficiency) restored the electron-transport reactions. ATP-dependent reversed electron flow from NNN'N'-tetramethyl-p-phenylenediamine to NADP+ or, via the membrane-bound hydrogenase, to H+ was likewise abolished by pentane extraction and restored by incorporation of phylloquinone. Participation of the incorporated quinones in the respiratory electron-transport reactions of reconstituted particles was confirmed by measuring the degree of steady-state reduction of the quinones. Isolation and identification of the quinones present in native Anacystis membranes yielded mainly plastoquinone-9 and phylloquinone; neither menaquinone nor alpha-tocopherolquinone could be detected. Together with the results from reconstitution experiments this suggests that phylloquinone might function as the main respiratory quinone in Anacystis nidulans.
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Hon-nami K, Oshima T. Cytochrome oxidase from an extreme thermophile. Thermus thermophilus HB8. Biochem Biophys Res Commun 1980; 92:1023-9. [PMID: 6244813 DOI: 10.1016/0006-291x(80)90804-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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de Hollander JA, Bettenhaussen CW, Stouthamer AH. Growth yields, polysaccharide production and energy conservation in chemostat cultures of Rhizobium trifolii. Antonie Van Leeuwenhoek 1979; 45:401-15. [PMID: 122050 DOI: 10.1007/bf00443279] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhizobium trifolii was grown in a defined medium in chemostat cultures. Extracellular polysaccharide production was found in carbon-sufficient as well as in carbon-limited cultures. Extracellular polysaccharide production in carbon-limited cultures was strongly dependent on the growth rate. In mannitol-limited cultures, asparagine was always totally depleted from the culture medium. Only when the asparagine supply was not sufficient to meet the nitrogen need of the culture, ammonia assimilation took place. Excess organic nitrogen was excreted as ammonia. Whether ammonia assimilation or ammonia excretion took place was also dependent on the growth rate. Respiration-coupled proton translocation measurements showed the presence of three energy conserving sites in an electron transport chain which is branched. Assuming a H+/P ratio of 4, a P/O ratio of 2.33 was found. Growth yield calculations indicated a P/O ratio of approximately 2. Sulphate limitation in the chemostat culture resulted in a decrease in the efficiency of oxidative phosphorylation and in a less stringent coupling between growth and energy yielding processes.
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Stoeckenius W, Lozier RH, Bogomolni RA. Bacteriorhodopsin and the purple membrane of halobacteria. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 505:215-78. [PMID: 35226 DOI: 10.1016/0304-4173(79)90006-5] [Citation(s) in RCA: 781] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Lillich TT, Calmes R. Cytochromes and dehydrogenases in membranes of a new human periodontal bacterial pathogen, Capnocytophaga ochracea. Arch Oral Biol 1979; 24:699-702. [PMID: 231958 DOI: 10.1016/0003-9969(79)90120-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Yang TY, Jurtshuk P. Studies on the red oxidase (cytochrome o) of Azotobacter vinelandii. Biochem Biophys Res Commun 1978; 81:1032-9. [PMID: 666783 DOI: 10.1016/0006-291x(78)91454-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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34
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Sweet WJ, Peterson JA. Changes in cytochrome content and electron transport patterns in Pseudomonas putida as a function of growth phase. J Bacteriol 1978; 133:217-24. [PMID: 618838 PMCID: PMC221997 DOI: 10.1128/jb.133.1.217-224.1978] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Optical absorbance difference spectra of membrane vesicles prepared from aerobically grown Pseudomonas putida indicated that, when harvested in logarithmic phase, the cells contained one c-type cytochrome and two or three b-type cytochromes, one of which was cytochrome o. As the cells grew into stationary phase and the oxygen concentration of the medium dropped to essentially zero, an additional component believed to be cytochrome d was produced. Both the o- and d-type cytochromes might function as terminal oxidases. No a-type cytochromes could be detected at any stage of growth. Polarographic measurement of oxygen utilization revealed that cyanide and azide are effective inhibitors of the oxidation of ascorbate coupled with 2,6-dichlorophenolindophenol or N,N,N',N'-tetramethyl-p-phenylenediamine in respiratory particles from either log-phase or stationary-phase cells. Reduced nicotinamide adenine dinucleotide- or succinate-dependent oxygen utilization, however, was sensitive to these inhibitors only in log-phase particles. These results indicate that an alternate terminal oxidase may be synthesized by this organism in response to restricted oxygen availability and that branching of the respiratory system may result.
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36
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Bayley ST, Morton RA. Recent developments in the molecular biology of extremely halophilic bacteria. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1978; 6:151-205. [PMID: 365457 DOI: 10.3109/10408417809090622] [Citation(s) in RCA: 108] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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John P, Whatley FR. The bioenergetics of Paracoccus denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 463:129-53. [PMID: 20140 DOI: 10.1016/0304-4173(77)90006-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Thauer RK, Jungermann K, Decker K. Energy conservation in chemotrophic anaerobic bacteria. BACTERIOLOGICAL REVIEWS 1977; 41:100-80. [PMID: 860983 PMCID: PMC413997 DOI: 10.1128/br.41.1.100-180.1977] [Citation(s) in RCA: 1326] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Anaerobic Electron Transfer and Active Transport in Bacteria. CURRENT TOPICS IN MEMBRANES AND TRANSPORT 1977. [DOI: 10.1016/s0070-2161(08)60679-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Sinclair PR, White DC, Smith L. Oxidation and reduction of membrane-bound cytochrome c in Hemophilus parainfluenzae. Reaction with oxygen, hydrogen peroxide and nitrate. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 449:37-47. [PMID: 184842 DOI: 10.1016/0005-2728(76)90005-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochromes of the a-, b-, c- and d-type become reduced when intact cells of Hemophilus parainfluenzae have become anaerobic following respiration with substrates such as formate or succinate, as shown previously (J. Biol. Chem. (1970) 254, 5096-5100). In the presence of formate after depletion of O2, there is an unusual two-step time course of reduction of the membrane-bound cytochrome c. The proportion of the cytochrome c which is reduced during the second stage is oxidizable by either nitrate or H2O2 and is reduced again when the nitrate or H2O2 have been depleted. We conclude that the observed two-stage reduction of cytochrome c results from the presence of an oxidant, probably H2O2, produced by reaction of formate dehydrogenase with O2. This was shown by the effects of cyanide, catalase and O2. In addition, no evidence for the production of the oxidant is seen when succinate is the substrate oxidized. Although measurements of absorption spectra indicated only one species of cytochrome c, kinetic evidence is presented for some separation of the cytochrome c into more than one electron transport pathway.
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Abstract
The membrane-bound respiratory system of the gram-negative bacterium Spirillum itersonii was investigated. It contains cytochromes b (558), c (550), and o (558) and beta-dihydro-nicotinamide adenine dinucleotide (NADH) and succinate oxidase activities under all growth conditions. It is also capable of producing D-lactate and alpha-glycerophosphate dehydrogenases when grown with lactate or glycerol as sole carbon source. Membrane-bound malate dehydrogenase was not detectable under any conditions, although there is high activity of soluble nicotinamide adenine dinucleotide: malate dehydrogenase. When grown with oxygen as the sole terminal electron acceptor, approximately 60% of the total b-type cytochrome is present as cytochrome o, whereas only 40% is present as cytochrome o in cells grown with nitrate in the presence of oxygen. Both NADH and succinate oxidase are inhibited by azide, cyanide, antimycin A, and 2-n-heptyl-4-hydroxyquinoline-N-oxidase at low concentrations. The ability of these inhibitors to completely inhibit oxidase activity at low concentrations and their effects upon the aerobic steady-state reduction levels of b- and c-type cytochromes as well as the aerobic steady-state reduction levels obtained with NADH, succinate, and ascorbate-dichlorophenolindophenol suggest that presence of an unbranched respiratory chain in S. itersonii with the order ubiquinone leads to b leads to c leads to c leads to oxygen.
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Zannoni D, Melandri BA, Baccarini-Melandri A. Energy transduction in photosynthetic bacteria. X. Composition and function of the branched oxidase system in wild type and respiration deficient mutants of Rhodopseudomonas capsulata. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 423:413-30. [PMID: 177045 DOI: 10.1016/0005-2728(76)90197-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The respiratory chain of Rhodopseudomonas capsulata, strain St. Louis and of two respiration deficient mutants (M6 and M7) has been investigated by examining the redox and spectral characteristics of the cytochromes and their response to substrates and to specific respiratory inhibitors. Since the specific lesions of M6 and M7 have been localized on two different branches of the multiple oxidase system of the wild type strain, the capability for aerobic growth of these mutants can be considered as a proof of the physiological significance of both branched systems "in vivo". Using M6 and M7 mutants the response of the branched chain to respiratory inhibitors could be established. Cytochrome oxidase activity, a specific function of an high potential cytochrome b (E'0 = +413 mV) is sensitive to low concentrations of KCN (5-10(-5) M); CO is a specific inhibitor of an alternative oxidase, which is also inhibited by high concentrations of KCN (10(-3) M). Antimycin A inhibits preferentially the branch of the chain affected by low concentrations of cyanide. Redox titrations and spectral data indicate the presence in the membrane of three cytochromes of b type (E'0 = +413, +260, +47 vM) and two cytochromes of c type (E'0 = +342, +94 mV). A clear indication of the involvement in respiration of cytochrome b413, cytochrome c342 and cytochrome b47 has been obtained. Only 50% of the dithionite reducible cytochrome b can be reduced by respiratory substrates also in the presence of high concentrations of KCN or in anaerobiosis. The presence and function of quinones in the respiratory electron transport system has been clearly demonstrated. Quinones, which are reducible by NADH and succinate to about the same extent can be reoxidized through both branches of the respiratory chain, as shown by the response of their redox state to KCN. The possible site of the branching of the electron transport chain has been investigated comparing the per cent level of reduction of quinones and of cytochromes b and c as a function of KCN concentrations in membranes from wild type and M6 mutants cells. The site of the branching has been localized at the level of quinones-cytochrome b47. A tentative scheme of the respiratory chains operating in Rhodopseudomonas capsulata, St. Louis and in the two respiration deficient mutants, M6 and M7 is presented.
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Holländer R. Energy metabolism of some representatives of the Haemophilus group. Antonie Van Leeuwenhoek 1976; 42:429-44. [PMID: 1087860 DOI: 10.1007/bf00410174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The purpose of this investigation was to characterize the carbohydrate catabolism and the constellation of the respiratory chain components of Haemophilus influenzae RAMC 18 Bensted, H. parainfluenzae 1 Fleming, H. parainfluenzae 429 Pittman and H. aegyptius 180a Pittman. These strains represent several physiological types with respect to respiratory quinones and glucose catabolism. On addition of glucose or lactate to the complex growth medium a remarkable increase in cell mass was observed. Depending on the growth rate, carbohydrate degradation varied with the strains examined so that at the end of the exponential growth phase only small amounts of the supplements could be demonstrated. All strains were found to possess functional enzymes of Embden-Meyerhof-Parnas-, Entner-Doudoroff-pathways, hexosemonophosphate shunt, tricarboxylic acid cycle and gluconeogenesis with an extremely high activity of malate dehydrogenase. The concentration of cytochromes varied according to culture conditions. The cytochromes a1, d, o and b + c were found to occur under aerobic conditions. In cells grown anaerobically in the presence of fumarate cytochromes a1 and d could not be demonstrated. Under aerobic conditions preparations of H. parainfluenzae 1 Fleming exhibited an alpha-maximum at 558 nm, whereas under anaerobic culture conditions with fumarate as terminal electron acceptor an alpha-maximum at 552 nm occurred, suggesting different roles of b and c type cytochromes in aerobic and anaerobic electron transport to fumarate, respectively.
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Jurtshuk P, Mueller TJ, Acord WC. Bacterial terminal oxidases. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1975; 3:399-468. [PMID: 166799 DOI: 10.3109/10408417509108757] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The electron transport system in Brucella abortus has been characterized. Spectral studies of membrane preparations have indicated the presence of cytochromes a + a3 (maxima at 612 nm), cytochrome b (maxima at 560, 530, and 428 nm), cytochrome c (maxima at 552 and 522 nm), cytochrome o (maxima of carbon monoxide complex at 418 nm), and flavoproteins (minimum at 582 and 450 nm). Cytochromes a + a3 appeared only after cells had reached late log phase, possibly due to lowered oxygen tension in the medium. Dehydrogenases were shown to be present for D-erythritol 1-phosphate, L-lactate, reduced nicotinamide adenine dinucleotide, and succinate. All of the above substrates reduced the electron transport chain and at least some of the flavoproteins, indicating similar pathways of electron transport. N-ethylmaleimide, p-chloromercuribenzoate, and KCN were the only electron transport inhibitors that blocked electron transport by 100%. The system seemed to be uniquely resistant to other electron transport inhibitors.
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Focht DD, Chang AC. Nitrification and denitrification processes related to waste water treatment. ADVANCES IN APPLIED MICROBIOLOGY 1975; 19:153-86. [PMID: 242195 DOI: 10.1016/s0065-2164(08)70428-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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