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Katsyv A, Müller V. Overcoming Energetic Barriers in Acetogenic C1 Conversion. Front Bioeng Biotechnol 2020; 8:621166. [PMID: 33425882 PMCID: PMC7793690 DOI: 10.3389/fbioe.2020.621166] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions. Microbiol Spectr 2017; 5. [PMID: 28597820 DOI: 10.1128/microbiolspec.tbtb2-0014-2016] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.
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Lee JH, Park SW, Kim YM, Oh JI. Identification and characterization of the genes encoding carbon monoxide dehydrogenase in Terrabacter carboxydivorans. Res Microbiol 2017; 168:431-442. [PMID: 28161485 DOI: 10.1016/j.resmic.2017.01.004] [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: 09/08/2016] [Revised: 01/18/2017] [Accepted: 01/20/2017] [Indexed: 11/28/2022]
Abstract
Terrabacter carboxydivorans is able to grow aerobically at low concentrations of carbon monoxide (CO) as a sole source of carbon and energy. The genes for carbon monoxide dehydrogenase (CO-DH) were cloned from T. carboxydivorans and analyzed. The operon encoding T. carboxydivorans CO-DH was composed of three structural genes with the transcriptional order of cutB, cutC and cutA, as well as an additional accessory gene (orf4). Phylogenetic analysis of CutA revealed that T. carboxydivorans CO-DH was classified into a group distinct from previously characterized CO-DHs. Expression of antisense RNA for the cutB or cutA gene in T. carboxydivorans led to a decrease in CO-DH activity, confirming that cutBCA genes are the functional genes encoding CO-DH. The CO-DH operon was expressed even in the absence of CO and further inducible by CO. In addition, CO-DH synthesis was increased in the stationary phase compared to the exponential phase during heterotrophic growth on glucose and glycerol. Point mutations of a partially inverted repeat sequence (TCGGA-N6-GCCCA) in the upstream region of the cutB gene almost abolished expression of the CO-DH operon, indicating that the inverted-repeat sequence might be a cis-acting regulatory site for the positive regulation of the CO-DH operon.
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Affiliation(s)
- Jae Ho Lee
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Sae Woong Park
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Young Min Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea.
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Lee JH, Park SW, Kim YM, Oh JI. Functional characterization of the cutI gene for the transcription of carbon monoxide dehydrogenase genes in Mycobacterium sp. strain JC1 DSM 3803. J Microbiol 2016; 55:31-36. [PMID: 28035599 DOI: 10.1007/s12275-017-6572-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
Abstract
Carbon monoxide dehydrogenase (CO-DH) in Mycobacterium sp. strain JC1 is a key enzyme for the carboxydotrophic growth, when carbon monoxide (CO) is supplied as a sole source of carbon and energy. This enzyme is also known to act as nitric oxide dehydrogenase (NO-DH) for the detoxification of NO. Several accessory genes such as cutD, cutE, cutF, cutG, cutH, and cutI, are clustered together with two copies of the CO-DH structural genes (cutB1C1A1 and cutB2C2A2) in Mycobacterium sp. strain JC1 and are well conserved in carboxydotrophic mycobacteria. Transcription of the CO-DH structural and accessory genes was demonstrated to be increased significantly by acidified sodium nitrate as a source of NO. A cutI deletion (ΔcutI) mutant of Mycobacterium sp. strain JC1 was generated to identity the function of CutI. Lithoautotrophic growth of the ΔcutI mutant was severely affected in mineral medium supplemented with CO, while the mutant grew normally with glucose. Western blotting, CO-DH activity staining, and CO-DH-specific enzyme assay revealed a significant decrease in the cellular level of CO-DH in the ΔcutI mutant. Northern blot analysis and promoter assay showed that expression of the cutB1 and cutB2 genes was significantly reduced at the transcriptional level in the ΔcutI mutant, compared to that of the wildtype strain. The ΔcutI mutant was much more susceptible to NO than was the wild type.
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Affiliation(s)
- Jae Ho Lee
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sae Woong Park
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Young Min Kim
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
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Abstract
Mycobacteria inhabit a wide range of intracellular and extracellular environments. Many of these environments are highly dynamic and therefore mycobacteria are faced with the constant challenge of redirecting their metabolic activity to be commensurate with either replicative growth or a non-replicative quiescence. A fundamental feature in this adaptation is the ability of mycobacteria to respire, regenerate reducing equivalents and generate ATP via oxidative phosphorylation. Mycobacteria harbor multiple primary dehydrogenases to fuel the electron transport chain and two terminal respiratory oxidases, an aa3 -type cytochrome c oxidase and cytochrome bd-type menaquinol oxidase, are present for dioxygen reduction coupled to the generation of a protonmotive force. Hypoxia leads to the downregulation of key respiratory complexes, but the molecular mechanisms regulating this expression are unknown. Despite being obligate aerobes, mycobacteria have the ability to metabolize in the absence of oxygen and a number of reductases are present to facilitate the turnover of reducing equivalents under these conditions (e.g. nitrate reductase, succinate dehydrogenase/fumarate reductase). Hydrogenases and ferredoxins are also present in the genomes of mycobacteria suggesting the ability of these bacteria to adapt to an anaerobic-type of metabolism in the absence of oxygen. ATP synthesis by the membrane-bound F1FO-ATP synthase is essential for growing and non-growing mycobacteria and the enzyme is able to function over a wide range of protonmotive force values (aerobic to hypoxic). The discovery of lead compounds that target respiration and oxidative phosphorylation in Mycobacterium tuberculosis highlights the importance of this area for the generation of new front line drugs to combat tuberculosis.
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Berney M, Cook GM. Respiration and Oxidative Phosphorylation in Mycobacteria. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Kim YM, Park SW. Microbiology and genetics of CO utilization in mycobacteria. Antonie van Leeuwenhoek 2012; 101:685-700. [PMID: 22277984 DOI: 10.1007/s10482-012-9698-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/06/2012] [Indexed: 11/29/2022]
Abstract
Although extensive studies on the oxidation of carbon monoxide (CO) in aerobic carboxydotrophic bacteria have been carried out for over 30 years, utilization of CO as a source of carbon and energy by mycobacteria was recognized only recently. Studies on pathogenic and nonpathogenic mycobacteria have revealed that the basis for CO utilization in these bacteria is different in many aspects from that of other aerobic carboxydobacteria. We review the basis for CO utilization in mycobacterial carboxydobacteria, which is unique from physiological, biochemical, molecular, genetic and phylogenetic points of view.
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Affiliation(s)
- Young Min Kim
- Molecular Microbiology Laboratory, Department of Systems Biology, Yonsei University, Seoul, Korea.
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Identification of trans- and cis-control elements involved in regulation of the carbon monoxide dehydrogenase genes in Mycobacterium sp. strain JC1 DSM 3803. J Bacteriol 2010; 192:3925-33. [PMID: 20511503 DOI: 10.1128/jb.00286-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cutR gene was identified 314 bp upstream of the divergently oriented cutB1C1A1 operon encoding carbon monoxide (CO) dehydrogenase in Mycobacterium sp. strain JC1. Its deduced product was composed of 320 amino acid residues with a calculated molecular mass of 34.1 kDa and exhibits a basal sequence similarity to the regulatory proteins belonging to the LysR family. Using a cutR deletion mutant, it was demonstrated that CutR is required for the efficient utilization of CO by Mycobacterium sp. strain JC1 growing with CO as the sole source of carbon and energy. CutR served as a transcriptional activator for expression of the duplicated cutBCA operons (cutB1C1A1 and cutB2C2A2) and was involved in the induction of the cutBCA operons by CO. The cutBCA operons were also subjected to catabolite repression. An inverted repeat sequence (TGTGA-N(6)-TCACA) with a perfect match with the binding motif of cyclic AMP receptor protein was identified immediately upstream of and overlapping with the translational start codons of cutB1 and cutB2. This palindrome sequence was shown to be involved in catabolite repression of the cutBCA operons. The transcription start point of cutR was determined to be the nucleotide G located 36 bp upstream of the start codon of cutR. Expression of cutR was higher in Mycobacterium sp. strain JC1 grown with glucose than that grown with CO.
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Song T, Park SW, Park SJ, Kim JH, Yu JY, Oh JI, Kim YM. Cloning and expression analysis of the duplicated genes for carbon monoxide dehydrogenase of Mycobacterium sp. strain JC1 DSM 3803. Microbiology (Reading) 2010; 156:999-1008. [DOI: 10.1099/mic.0.034769-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide dehydrogenase (CO-DH) is an enzyme catalysing the oxidation of CO to carbon dioxide in Mycobacterium sp. strain JC1 DSM 3803. Cloning of the genes encoding CO-DH from the bacterium and sequencing of overlapping clones revealed the presence of duplicated sets of genes for three subunits of the enzyme, cutB1C1A1 and cutB2C2A2, in operons, and a cluster of genes encoding proteins that may be involved in CO metabolism, including a possible transcriptional regulator. Phylogenetic analysis based on the amino acid sequences of large subunits of CO-DH suggested that the CO-DHs of Mycobacterium sp. JC1 and other mycobacteria are distinct from those of other types of bacteria. The growth phenotype of mutant strains lacking cutA genes and of a corresponding complemented strain showed that both of the duplicated sets of CO-DH genes were functional in this bacterium. Transcriptional fusions of the cutB genes with lacZ revealed that the cutBCA operons were expressed regardless of the presence of CO and were further inducible by CO. Primer extension analysis indicated two promoters, one expressed in the absence of CO and the other induced in the presence of CO. This is believed to be the first report to show the presence of multiple copies of CO-DH genes with identical sequences and in close proximity in carboxydobacteria, and to present the genetic evidence for the function of the genes in mycobacteria.
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Affiliation(s)
- Taeksun Song
- Genome Research Center for Respiratory Pathogens, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Sae Woong Park
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Su-Jeong Park
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Ji Hyang Kim
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Ji Young Yu
- Genome Research Center for Respiratory Pathogens, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Young M. Kim
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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Kim SM, Park SW, Park ST, Kim YM. Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete. Int J Syst Evol Microbiol 2010; 61:482-486. [PMID: 20207805 DOI: 10.1099/ijs.0.020826-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, PY2(T), capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2(T) was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26(T) (99.1 % similarity). Strain PY2(T) was characterized chemotaxonomically as having iso-C(15 : 0) as the predominant fatty acid, MK-8(H(4)) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA-DNA relatedness values between strain PY2(T) and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA-DNA hybridization experiments, it is proposed that strain PY2(T) represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2(T) (=KCCM 42922(T)=JCM 16259(T)).
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Affiliation(s)
- Sung M Kim
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Sae W Park
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Sang T Park
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Young M Kim
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia. Int J Syst Evol Microbiol 2008; 58:2475-8. [DOI: 10.1099/ijs.0.65765-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Park SW, Song T, Kim SY, Kim E, Oh JI, Eom CY, Kim YM. Carbon monoxide dehydrogenase in mycobacteria possesses a nitric oxide dehydrogenase activity. Biochem Biophys Res Commun 2007; 362:449-53. [PMID: 17707766 DOI: 10.1016/j.bbrc.2007.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 11/26/2022]
Abstract
CO dehydrogenase (CO-DH) catalyzes the oxidation of CO to CO(2) in carboxydobacteria. Cell-free extracts prepared from several mycobacteria, including Mycobacterium tuberculosis H37Ra, showed NO dehydrogenase (NO-DH) activity in a reaction mixture containing sodium nitroprusside (SNP) as the source of NO. The association of the NO-DH activity with CO-DH was revealed by activity staining and confirmed by enzyme assay with purified CO-DH from Mycobacterium sp. strain JC1, a carboxydotrophic mycobacterium. SNP stimulated the production of CO-DH with a coincidental increase in NO-DH activity in the bacterium, further supporting this association and implying the existence of a possible SNP-induced CO-DH gene expression. The addition of purified CO-DH to cultures of Escherichia coli revealed that the enzyme protected E. coli from SNP-induced killing in a dose-dependant way. The present results indicate that mycobacterial CO-DH also acts as a NO-DH, which may function in the protection of mycobacterial pathogens from nitrosative stress during infection.
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Affiliation(s)
- Sae Woong Park
- Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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Jensen A, Finster K. Isolation and characterization of Sulfurospirillum carboxydovorans sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium. Antonie van Leeuwenhoek 2005; 87:339-53. [PMID: 15928986 DOI: 10.1007/s10482-004-6839-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Accepted: 11/26/2004] [Indexed: 11/29/2022]
Abstract
A new microaerophilic, Gram-negative, motile, 2-3 microm long and 0.3 microm wide, vibrioid to spirillum-shaped, CO oxidizing bacterium, designated strain MV, isolated from marine sediment (The North Sea) is described. Strain MV was able to couple the oxidation of CO to the reduction of elemental sulphur, DMSO and thiosulphate. Growth occurred with up to 100% (v/v) CO in the headspace. Acetate was needed as carbon source. No growth on CO was observed with nitrate and selenate as electron acceptor. Sulphite, elemental sulphur, DMSO, thiosulphate, nitrate, nitrite, perchloroethylene, arsenate and selenate were used as electron acceptors with pyruvate as energy and carbon source. Microaerophilic growth was observed. In non-agitated cultures growth occurred at atmospheric oxygen concentrations in the headspace. Hydrogen (with acetate as carbon source), formate (with acetate as carbon source), pyruvate, lactate, succinate, fumarate, malate alpha-ketoglutaric acid, aspartate and yeast extract (1% (w/v)) supported growth with nitrate as electron acceptor. Fumarate and malate were fermented. Vitamins were not required for growth. The strain was cytochrome C oxidase and catalase positive. The DNA mol G+C content was 30.5%. 16S rRNA gene sequence comparison showed that strain MV grouped within the genus Sulfurospirillum with Sulfurospirillum arcachonense (sequence similarity 98.3%) as closest relative. The relative DNA-DNA relatedness between strain MV and S. arcachonense was 33.1%. Based on a detailed phenotypic and phylogenetic analysis, inclusion of strain MV in the genus Sulfurospirillum as a well separated new species is proposed. As species name we propose Sulfurospirillum carboxydovorans. The type strain is strain MV (ATCC BAA-937 = DSM 16295, GenBank accession number: AY740528).
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Affiliation(s)
- Anders Jensen
- Department of Microbiology, Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Bldg. 540, Dk-8000, Aarhus C, Denmark
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Abstract
Carbon monoxide (CO) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for CO. This article reviews the current evidence for a variety of proteins with demonstrated or potential CO-sensing ability. Particular emphasis is placed on the molecular description of CooA, a heme-containing CO sensor from Rhodospirillum rubrum, since its biological role as a CO sensor is clear and we have substantial insight into the basis of its sensing ability.
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Affiliation(s)
- Gary P Roberts
- Department of Bacteriology, 420 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Park SW, Hwang EH, Park H, Kim JA, Heo J, Lee KH, Song T, Kim E, Ro YT, Kim SW, Kim YM. Growth of mycobacteria on carbon monoxide and methanol. J Bacteriol 2003; 185:142-7. [PMID: 12486050 PMCID: PMC141938 DOI: 10.1128/jb.185.1.142-147.2003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several mycobacterial strains, such as Mycobacterium flavescens, Mycobacterium gastri, Mycobacterium neoaurum, Mycobacterium parafortuitum, Mycobacterium peregrinum, Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium vaccae, were found to grow on carbon monoxide (CO) as the sole source of carbon and energy. These bacteria, except for M. tuberculosis, also utilized methanol as the sole carbon and energy source. A CO dehydrogenase (CO-DH) assay, staining by activity of CO-DH, and Western blot analysis using an antibody raised against CO-DH of Mycobacterium sp. strain JC1 (formerly Acinetobacter sp. strain JC1 [J. W. Cho, H. S. Yim, and Y. M. Kim, Kor. J. Microbiol. 23:1-8, 1985]) revealed that CO-DH is present in extracts of the bacteria prepared from cells grown on CO. Ribulose bisphosphate carboxylase/oxygenase (RubisCO) activity was also detected in extracts prepared from all cells, except M. tuberculosis, grown on CO. The mycobacteria grown on methanol, except for M. gastri, which showed hexulose phosphate synthase activity, did not exhibit activities of classic methanol dehydrogenase, hydroxypyruvate reductase, or hexulose phosphate synthase but exhibited N,N-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase and RuBisCO activities. Cells grown on methanol were also found to have dihydroxyacetone synthase. Double immunodiffusion revealed that the antigenic sites of CO-DHs, RuBisCOs, and dihydroxyacetone synthases in all mycobacteria tested are identical with those of the Mycobacterium sp. strain JC1 enzymes.
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Affiliation(s)
- Sae W Park
- Department of Biology, Yonsei University, Seoul 120-749, Korea
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Kang BS, Kim YM. Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava. J Bacteriol 1999; 181:5581-90. [PMID: 10482497 PMCID: PMC94076 DOI: 10.1128/jb.181.18.5581-5590.1999] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon monoxide dehydrogenases (CO-DH) are the enzymes responsible for the oxidation of CO to carbon dioxide in carboxydobacteria and consist of three nonidentical subunits containing molybdopterin flavin adenine dinucleotide (FAD), and two different iron-sulfur clusters (O. Meyer, K. Frunzke, D. Gadkari, S. Jacobitz, I. Hugendieck, and M. Kraut, FEMS Microbiol. Rev. 87:253-260, 1990). The three structural genes of CO-DH in Hydrogenophaga pseudoflava were cloned and characterized. The genes were clustered on the chromosome in the transcriptional order cutM-cutS-cutL. The cloned cutM, cutS, and cutL genes had open reading frames of 864, 492, and 2,412 nucleotides, coding for proteins with calculated molecular weights of 30,694, 17,752, and 87,224, respectively. The overall identities in the nucleotide sequence of the genes and the amino acid sequence of the subunits with those of other carboxydobacteria were 64.5 to 74.3% and 62.8 to 72.3%, respectively. Primer extension analysis revealed that the transcriptional start site of the genes was the nucleotide G located 47 bp upstream of the cutM start codon. The deduced amino acid sequences of the three subunits of CO-DH implied the presence of molybdenum cofactor, FAD, and iron-sulfur centers in CutL, CutM, and CutS, respectively. Fluorometric analysis coupled with denaturing polyacrylamide gel electrophoresis of fractions from hydroxyapatite column chromatography in the presence of 8 M urea of active CO-DH and from gel filtration of spontaneously inactivated enzyme revealed that the large and medium subunits of CO-DH in H. pseudoflava bind molybdopterin and FAD cofactors, respectively. Iron-sulfur centers of the enzyme were identified to be present in the small subunit on the basis of the iron content in each subunit eluted from the denaturing polyacrylamide gels.
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Affiliation(s)
- B S Kang
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Korea
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Fontecilla-Camps JC, Ragsdale SW. Nickel–Iron–Sulfur Active Sites: Hydrogenase and Co Dehydrogenase. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60081-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ro YT, Eom CY, Song T, Cho JW, Kim YM. Dihydroxyacetone synthase from a methanol-utilizing carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803. J Bacteriol 1997; 179:6041-7. [PMID: 9324250 PMCID: PMC179506 DOI: 10.1128/jb.179.19.6041-6047.1997] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Acinetobacter sp. strain JC1 DSM 3803, a carboxydobacterium, grown on methanol was found to show dihydroxyacetone synthase, dihydroxyacetone kinase, and ribulose 1,5-bisphosphate carboxylase, but no hydroxypyruvate reductase and very low hexulose 6-phosphate synthase, activities. The dihydroxyacetone synthase was found to be expressed earlier than the ribulose 1,5-bisphosphate carboxylase. The dihydroxyacetone synthase was purified 19-fold in eight steps to homogeneity, with a yield of 9%. The final specific activity of the purified enzyme was 1.12 micromol of NADH oxidized per min per mg of protein. The molecular weight of the native enzyme was determined to be 140,000. Sodium dodecyl sulfate-gel electrophoresis revealed a subunit of molecular weight 73,000. The optimum temperature and pH were 30 degrees C and 7.0, respectively. The enzyme was inactivated very rapidly at 70 degrees C. The enzyme required Mg2+ and thiamine pyrophosphate for maximal activity. Xylulose 5-phosphate was found to be the best substrate when formaldehyde was used as a glycoaldehyde acceptor. Erythrose 4-phosphate, glycolaldehyde, and formaldehyde were found to act as excellent substrates when xylulose 5-phosphate was used as a glycoaldehyde donor. The Kms for formaldehyde and xylulose 5-phosphate were 1.86 mM and 33.3 microM, respectively. The enzyme produced dihydroxyacetone from formaldehyde and xylulose 5-phosphate. The enzyme was found to be expressed only in cells grown on methanol and shared no immunological properties with the yeast dihydroxyacetone synthase.
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Affiliation(s)
- Y T Ro
- Department of Biology, Yonsei University, Seoul, Korea
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19
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Henry SM, Grbić-Galić D. Inhibition of trichloroethylene oxidation by the transformation intermediate carbon monoxide. Appl Environ Microbiol 1991; 57:1770-6. [PMID: 1908211 PMCID: PMC183466 DOI: 10.1128/aem.57.6.1770-1776.1991] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Inhibition of trichloroethylene (TCE) oxidation by the transformation intermediate carbon monoxide (CO) was evaluated with the aquifer methanotroph Methylomonas sp. strain MM2. CO was a TCE transformation intermediate. During TCE oxidation, approximately 9 mol% of the TCE was transformed to CO. CO was oxidized by Methylomonas sp. strain MM2, and when formate was provided as an electron donor, the CO oxidation rate doubled. The rate of CO oxidation without formate was 4.6 liter mg (dry weight)-1 day-1, and the rate with formate was 10.2 liter mg (dry weight)-1 day-1. CO inhibited TCE oxidation, both by exerting a demand for reductant and through competitive inhibition. The Ki for CO inhibition of TCE oxidation, 4.2 microM, was much less than the Ki for methane inhibition of TCE oxidation, 116 microM. CO also inhibited methane oxidation, and the degree of inhibition increased with increasing CO concentration. When CO was present, formate amendment was necessary for methane oxidation to occur and both substrates were simultaneously oxidized. CO at a concentration greater than that used in the inhibition studies was not toxic to Methylomonas sp. strain MM2.
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Affiliation(s)
- S M Henry
- Department of Civil Engineering, Stanford University, California 94305-4020
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20
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Frunzke K, Meyer O. Nitrate respiration, denitrification, and utilization of nitrogen sources by aerobic carbon monoxide-oxidizing bacteria. Arch Microbiol 1990. [DOI: 10.1007/bf00423328] [Citation(s) in RCA: 14] [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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21
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Do YS, Kim E, Kim YM. Carbon monoxide dehydrogenase inhibitor in cell extracts of Pseudomonas carboxydovorans. J Bacteriol 1990; 172:1267-70. [PMID: 2106505 PMCID: PMC208593 DOI: 10.1128/jb.172.3.1267-1270.1990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Extracts of heterotrophically grown cells of Pseudomonas carboxydovorans were found to contain an inhibitor of carbon monoxide dehydrogenase (CO-DH). The inhibitor activity was not detected in CO-autotrophically grown cells. The inhibitor was extremely stable to heat treatment based on the extent of inhibition of CO-DH activity. The extent of inhibition was proportional to the amount of cell extract added to the reaction mixture. The inhibition was independent of a prior incubation period of the extracts with CO-DH. The inhibitor was precipitable with ammonium sulfate, phenol, and trichloroacetic acid. It was passed through benzoylated dialysis tubing and Amicon ultrafiltration membrane YM2. Denaturing and nondenturing polyacrylamide gel electrophoresis of CO-DH inactivated by inhibitor revealed that the mobilities of native enzyme and subunits were identical to those of active CO-DH. The inhibitor-treated CO-DH retained its original antigenic sites and exhibited enzyme activity upon activity staining. The CO-DH inhibitor of P. carboxydovorans was also active on CO-DHs from Pseudomonas carboxydohydrogena, Acinetobacter sp. strain JC1, and Pseudomonas carboxydoflava.
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Affiliation(s)
- Y S Do
- Department of Biology, College of Science, Yonset University, Seoul, Korea
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22
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Kraut M, Hugendieck I, Herwig S, Meyer O. Homology and distribution of CO dehydrogenase structural genes in carboxydotrophic bacteria. Arch Microbiol 1989; 152:335-41. [PMID: 2818128 DOI: 10.1007/bf00425170] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 17 (S), 30 (M) and 87 kDa (L) subunits of CO dehydrogenases from the CO-oxidizing bacteria Pseudomonas carboxydoflava, Pseudomonas carboxydohydrogena and Pseudomonas carboxydovorans OM5 were isolated and purified. The N-terminal sequences of same subunits from different bacteria showed distinct homologies. Dot blot hybridization employing oligonucleotide probes derived from the sequences of the S-subunit of P. carboxydovorans OM5 and the M-subunit of P. carboxydohydrogena and DNA of the plasmid-containing CO-oxidizing bacteria Alcaligenes carboxydus, Azomonas B1, P. carboxydoflava, P. carboxydovorans OM2, OM4 and OM5 indicated that all genes encoding these subunits reside on plasmids. That in P. carboxydovorans OM5 CO dehydrogenase structural genes are located entirely on plasmid pHCG3 was evident from the absence of hybridization employing DNA from the cured mutant strain OM5-12. CO dehydrogenase structural genes could be identified on the chromosome of the plasmid-free bacteria Arthrobacter 11/x, Bacillus schlegelii, P. carboxydohydrogena and P. carboxydovorans OM3. There was no example of a plasmid-harboring carboxydotrophic bacterium that did not carry CO dehydrogenase structural genes on the plasmid. The N-terminal sequences of CO dehydrogenase structural genes were found to be conserved among carboxydotrophic bacteria of distinct taxonomic position, independent of the presence of plasmids. It is discussed whether this might be the consequence of horizontal gene transfer.
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Affiliation(s)
- M Kraut
- Lehrstuhl für Mikrobiologie der Universität Bayreuth, Federal Republic of Germany
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Bonam D, Lehman L, Roberts GP, Ludden PW. Regulation of carbon monoxide dehydrogenase and hydrogenase in Rhodospirillum rubrum: effects of CO and oxygen on synthesis and activity. J Bacteriol 1989; 171:3102-7. [PMID: 2498285 PMCID: PMC210021 DOI: 10.1128/jb.171.6.3102-3107.1989] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Exposure of the photosynthetic bacterium Rhodospirillum rubrum to carbon monoxide led to increased carbon monoxide dehydrogenase and hydrogenase activities due to de novo protein synthesis of both enzymes. Two-dimensional gels of [35S]methionine-pulse-labeled cells showed that induction of CO dehydrogenase synthesis was rapidly initiated (less than 5 min upon exposure to CO) and was inhibited by oxygen. Both CO dehydrogenase and the CO-induced hydrogenase were inactivated by oxygen in vivo and in vitro. In contrast to CO dehydrogenase, the CO-induced hydrogenase was 95% inactivated by heating at 70 degrees C for 5 min. Unlike other hydrogenases, this CO-induced hydrogenase was inhibited only 60% by a 100% CO gas phase.
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Affiliation(s)
- D Bonam
- Department of Biochemistry, University of Wisconsin, Madison 53706-1569
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Kim Y, Kim Y. Induction of carbon monoxide dehydrogenase during heterotrophic growth of Acinetobacter sp. strain JC1 DSM 3803 in the presence of carbon monoxide. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03111.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Kim KS, Ro YT, Kim YM. Purification and some properties of carbon monoxide dehydrogenase from Acinetobacter sp. strain JC1 DSM 3803. J Bacteriol 1989; 171:958-64. [PMID: 2536687 PMCID: PMC209688 DOI: 10.1128/jb.171.2.958-964.1989] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A brown carbon monoxide dehydrogenase from CO-autotrophically grown cells of Acinetobacter sp. strain JC1, which is unstable outside the cells, was purified 80-fold in seven steps to better than 95% homogeneity, with a yield of 44% in the presence of the stabilizing agents iodoacetamide (1 mM) and ammonium sulfate (100 mM). The final specific activity was 474 mumol of acceptor reduced per min per mg of protein as determined by an assay based on the CO-dependent reduction of thionin. Methyl viologen, NAD(P), flavin mononucleotide, flavin adenine dinucleotide, and ferricyanide were not reduced by the enzyme, but methylene blue, thionin, and dichlorophenolindophenol were reduced. The molecular weight of the native enzyme was determined to be 380,000. Sodium dodecyl sulfate-gel electrophoresis revealed at least three nonidentical subunits of molecular weights 16,000 (alpha), 34,000 (beta), and 85,000 (gamma). The purified enzyme contained particulate hydrogenase-like activity. Selenium did not stimulate carbon monoxide dehydrogenase activity. The isoelectic point of the native enzyme was found to be 5.8; the Km of CO was 150 microM. The enzyme was rapidly inactivated by methanol. One mole of native enzyme was found to contain 2 mol of each of flavin adenine dinucleotide and molybdenum and 8 mol each of nonheme iron and labile sulfide, which indicated that the enzyme was a molybdenum-containing iron-sulfur flavoprotein. The ratio of densities of each subunit after electrophoresis (alpha:beta:gamma = 1:2:6) and the number of each cofactor in the native enzyme suggest a alpha 2 beta 2 gamma 2 structure of the enzyme. The carbon monoxide dehydrogenase of Acinetobacter sp. strain JC1 was found to have no immunological relationship with enzymes of Pseudomonas carboxydohydrogena and Pseudomonas carboxydovorans.
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Affiliation(s)
- K S Kim
- Department of Biology, College of Science, Yonsei University, Seoul, Korea
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26
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Auling G, Busse J, Hahn M, Hennecke H, Kroppenstedt RM, Probst A, Stackebrandt E. Phylogenetic Heterogeneity and Chemotaxonomic Properties of Certain Gram-negative Aerobic Carboxydobacteria. Syst Appl Microbiol 1988. [DOI: 10.1016/s0723-2020(88)80011-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bonam D, Ludden P. Purification and characterization of carbon monoxide dehydrogenase, a nickel, zinc, iron-sulfur protein, from Rhodospirillum rubrum. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61456-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Kwon M, Chung I, Kim Y. Role of a small plasmid in the modification of carbon monoxide dehydrogenase inPseudomonas carboxydovorans. FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01777.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Meyer O, Jacobitz S, Krüger B. Biochemistry and physiology of aerobic carbon monoxide-utilizing bacteria. FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01858.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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31
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Kwon M, Kim Y. Relationship between carbon monoxide dehydrogenase and a small plasmid inPseudomonas carboxydovorans. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb00852.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Immunocytochemical localization of carbon monoxide oxidase in Pseudomonas carboxydovorans. The enzyme is attached to the inner aspect of the cytoplasmic membrane. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42672-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Krzycki JA, Zeikus JG. Characterization and purification of carbon monoxide dehydrogenase from Methanosarcina barkeri. J Bacteriol 1984; 158:231-7. [PMID: 6425262 PMCID: PMC215403 DOI: 10.1128/jb.158.1.231-237.1984] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Carbon monoxide-dependent production of H2, CO2, and CH4 was detected in crude cell extracts of acetate-grown Methanosarcina barkeri. This metabolic transformation was associated with an active methyl viologen-linked CO dehydrogenase activity (5 to 10 U/mg of protein). Carbon monoxide dehydrogenase activity was inhibited 85% by 10 microM KCN and was rapidly inactivated by O2. The enzyme was nearly homogeneous after 20-fold purification, indicating that a significant proportion of soluble cell protein was CO dehydrogenase (ca. 5%). The native purified enzyme displayed a molecular weight of 232,000 and a two-subunit composition of 92,000 and 18,000 daltons. The enzyme was shown to contain nickel by isolation of radioactive CO dehydrogenase from cells grown in 63Ni. Analysis of enzyme kinetic properties revealed an apparent Km of 5 mM for CO and a Vmax of 1,300 U/mg of protein. The spectral properties of the enzyme were similar to those published for CO dehydrogenase from acetogenic anaerobes. The physiological functions of the enzyme are discussed.
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Turner A, Aston W, Higgins I, Bell J, Colby J, Davis G, Hill H. Carbon monoxide :acceptor oxidoreductase from Pseudomonas thermocarboxydovorans strain C2 and its use in a carbon monoxide sensor. Anal Chim Acta 1984. [DOI: 10.1016/s0003-2670(00)81505-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cypionka H, Meyer O. Carbon monoxide-insensitive respiratory chain of Pseudomonas carboxydovorans. J Bacteriol 1983; 156:1178-87. [PMID: 6315679 PMCID: PMC217965 DOI: 10.1128/jb.156.3.1178-1187.1983] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Experiments employing electron transport inhibitors, room- and low-temperature spectroscopy, and photochemical action spectra have led to a model for the respiratory chain of Pseudomonas carboxydovorans. The chain is branched at the level of b-type cytochromes or ubiquinone. One branch (heterotrophic branch) contained cytochromes b558, c, and a1; the second branch (autotrophic branch) allowed growth in the presence of CO and contained cytochromes b561 and o (b563). Electrons from the oxidation of organic substrates were predominantly channelled into the heterotrophic branch, whereas electrons derived from the oxidation of CO or H2 could use both branches. Tetramethyl-p-phenylenediamine was oxidized via cytochromes c and a exclusively. The heterotrophic branch was sensitive to antimycin A, CO, and micromolar concentrations of cyanide. The autotrophic branch was sensitive to 2-n-heptyl-4-hydroxyquinoline-N-oxide, insensitive to CO, and inhibited only by millimolar concentrations of cyanide. The functioning of cytochrome a1 as a terminal oxidase was established by photochemical action spectra. Reoxidation experiments established the functioning of cytochrome o as an alternative CO-insensitive terminal oxidase of the autotrophic branch.
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