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Acetoacetate Production from CO2 and Acetone with Acetone Carboxylase from Photosynthetic Bacteria Rhodobacter Capsulatus. CATALYSIS SURVEYS FROM ASIA 2022. [DOI: 10.1007/s10563-022-09371-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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Alviz-Gazitua P, Durán RE, Millacura FA, Cárdenas F, Rojas LA, Seeger M. Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium. Microorganisms 2022; 10:microorganisms10020484. [PMID: 35208938 PMCID: PMC8879955 DOI: 10.3390/microorganisms10020484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II).
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Affiliation(s)
- Pablo Alviz-Gazitua
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5311890, Chile
| | - Roberto E. Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
| | - Felipe A. Millacura
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK
| | - Franco Cárdenas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Centro Regional de Estudios en Alimentos Saludables (CREAS), Avenida Universidad 330, Curauma, Valparaíso 2373223, Chile
| | - Luis A. Rojas
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte, Avenida Angamos 610, Antofagasta 1270709, Chile;
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (P.A.-G.); (R.E.D.); (F.A.M.); (F.C.)
- Correspondence: or
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Mus F, Eilers BJ, Alleman AB, Kabasakal BV, Wells JN, Murray JW, Nocek BP, DuBois JL, Peters JW. Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation. Sci Rep 2017; 7:7234. [PMID: 28775283 PMCID: PMC5543143 DOI: 10.1038/s41598-017-06973-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/21/2017] [Indexed: 01/07/2023] Open
Abstract
Microorganisms use carboxylase enzymes to form new carbon-carbon bonds by introducing carbon dioxide gas (CO2) or its hydrated form, bicarbonate (HCO3-), into target molecules. Acetone carboxylases (ACs) catalyze the conversion of substrates acetone and HCO3- to form the product acetoacetate. Many bicarbonate-incorporating carboxylases rely on the organic cofactor biotin for the activation of bicarbonate. ACs contain metal ions but not organic cofactors, and use ATP to activate substrates through phosphorylation. How the enzyme coordinates these phosphorylation events and new C-C bond formation in the absence of biotin has remained a mystery since these enzymes were discovered. The first structural rationale for acetone carboxylation is presented here, focusing on the 360 kDa (αβγ)2 heterohexameric AC from Xanthobacter autotrophicus in the ligand-free, AMP-bound, and acetate coordinated states. These structures suggest successive steps in a catalytic cycle revealing that AC undergoes large conformational changes coupled to substrate activation by ATP to perform C-C bond ligation at a distant Mn center. These results illustrate a new chemical strategy for the conversion of CO2 into biomass, a process of great significance to the global carbon cycle.
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Affiliation(s)
- Florence Mus
- 0000 0001 2157 6568grid.30064.31Insitutite of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Brian J. Eilers
- 0000 0001 2156 6108grid.41891.35Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - Alexander B. Alleman
- 0000 0001 2157 6568grid.30064.31Insitutite of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Burak V. Kabasakal
- 0000 0001 2113 8111grid.7445.2Department of Life Sciences, Imperial College, London, SW7 2AZ UK
| | - Jennifer N. Wells
- 0000 0001 2113 8111grid.7445.2Department of Life Sciences, Imperial College, London, SW7 2AZ UK
| | - James W. Murray
- 0000 0001 2113 8111grid.7445.2Department of Life Sciences, Imperial College, London, SW7 2AZ UK
| | - Boguslaw P. Nocek
- 0000 0001 1939 4845grid.187073.aStructural Biology Center, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Jennifer L. DuBois
- 0000 0001 2156 6108grid.41891.35Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717 USA
| | - John W. Peters
- 0000 0001 2157 6568grid.30064.31Insitutite of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
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Fida TT, Gassara F, Voordouw G. Biodegradation of isopropanol and acetone under denitrifying conditions by Thauera sp. TK001 for nitrate-mediated microbially enhanced oil recovery. JOURNAL OF HAZARDOUS MATERIALS 2017; 334:68-75. [PMID: 28402896 DOI: 10.1016/j.jhazmat.2017.03.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/11/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
Amendment of reservoir fluid with injected substrates can enhance the growth and activity of microbes. The present study used isopropyl alcohol (IPA) or acetone to enhance the indigenous anaerobic nitrate-reducing bacterium Thauera sp. TK001. The strain was able to grow on IPA or acetone and nitrate. To monitor effects of strain TK001 on oil recovery, sand-packed columns containing heavy oil were flooded with minimal medium at atmospheric or high (400psi) pressure. Bioreactors were then inoculated with 0.5 pore volume (PV) of minimal medium containing Thauera sp. TK001 with 25mM of acetone or 22.2mM of IPA with or without 80mM nitrate. Incubation without flow for two weeks and subsequent injection with minimal medium gave an additional 17.0±6.7% of residual oil in place (ROIP) from low-pressure bioreactors and an additional 18.3% of ROIP from the high-pressure bioreactors. These results indicate that acetone or IPA, which are commonly used organic solvents, are good substrates for nitrate-mediated microbial enhanced oil recovery (MEOR), comparable to glucose, acetate or molasses, tested previously. This technology may be used for coupling biodegradation of IPA and/or acetone in waste streams to MEOR where these waste streams are generated in close proximity to an oil field.
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Affiliation(s)
- Tekle Tafese Fida
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - Fatma Gassara
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Gerrit Voordouw
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
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Kundu D, Hazra C, Chaudhari A. Biodegradation of 2,6-dinitrotoluene and plant growth promoting traits by Rhodococcus pyridinivorans NT2: Identification and toxicological analysis of metabolites and proteomic insights. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Heider J, Schühle K, Frey J, Schink B. Activation of Acetone and Other Simple Ketones in Anaerobic Bacteria. J Mol Microbiol Biotechnol 2016; 26:152-64. [PMID: 26958851 DOI: 10.1159/000441500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Acetone and other ketones are activated for subsequent degradation through carboxylation by many nitrate-reducing, phototrophic, and obligately aerobic bacteria. Acetone carboxylation leads to acetoacetate, which is subsequently activated to a thioester and degraded via thiolysis. Two different types of acetone carboxylases have been described, which require either 2 or 4 ATP equivalents as an energy supply for the carboxylation reaction. Both enzymes appear to combine acetone enolphosphate with carbonic phosphate to form acetoacetate. A similar but more complex enzyme is known to carboxylate the aromatic ketone acetophenone, a metabolic intermediate in anaerobic ethylbenzene metabolism in denitrifying bacteria, with simultaneous hydrolysis of 2 ATP to 2 ADP. Obligately anaerobic sulfate-reducing bacteria activate acetone to a four-carbon compound as well, but via a different process than bicarbonate- or CO2-dependent carboxylation. The present evidence indicates that either carbon monoxide or a formyl residue is used as a cosubstrate, and that the overall ATP expenditure of this pathway is substantially lower than in the known acetone carboxylase reactions.
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Affiliation(s)
- Johann Heider
- Laboratory of Microbiology, LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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Oosterkamp MJ, Boeren S, Atashgahi S, Plugge CM, Schaap PJ, Stams AJM. Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC. FEMS Microbiol Lett 2015; 362:fnv080. [PMID: 25977262 DOI: 10.1093/femsle/fnv080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 11/13/2022] Open
Abstract
Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor.
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Affiliation(s)
- Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Dreijenplein 3, 6703 HA Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057, Braga, Portugal
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Gutiérrez Acosta OB, Hardt N, Schink B. Carbonylation as a key reaction in anaerobic acetone activation by Desulfococcus biacutus. Appl Environ Microbiol 2013; 79:6228-35. [PMID: 23913429 PMCID: PMC3811201 DOI: 10.1128/aem.02116-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/29/2013] [Indexed: 01/23/2023] Open
Abstract
Acetone is activated by aerobic and nitrate-reducing bacteria via an ATP-dependent carboxylation reaction to form acetoacetate as the first reaction product. In the activation of acetone by sulfate-reducing bacteria, acetoacetate has not been found to be an intermediate. Here, we present evidence of a carbonylation reaction as the initial step in the activation of acetone by the strictly anaerobic sulfate reducer Desulfococcus biacutus. In cell suspension experiments, CO was found to be a far better cosubstrate for acetone activation than CO2. The hypothetical reaction product, acetoacetaldehyde, is extremely reactive and could not be identified as a free intermediate. However, acetoacetaldehyde dinitrophenylhydrazone was detected by mass spectrometry in cell extract experiments as a reaction product of acetone, CO, and dinitrophenylhydrazine. In a similar assay, 2-amino-4-methylpyrimidine was formed as the product of a reaction between acetoacetaldehyde and guanidine. The reaction depended on ATP as a cosubstrate. Moreover, the specific activity of aldehyde dehydrogenase (coenzyme A [CoA] acylating) tested with the putative physiological substrate was found to be 153 ± 36 mU mg(-1) protein, and its activity was specifically induced in extracts of acetone-grown cells. Moreover, acetoacetyl-CoA was detected (by mass spectrometry) after the carbonylation reaction as the subsequent intermediate after acetoacetaldehyde was formed. These results together provide evidence that acetoacetaldehyde is an intermediate in the activation of acetone by sulfate-reducing bacteria.
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Affiliation(s)
- Olga B. Gutiérrez Acosta
- Department of Biology
- Konstanz Research School of Chemical Biology, Universität Konstanz, Constance, Germany
| | - Norman Hardt
- Department of Chemistry
- Konstanz Research School of Chemical Biology, Universität Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology
- Konstanz Research School of Chemical Biology, Universität Konstanz, Constance, Germany
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Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. MICROBIOME 2013; 1:22. [PMID: 24450983 PMCID: PMC3971608 DOI: 10.1186/2049-2618-1-22] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/24/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. Recent 16S rRNA gene profiling indicates that members of the bacterial phylum Chloroflexi are common in sediment. Only the role of the class Dehalococcoidia, which degrade halogenated solvents, is well understood. Genomic sampling is available for only six of the approximate 30 Chloroflexi classes, so little is known about the phylogenetic distribution of reductive dehalogenation or about the broader metabolic characteristics of Chloroflexi in sediment. RESULTS We used metagenomics to directly evaluate the metabolic potential and diversity of Chloroflexi in aquifer sediments. We sampled genomic sequence from 86 Chloroflexi representing 15 distinct lineages, including members of eight classes previously characterized only by 16S rRNA sequences. Unlike in the Dehalococcoidia, genes for organohalide respiration are rare within the Chloroflexi genomes sampled here. Near-complete genomes were reconstructed for three Chloroflexi. One, a member of an unsequenced lineage in the Anaerolinea, is an aerobe with the potential for respiring diverse carbon compounds. The others represent two genomically unsampled classes sibling to the Dehalococcoidia, and are anaerobes likely involved in sugar and plant-derived-compound degradation to acetate. Both fix CO2 via the Wood-Ljungdahl pathway, a pathway not previously documented in Chloroflexi. The genomes each encode unique traits apparently acquired from Archaea, including mechanisms of motility and ATP synthesis. CONCLUSIONS Chloroflexi in the aquifer sediments are abundant and highly diverse. Genomic analyses provide new evolutionary boundaries for obligate organohalide respiration. We expand the potential roles of Chloroflexi in sediment carbon cycling beyond organohalide respiration to include respiration of sugars, fermentation, CO2 fixation, and acetogenesis with ATP formation by substrate-level phosphorylation.
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Affiliation(s)
- Laura A Hug
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Kelly C Wrighton
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Kyle R Frischkorn
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
| | - Kenneth H Williams
- Geophysics Department, Earth Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Susannah G Tringe
- Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA
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