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Reis PCJ, Correa-Garcia S, Tremblay J, Beaulieu-Laliberté A, Muench DG, Ahad JME, Yergeau E, Comte J, Martineau C. Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water. FEMS Microbiol Ecol 2023; 99:fiad153. [PMID: 38012121 PMCID: PMC10710301 DOI: 10.1093/femsec/fiad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal. Recent advances in genomics and analytical chemistry have provided insights into a better understanding of the metabolic pathways and genes involved in NA degradation. Here, we discuss the ecology of microbial NA degradation with a focus on CWTS and summarize the current knowledge related to the metabolic pathways and genes used by microorganisms to degrade NAs. Evidence to date suggests that NAs are mostly degraded aerobically through ring cleavage via the beta-oxidation pathway, which can be combined with other steps such as aromatization, alpha-oxidation, omega-oxidation, or activation as coenzyme A (CoA) thioesters. Anaerobic NA degradation has also been reported via the production of benzoyl-CoA as an intermediate and/or through the involvement of methanogens or nitrate, sulfate, and iron reducers. Furthermore, we discuss how genomic, statistical, and modeling tools can assist in the development of improved bioremediation practices.
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Affiliation(s)
- Paula C J Reis
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
| | - Sara Correa-Garcia
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
| | - Julien Tremblay
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Aurélie Beaulieu-Laliberté
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec city, QC G1K 9A9, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Québec city, QC G1V 4C7, Canada
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Zan S, Wang J, Fan J, Jin Y, Li Z, Du M. Cyclohexanecarboxylic acid degradation with simultaneous nitrate removal by Marinobacter sp. SJ18. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:34296-34305. [PMID: 36512278 DOI: 10.1007/s11356-022-24705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Naphthenic acid (NA) is a toxic pollutant with potential threat to human health. However, NA transformations in marine environments are still unclear. In this study, the characteristics and pathways of cyclohexanecarboxylic acid (CHCA) biodegradation were explored in the presence of nitrate. The results showed that CHCA was completely degraded with pseudo-first-order kinetic reaction under aerobic and anaerobic conditions, accompanied by nitrate removal rates exceeding 70%, which was positively correlated with CHCA degradation (P < 0.05). In the proposed CHCA degradation pathways, cyclohexane is dehydrogenated to form cyclohexene, followed by ring-opening by dioxygenase to generate fatty acid under aerobic conditions or cleavage of cyclohexene through β-oxidation under anaerobic conditions. Whole genome analysis indicated that nitrate was removed via assimilation and dissimilation pathways under aerobic conditions and via denitrification pathway under anaerobic conditions. These results provide a basis for alleviating combined pollution of NA and nitrate in marine environments with frequent anthropogenic activities.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
- Groundwater Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China.
| | - Jingfeng Fan
- Marine Ecology Department, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Yuan Jin
- Marine Ecology Department, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | - Miaomiao Du
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
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Sanz D, Díaz E. Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB. Environ Microbiol 2022; 24:4987-5004. [PMID: 35768954 PMCID: PMC9795900 DOI: 10.1111/1462-2920.16093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022]
Abstract
The alicyclic compound cyclohexane carboxylate (CHC) is anaerobically degraded through a peripheral pathway that converges with the central benzoyl-CoA degradation pathway of aromatic compounds in Rhodopseudomonas palustris (bad pathway) and some strictly anaerobic bacteria. Here we show that in denitrifying bacteria, e.g. Aromatoleum sp. CIB strain, CHC is degraded through a bad-ali pathway similar to that reported in R. palustris but that does not share common intermediates with the benzoyl-CoA degradation pathway (bzd pathway) of this bacterium. The bad-ali genes are also involved in the aerobic degradation of CHC in strain CIB, and orthologous bad-ali clusters have been identified in the genomes of a wide variety of bacteria. Expression of bad-ali genes in strain CIB is under control of the BadR transcriptional repressor, which was shown to recognize CHC-CoA, the first intermediate of the pathway, as effector, and whose operator region (CAAN4 TTG) was conserved in bad-ali clusters from Gram-negative bacteria. The bad-ali and bzd pathways generate pimelyl-CoA and 3-hydroxypimelyl-CoA, respectively, that are metabolized through a common aab pathway whose genetic determinants form a supraoperonic clustering with the bad-ali genes. A synthetic bad-ali-aab catabolic module was engineered and it was shown to confer CHC degradation abilities to different bacterial hosts.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
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Zan S, Wang J, Wang F, Li Z, Du M, Cai Y. A novel degradation mechanism of naphthenic acids by marine Pseudoalteromonas sp. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127534. [PMID: 34879524 DOI: 10.1016/j.jhazmat.2021.127534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Naphthenic acids (NAs) are a persistent toxic organic pollutant that occur in different environment worldwide and cause serious threat to the ecosystem and public health. However, knowledge on the behavior and fate of NAs in marine environments still remains unknown. In this study, the degradation mechanism of NAs (cyclohexylacetic acid, CHAA) was investigated using an common indigenous marine Pseudoalteromonas sp. The results showed that CHAA could be degraded completely under aerobic condition, but could not be utilized directly under anaerobic condition. Interestingly, transcriptome and key enzyme activity results showed the CHAA degradation pathway induced under aerobic condition could still work in anaerobic condition. The degradation was activated by acetyl-CoA transferase and sequentially formed the corresponding cyclohexene, alcohol, and ketone with the assistance of related enzymes, and finally cleaved by hydroxymethylglutarate-CoA lyase. Besides, there was a positive correlation between chemotaxis and aerobic degradation genes (r = 0.976, P < 0.05), the chemotaxis would enhance bacterium movement and NAs biodegradation. It is proposed that bacterium could translocate to NAs and accomplish biodegradation from aerobic to anaerobic environments, which was a new anaerobic degradation pathway of NAs. This study provides new insights into the fate of NAs and other organic contaminants in marine environment.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Fengbo Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Miaomiao Du
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Yingxue Cai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
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Yamamoto T, Hasegawa Y, Iwaki H. Identification and characterization of a novel class of self-sufficient cytochrome P450 hydroxylase involved in cyclohexanecarboxylate degradation in Paraburkholderia terrae strain KU-64. Biosci Biotechnol Biochem 2022; 86:199-208. [PMID: 34965585 DOI: 10.1093/bbb/zbab199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/15/2021] [Indexed: 11/14/2022]
Abstract
Cytochrome P450 monooxygenases play important roles in metabolism. Here, we report the identification and biochemical characterization of P450CHC, a novel self-sufficient cytochrome P450, from cyclohexanecarboxylate-degrading Paraburkholderia terrae KU-64. P450CHC was found to comprise a [2Fe-2S] ferredoxin domain, NAD(P)H-dependent FAD-containing reductase domain, FCD domain, and cytochrome P450 domain (in that order from the N terminus). Reverse transcription-polymerase chain reaction results indicated that the P450CHC-encoding chcA gene was inducible by cyclohexanecarboxylate. chcA overexpression in Escherichia coli and recombinant protein purification enabled functional characterization of P450CHC as a catalytically self-sufficient cytochrome P450 that hydroxylates cyclohexanecarboxylate. Kinetic analysis indicated that P450CHC largely preferred NADH (Km = 0.011 m m) over NADPH (Km = 0.21 m m). The Kd, Km, and kcat values for cyclohexanecarboxylate were 0.083 m m, 0.084 m m, and 15.9 s-1, respectively. The genetic and biochemical analyses indicated that the physiological role of P450CHC is initial hydroxylation in the cyclohexanecarboxylate degradation pathway.
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Affiliation(s)
- Taisei Yamamoto
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
| | - Yoshie Hasegawa
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
| | - Hiroaki Iwaki
- Department of Life Science and Biotechnology, Kansai University, Suita, Osaka, Japan
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Kung JW, Meier AK, Willistein M, Weidenweber S, Demmer U, Ermler U, Boll M. Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases. Chembiochem 2021; 22:3173-3177. [PMID: 34555236 PMCID: PMC9293079 DOI: 10.1002/cbic.202100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Indexed: 11/20/2022]
Abstract
The biologically important, FAD‐containing acyl‐coenzyme A (CoA) dehydrogenases (ACAD) usually catalyze the anti‐1,2‐elimination of a proton and a hydride of aliphatic CoA thioesters. Here, we report on the structure and function of an ACAD from anaerobic bacteria catalyzing the unprecedented 1,4‐elimination at C3 and C6 of cyclohex‐1‐ene‐1‐carboxyl‐CoA (Ch1CoA) to cyclohex‐1,5‐diene‐1‐carboxyl‐CoA (Ch1,5CoA) and at C3 and C4 of the latter to benzoyl‐CoA. Based on high‐resolution Ch1CoA dehydrogenase crystal structures, the unorthodox reactivity is explained by the presence of a catalytic aspartate base (D91) at C3, and by eliminating the catalytic glutamate base at C1. Moreover, C6 of Ch1CoA and C4 of Ch1,5CoA are positioned towards FAD‐N5 to favor the biologically relevant C3,C6‐ over the C3,C4‐dehydrogenation activity. The C1,C2‐dehydrogenation activity was regained by structure‐inspired amino acid exchanges. The results provide the structural rationale for the extended catalytic repertoire of ACADs and offer previously unknown biocatalytic options for the synthesis of cyclic 1,3‐diene building blocks.
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Affiliation(s)
- Johannes W Kung
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Anne-Katrin Meier
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Max Willistein
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Sina Weidenweber
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Ulrike Demmer
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Matthias Boll
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
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Yamamoto T, Hasegawa Y, Lau PCK, Iwaki H. Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369. J Biosci Bioeng 2021; 132:621-629. [PMID: 34583900 DOI: 10.1016/j.jbiosc.2021.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/18/2022]
Abstract
Cyclohexanecarboxylate (CHCA) is formed by oxidative microbial degradation of n-alkylcycloparaffins and anaerobic degradation of benzoate, and also known to be a synthetic intermediate or the starter unit of biosynthesis of cellular constituents and secondary metabolites. Although two degradation pathways have been proposed, genetic information has been limited to the β-oxidation-like pathway. In this study, we identified a gene cluster, designated chcC1XTC2B1B2RAaAbAc, that is responsible for the CHCA aromatization pathway in Sinomonas (formerly Corynebacterium) cyclohexanicum strain ATCC 51369. Reverse transcription-PCR analysis indicated that the chc gene cluster is inducible by CHCA and that it consists of two transcriptional units, chcC1XTC2B1B2R and chcAaAbAc. Overexpression of the various genes in Escherichia coli, and purification of the recombinant proteins led to the functional characterization of ChcAaAbAc as subunits of a cytochrome P450 system responsible for CHCA hydroxylation; ChcB1 and ChcB2 as trans-4-hydroxyCHCA and cis-4-hydroxyCHCA dehydrogenases, respectively; ChcC1 was identified as a 4-oxoCHCA desaturase containing a covalently bound FAD; and ChcC2 was identified as a 4-oxocyclohexenecarboxylate desaturase. The binding constant of ChcAa for CHCA was found to be 0.37 mM. Kinetic parameters established for ChcB1 indicated that it has a high catalytic efficiency towards 4-oxoCHCA compared to trans- or cis-4-hydroxyCHCA. The Km and Kcat values of ChcC1 for 4-oxoCHCA were 0.39 mM and 44 s-1, respectively. Taken together with previous work on the identification of a pobA gene encoding a 4-hydroxybenzoate hydroxylase, we have now localized the remaining set of genes for the final degradation of protocatechuate before entry into the tricarboxylic acid cycle.
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Affiliation(s)
- Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Peter C K Lau
- Department of Microbiology & Immunology, McGill University, Montréal, Québec, H3A 2B4, Canada
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan.
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Weiten A, Kalvelage K, Becker P, Reinhardt R, Hurek T, Reinhold-Hurek B, Rabus R. Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T. Microb Physiol 2021; 31:16-35. [PMID: 33477134 DOI: 10.1159/000513167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/17/2020] [Indexed: 11/19/2022]
Abstract
The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.41 Mbp) and Ar. bremense PbN1T (4.38 Mbp), which cover the phylogenetic breadth of the genus Aromatoleum together with previously genome sequenced Ar. aromaticum EbN1T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27-36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1T only) compounds are scattered across the genomes of strains ToN1T and PbN1T. The richness in mobile genetic elements is shared with other Aromatoleum spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1T and PbN1T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1T) and toluene/monoterpenes (strain ToN1T) share high similarity with their counterparts in Ar. aromaticum strains EbN1T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1T, PbN1T, and EbN1T. The diazotrophic, endophytic lifestyle of closest related genus Azoarcus is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1T, PbN1T, and EbN1T lack nif genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1T and EbN1T do not possess tss genes for T6SS, while strain ToN1T does and facultative endophytic "Aromatoleum" sp. CIB is known to even have both. These findings underpin the functional heterogeneity among Aromatoleum members, correlating with the high plasticity of their genomes.
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Affiliation(s)
- Arne Weiten
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kristin Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Patrick Becker
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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Soares-Castro P, Soares F, Santos PM. Current Advances in the Bacterial Toolbox for the Biotechnological Production of Monoterpene-Based Aroma Compounds. Molecules 2020; 26:molecules26010091. [PMID: 33379215 PMCID: PMC7794910 DOI: 10.3390/molecules26010091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Monoterpenes are plant secondary metabolites, widely used in industrial processes as precursors of important aroma compounds, such as vanillin and (-)-menthol. However, the physicochemical properties of monoterpenes make difficult their conventional conversion into value-added aromas. Biocatalysis, either by using whole cells or enzymes, may overcome such drawbacks in terms of purity of the final product, ecological and economic constraints of the current catalysis processes or extraction from plant material. In particular, the ability of oxidative enzymes (e.g., oxygenases) to modify the monoterpene backbone, with high regio- and stereo-selectivity, is attractive for the production of "natural" aromas for the flavor and fragrances industries. We review the research efforts carried out in the molecular analysis of bacterial monoterpene catabolic pathways and biochemical characterization of the respective key oxidative enzymes, with particular focus on the most relevant precursors, β-pinene, limonene and β-myrcene. The presented overview of the current state of art demonstrates that the specialized enzymatic repertoires of monoterpene-catabolizing bacteria are expanding the toolbox towards the tailored and sustainable biotechnological production of values-added aroma compounds (e.g., isonovalal, α-terpineol, and carvone isomers) whose implementation must be supported by the current advances in systems biology and metabolic engineering approaches.
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10
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Lv X, Ma B, Cologgi D, Lee K, Ulrich A. Naphthenic acid anaerobic biodegrading consortia enriched from pristine sediments underlying oil sands tailings ponds. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122546. [PMID: 32203719 DOI: 10.1016/j.jhazmat.2020.122546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/06/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
Seepage from oil sands tailings ponds (OSTP), which contain toxic naphthenic acids (NAs), can infiltrate into groundwater. Clay sediment layer beneath is a critical barrier for reducing the infiltration of NAs into the sand sediment layer, where groundwater channels reside. Biodegradation has great potential as a strategy for NAs removal, but little is known about NAs biodegradability and potential functional microbes in these pristine sediments. This study investigated the potential for anaerobic biodegradation of NAs by microbial consortia enriched from clay and sand sediments underlying OSTP, amended with either acid extracted organics or Merichem NAs, under nitrate- and sulfate-reducing conditions. Degradation of NAs only be detected after DOC concentration reached to steady state after 163 days. Microbial community analysis shows that different electron acceptors, sediment types, and NAs sources associated with specific microbial taxa and can explain 14.8, 13.9 % and 5% of variation of microbial community structures, respectively. The DOC and methane were the most important geochemical properties for microbial community variations. This study approved the potential capability of indigenous microbial communities from the pristine sediments in NA degradation, demonstrating the barrier function of pristine clay sediments underlying OSTP in prohibiting organic contaminants from entering into groundwater.
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Affiliation(s)
- Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Dena Cologgi
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
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Yu X, Lee K, Ulrich AC. Model naphthenic acids removal by microalgae and Base Mine Lake cap water microbial inoculum. CHEMOSPHERE 2019; 234:796-805. [PMID: 31247489 DOI: 10.1016/j.chemosphere.2019.06.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/27/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Naphthenic acids (NAs) originate from bitumen and are considered a major contributor to acute toxicity in oil sands process-affected water (OSPW) produced from bitumen extraction processes. To reclaim oil sands tailings and remediate OSPW, in-pit fluid fine tailings can be water-capped as end pit lakes (EPL). Addressing NAs present in OSPW, either through removal, dilution or degradation, is an objective for oil sands reclamation. EPLs can remediate NAs through degradation or dilution or both. To assess and understand degradation potential, Chlorella kessleri and Botryococcus braunii were tested for their tolerance to, and ability to biodegrade, three model NAs (cyclohexanecarboxylic acid, cyclohexaneacetic acid, and cyclohexanebutyric acid). Water sourced from the industry's first EPL, the Base Mine Lake (BML), was used alone as an inoculum or co-cultured with C. kessleri to biodegrade cyclohexanecarboxylic acid and cyclohexanebutyric acid. All cultures metabolized the model compounds via β-oxidation. Biodegradation by the co-culture of C. kessleri and BML inoculum was most effective and rapid: the cyclohexaneacetic acid generated from cyclohexanebutyric acid could be further degraded by the co-culture, while the cyclohexaneacetic acid generated could not be consumed by pure algal cultures or BML inoculum alone. Adding C. kessleri greatly increased the diversity of the microbial community in the BML inoculum; many known hydrocarbon and NA degraders were identified from the 16S rRNA gene sequencing from this co-culture. This more diverse microbial community could have potential for EPL remediation.
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Affiliation(s)
- Xiaoxuan Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
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12
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James KL, Kung JW, Crable BR, Mouttaki H, Sieber JR, Nguyen HH, Yang Y, Xie Y, Erde J, Wofford NQ, Karr EA, Loo JA, Ogorzalek Loo RR, Gunsalus RP, McInerney MJ. Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids. Environ Microbiol 2019; 21:1833-1846. [PMID: 30895699 PMCID: PMC6488403 DOI: 10.1111/1462-2920.14601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Syntrophy is essential for the efficient conversion of organic carbon to methane in natural and constructed environments, but little is known about the enzymes involved in syntrophic carbon and electron flow. Syntrophus aciditrophicus strain SB syntrophically degrades benzoate and cyclohexane-1-carboxylate and catalyses the novel synthesis of benzoate and cyclohexane-1-carboxylate from crotonate. We used proteomic, biochemical and metabolomic approaches to determine what enzymes are used for fatty, aromatic and alicyclic acid degradation versus for benzoate and cyclohexane-1-carboxylate synthesis. Enzymes involved in the metabolism of cyclohex-1,5-diene carboxyl-CoA to acetyl-CoA were in high abundance in S. aciditrophicus cells grown in pure culture on crotonate and in coculture with Methanospirillum hungatei on crotonate, benzoate or cyclohexane-1-carboxylate. Incorporation of 13 C-atoms from 1-[13 C]-acetate into crotonate, benzoate and cyclohexane-1-carboxylate during growth on these different substrates showed that the pathways are reversible. A protein conduit for syntrophic reverse electron transfer from acyl-CoA intermediates to formate was detected. Ligases and membrane-bound pyrophosphatases make pyrophosphate needed for the synthesis of ATP by an acetyl-CoA synthetase. Syntrophus aciditrophicus, thus, uses a core set of enzymes that operates close to thermodynamic equilibrium to conserve energy in a novel and highly efficient manner.
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Affiliation(s)
- Kimberly L. James
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Johannes W. Kung
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Bryan R. Crable
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Housna Mouttaki
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Jessica R. Sieber
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Hong H. Nguyen
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Yanan Yang
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Yongming Xie
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Jonathan Erde
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Neil Q. Wofford
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Elizabeth A. Karr
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
- Price Family Foundation Institute of Structural Biology,
University of Oklahoma, Norman, OK, 73019
| | - Joseph A. Loo
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Rachel R. Ogorzalek Loo
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular
Genetics, University of California, Los Angeles, CA, USA
- UCLA-Molecular Biology Institute, University of California,
Los Angeles, CA USA
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
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13
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Fungal biotransformation of short-chain n-alkylcycloalkanes. Appl Microbiol Biotechnol 2019; 103:4137-4151. [PMID: 30941461 DOI: 10.1007/s00253-019-09749-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
The cycloalkanes, comprising up to 45% of the hydrocarbon fraction, occur in crude oil or refined oil products (e.g., gasoline) mainly as alkylated cyclohexane derivatives and have been increasingly found in environmental samples of soil and water. Furthermore, short-chain alkylated cycloalkanes are components of the so-called volatile organic compounds (VOCs). This study highlights the biotransformation of methyl- and ethylcyclohexane by the alkane-assimilating yeast Candida maltosa and the phenol- and benzoate-utilizing yeast Trichosporon mucoides under laboratory conditions. In the course of this biotransformation, we detected 25 different metabolites, which were analyzed by HPLC and GC-MS. The biotransformation process of methylcyclohexane in both yeasts involve (A) ring hydroxylation at different positions (C2, C3, and C4) and subsequent oxidation to ketones as well as (B) oxidation of the alkyl side chain to hydroxylated and acid products. The yeast T. mucoides additionally performs ring hydroxylation at the C1-position and (C) oxidative decarboxylation and (D) aromatization of cyclohexanecarboxylic acid. Both yeasts also oxidized the saturated ring system and the side chain of ethylcyclohexane. However, the cyclohexylacetic acid, which was formed, seemed not to be substrate for aromatization. This is the first report of several new transformation reactions of alkylated cycloalkanes for eukaryotic microorganisms.
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14
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Dörries M, Wöhlbrand L, Kube M, Reinhardt R, Rabus R. Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059. BMC Genomics 2016; 17:918. [PMID: 27846794 PMCID: PMC5109826 DOI: 10.1186/s12864-016-3236-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated. A metabolically versatile representative of this family is Desulfococcus multivorans that is able to completely oxidize (to CO2) a variety of organic acids, including fatty acids up to C14, as well as aromatic compounds. RESULTS In this study the complete 4.46 Mbp and manually annotated genome of metabolically versatile Desulfococcus multivorans DSM 2059 is presented with particular emphasis on a proteomics-driven metabolic reconstruction. Proteomic profiling covered 17 substrate adaptation conditions (6 aromatic and 11 aliphatic compounds) and comprised 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fractions. This comprehensive proteogenomic dataset allowed for reconstructing a metabolic network of degradation pathways and energy metabolism that consists of 170 proteins (154 detected; ~91 % coverage). Peripheral degradation routes feed via central benzoyl-CoA, (modified) β-oxidation or methylmalonyl-CoA pathways into the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO2. Dissimilatory sulfate reduction is fueled by a complex electron transfer network composed of cytoplasmic components (e.g., electron transfer flavoproteins) and diverse membrane redox complexes (Dsr, Qmo, Hmc, Tmc, Qrc, Nuo and Rnf). Overall, a high degree of substrate-specific formation of catabolic enzymes was observed, while most complexes involved in electron transfer appeared to be constitutively formed. CONCLUSIONS A highly dynamic genome structure in combination with substrate-specifically formed catabolic subproteomes and a constitutive subproteome for energy metabolism and electron transfer appears to be a common trait of Desulfobacteraceae members.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Michael Kube
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | | | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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15
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An W, Guo F, Song Y, Gao N, Bai S, Dai J, Wei H, Zhang L, Yu D, Xia M, Yu Y, Qi M, Tian C, Chen H, Wu Z, Zhang T, Qiu D. Comparative genomics analyses on EPS biosynthesis genes required for floc formation of Zoogloea resiniphila and other activated sludge bacteria. WATER RESEARCH 2016; 102:494-504. [PMID: 27403872 DOI: 10.1016/j.watres.2016.06.058] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Activated sludge (AS) process has been widely utilized for municipal sewage and industrial wastewater treatment. Zoolgoea and its related floc-forming bacteria are required for formation of AS flocs which is the key to gravitational effluent-and-sludge separation and AS recycling. However, little is known about the genetics, biochemistry and physiology of Zoogloea and its related bacteria. This report deals with the comparative genomic analyses on two Zoogloea resiniphila draft genomes and the closely related proteobacterial species commonly found in AS. In particular, the metabolic processes involved in removal of organic matters, nitrogen and phosphorus were analyzed. Furthermore, it is revealed that a large gene cluster, encoding eight glycosyltransferases and other proteins involved in biosynthesis and export of extracellular polysaccharides (EPS), was required for floc formation. One of the two asparagine synthase paralogues, associated with this EPS biosynthesis gene cluster, was required for floc formation in Zoogloea. Similar EPS biosynthesis gene cluster(s) were identified in the genome of other AS proteobacteria including polyphosphate-accumulating Candidatus Accumulibacter phosphatis (CAP) and nitrifying Nitrosopira and Nitrosomonas bacteria, but the gene composition varies interspecifically and intraspecifically. Our results indicate that floc formation of desired AS bacteria, including CAP strains, facilitate their recruitment into AS and gradual enrichment via repeated AS settling and recycling processes.
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Affiliation(s)
- Weixing An
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Guo
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Yulong Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Bai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Institute of Deep-sea Science and Technology, Chinese Academy of Sciences, Sanya 572000, China
| | - Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hehong Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dianzhen Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yu
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Qi
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyuan Tian
- School of Life Sciences and Technology, Hubei Engineering University, Xiaogan 43200, China
| | - Haofeng Chen
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenbin Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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16
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Boll M, Kung JW, Ermler U, Martins BM, Buckel W. Fermentative Cyclohexane Carboxylate Formation in Syntrophus aciditrophicus. J Mol Microbiol Biotechnol 2016; 26:165-79. [PMID: 26959729 DOI: 10.1159/000440881] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids such as acetic, propionic, butyric or lactic acids are typical primary fermentation products in the anaerobic feeding chain. Fifteen years ago, a novel fermentation type was discovered in the obligately anaerobic Deltaproteobacterium Syntrophus aciditrophicus. During fermentative growth with crotonate and/or benzoate, acetate is formed in the oxidative branch and cyclohexane carboxylate in the reductive branch. In both cases cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA) is a central intermediate that is either formed by a class II benzoyl-CoA reductase (fermentation of benzoate) or by reverse reactions of the benzoyl-CoA degradation pathway (fermentation of crotonate). Here, we summarize the current knowledge of the enzymology involved in fermentations yielding cyclohexane carboxylate as an excreted product. The characteristic enzymes involved are two acyl-CoA dehydrogenases specifically acting on Ch1,5CoA and cyclohex-1-ene-1-carboxyl-CoA. Both enzymes are also employed during the syntrophic growth of S. aciditrophicus with cyclohexane carboxylate as the carbon source in coculture with a methanogen. An investigation of anabolic pathways in S. aciditrophicus revealed a rather unusual pathway for glutamate synthesis involving a Re-citrate synthase. Future work has to address the unresolved question concerning which components are involved in reoxidation of the NADH formed in the oxidative branch of the unique cyclohexane carboxylate fermentation pathway in S. aciditrophicus.
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Affiliation(s)
- Matthias Boll
- Mikrobiologie, Fakultx00E4;t fx00FC;r Biologie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
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17
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Boll M, Einsle O, Ermler U, Kroneck PMH, Ullmann GM. Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase. J Mol Microbiol Biotechnol 2016; 26:119-37. [PMID: 26959374 DOI: 10.1159/000440805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In biology, tungsten (W) is exclusively found in microbial enzymes bound to a bis-pyranopterin cofactor (bis-WPT). Previously known W enzymes catalyze redox oxo/hydroxyl transfer reactions by directly coordinating their substrates or products to the metal. They comprise the W-containing formate/formylmethanofuran dehydrogenases belonging to the dimethyl sulfoxide reductase (DMSOR) family and the aldehyde:ferredoxin oxidoreductase (AOR) families, which form a separate enzyme family within the Mo/W enzymes. In the last decade, initial insights into the structure and function of two unprecedented W enzymes were obtained: the acetaldehyde forming acetylene hydratase (ACH) belongs to the DMSOR and the class II benzoyl-coenzyme A (CoA) reductase (BCR) to the AOR family. The latter catalyzes the reductive dearomatization of benzoyl-CoA to a cyclic diene. Both are key enzymes in the degradation of acetylene (ACH) or aromatic compounds (BCR) in strictly anaerobic bacteria. They are unusual in either catalyzing a nonredox reaction (ACH) or a redox reaction without coordinating the substrate or product to the metal (BCR). In organic chemical synthesis, analogous reactions require totally nonphysiological conditions depending on Hg2+ (acetylene hydration) or alkali metals (benzene ring reduction). The structural insights obtained pave the way for biological or biomimetic approaches to basic reactions in organic chemistry.
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Affiliation(s)
- Matthias Boll
- Fakultx00E4;t fx00FC;r Biologie/Mikrobiologie, Institut fx00FC;r Biochemie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
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18
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Wang C, Shi S, Chen H. Study of kinetics of degradation of cyclohexane carboxylic acid by acclimated activated sludge. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:2552-2558. [PMID: 27191578 DOI: 10.2166/wst.2016.114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Activated sludge contains complex microorganisms, which are highly effective biodegrading agents. In this study, the kinetics of biodegradation of cyclohexane carboxylic acid (CHCA) by an acclimated aerobic activated sludge were investigated. The results showed that after 180 days of acclimation, the activated sludge could steadily degrade >90% of the CHCA in 120 h. The degradation of CHCA by the acclimated activated sludge could be modeled using a first-order kinetics equation. The equations for the degradation kinetics for different initial CHCA concentrations were also obtained. The kinetics constant, kd, decreased with an increase in the CHCA concentration, indicating that, at high concentrations, CHCA had an inhibiting effect on the microorganisms in the activated sludge. The effects of pH on the degradation kinetics of CHCA were also investigated. The results showed that a pH of 10 afforded the highest degradation rate, indicating that basic conditions significantly promoted the degradation of CHCA. Moreover, it was found that the degradation efficiency for CHCA increased with an increase in temperature and concentration of dissolved oxygen under the experimental conditions.
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Affiliation(s)
- Chunhua Wang
- Department of Chemical Engineering, Huizhou University, Huizhou, Guangdong, China E-mail:
| | - Shuian Shi
- Department of Chemical Engineering, Huizhou University, Huizhou, Guangdong, China E-mail:
| | - Hongyan Chen
- Department of Chemical Engineering, Huizhou University, Huizhou, Guangdong, China E-mail:
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19
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BadR and BadM Proteins Transcriptionally Regulate Two Operons Needed for Anaerobic Benzoate Degradation by Rhodopseudomonas palustris. Appl Environ Microbiol 2015; 81:4253-62. [PMID: 25888170 DOI: 10.1128/aem.00377-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/09/2015] [Indexed: 11/20/2022] Open
Abstract
The bacterium Rhodopseudomonas palustris grows with the aromatic acid benzoate and the alicyclic acid cyclohexanecarboxylate (CHC) as sole carbon sources. The enzymatic steps in an oxygen-independent pathway for CHC degradation have been elucidated, but it was unknown how the CHC operon (badHI aliAB badK) encoding the enzymes for CHC degradation was regulated. aliA and aliB encode enzymes for the conversion of CHC to cyclohex-1-enecarboxyl-coenzyme A (CHene-CoA). At this point, the pathway for CHC degradation merges with the pathway for anaerobic benzoate degradation, as CHene-CoA is an intermediate in both degradation pathways. Three enzymes, encoded by badK, badH, and badI, prepare and cleave the alicyclic ring of CHene-CoA to yield pimelyl-CoA. Here, we show that the MarR transcription factor family member, BadR, represses transcription of the CHC operon by binding near the transcription start site of badH. 2-Ketocyclohexane-1-carboxyl-CoA, an intermediate of CHC and benzoate degradation, interacts with BadR to abrogate repression. We also present evidence that the transcription factor BadM binds to the promoter of the badDEFGAB (Bad) operon for the anaerobic conversion of benzoate to CHene-CoA to repress its expression. Contrary to previous reports, BadR does not appear to control expression of the Bad operon. These data enhance our view of the transcriptional regulation of anaerobic benzoate degradation by R. palustris.
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20
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Schmid G, René SB, Boll M. Enzymes of the benzoyl-coenzyme A degradation pathway in the hyperthermophilic archaeon Ferroglobus placidus. Environ Microbiol 2015; 17:3289-300. [PMID: 25630364 DOI: 10.1111/1462-2920.12785] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 12/28/2022]
Abstract
The Fe(III)-respiring Ferroglobus placidus is the only known archaeon and hyperthermophile for which a complete degradation of aromatic substrates to CO2 has been reported. Recent genome and transcriptome analyses proposed a benzoyl-coenzyme A (CoA) degradation pathway similar to that found in the phototrophic Rhodopseudomonas palustris, which involves a cyclohex-1-ene-1-carboxyl-CoA (1-enoyl-CoA) forming, ATP-dependent key enzyme benzoyl-CoA reductase (BCR). In this work, we demonstrate, by first in vitro studies, that benzoyl-CoA is ATP-dependently reduced by two electrons to cyclohexa-1,5-dienoyl-CoA (1,5-dienoyl-CoA), which is further degraded by hydration to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA (6-OH-1-enoyl-CoA); upon addition of NAD(+) , the latter was subsequently converted to β-oxidation intermediates. The four candidate genes of BCR were heterologously expressed, and the enriched, oxygen-sensitive enzyme catalysed the two-electron reduction of benzoyl-CoA to 1,5-dienoyl-CoA. A gene previously assigned to a 2,3-didehydropimeloyl-CoA hydratase was heterologously expressed and shown to act as a typical 1,5-dienoyl-CoA hydratase that does not accept 1-enoyl-CoA. A gene previously assigned to a 1-enoyl-CoA hydratase was heterologously expressed and identified to code for a bifunctional crotonase/3-OH-butyryl-CoA dehydrogenase. In summary, the results consistently provide biochemical evidence that F. placidus and probably other archaea predominantly degrade aromatics via the Thauera/Azoarcus type and not or only to a minor extent via the predicted R. palustris-type benzoyl-CoA degradation pathway.
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Affiliation(s)
- Georg Schmid
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
| | - Sandra Bosch René
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
| | - Matthias Boll
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
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