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Du M, Jin Y, Fan J, Zan S, Gu C, Wang J. A new pathway for anaerobic biotransformation of marine toxin domoic acid. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:5150-5160. [PMID: 35974277 DOI: 10.1007/s11356-022-22368-3] [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: 04/09/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Domoic acid (DA) is a harmful algal toxin produced by marine diatom Pseudo-nitzschia and seriously threatens ecosystem and human health. However, the current knowledge on its biotransformation behavior in coastal anaerobic environment is lacking. This study investigated the anaerobic biotransformation of DA by a new marine consortium GH1. The results demonstrated that 90% of DA (1 mg L-1) was cometabolically biotransformed under sulfate-reducing condition. A new anaerobic biotransformation pathway involving DA hydration, dehydrogenation, and C-C bond cleavage was proposed, where the conjugated double-bond of DA was interrupted, resulting in the corresponding alcohols and ketones, subsequently cleaved hydrolytically, and yielding the lower molecular weight products. Desulfovibrio and Clostridiales were markedly enriched in the anaerobic biotransformation of DA, which might jointly contribute to the elevated bacterial consortium resistance and degradation to DA. This study could deepen understanding of behavior and fate for DA in marine environments.
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Affiliation(s)
- 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, People's Republic of China
| | - Yuan Jin
- Marine Ecology Department, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jingfeng Fan
- Marine Ecology Department, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - 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, People's Republic of China
| | - Chen Gu
- 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, People's Republic of 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, People's Republic of China.
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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Solís-González CJ, Loza-Tavera H. Alicycliphilus: current knowledge and potential for bioremediation of xenobiotics. J Appl Microbiol 2019; 126:1643-1656. [PMID: 30661281 DOI: 10.1111/jam.14207] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/28/2018] [Accepted: 01/15/2019] [Indexed: 01/31/2023]
Abstract
Alicycliphilus is a promising candidate for participating in the development of novel xenobiotics bioremediation processes. Members of the Alicycliphilus genus are environmental bacteria mostly found in polluted sites such as landfills and contaminated watercourses, and in sewage sludges from wastewater treatment plants. They exhibit a versatile metabolism and the ability to use oxygen, nitrate and chlorate as terminal electron acceptors, which allow them to biodegrade xenobiotics under oxic or anoxic conditions. Pure cultures of Alicycliphilus strains are able to biodegrade some pollutants such as industrial solvents (acetone, cyclohexanol and N-methylpyrrolidone), aromatic hydrocarbons (benzene, toluene and anthracene), as well as polyurethane varnishes and foams, and they can even transform Cr(VI) to Cr(III). In addition, Alicycliphilus has also been identified in bacterial communities involved in wastewater treatment plants for denitrification, and the degradation of emerging pollutants such as triclosan, nonylphenol, N-heterocyclic aromatic compounds (indole and quinoline), and antibiotics (tetracycline and oxytetracycline). This work summarizes the current knowledge on the Alicycliphilus genus, describing its different metabolic characteristics, focusing on its xenobiotic biodegradation abilities and examining the distinct pathways and molecular bases that sustain them. We also discuss the progress made in genetic manipulation and 'omics' analyses, as well as Alicycliphilus participation in novel bioremediation strategies.
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Affiliation(s)
- C J Solís-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - H Loza-Tavera
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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The use of marine-derived fungi for preparation of enantiomerically pure alcohols. Appl Microbiol Biotechnol 2017; 102:1317-1330. [DOI: 10.1007/s00253-017-8707-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/27/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
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Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment. ISME JOURNAL 2016; 10:1967-83. [PMID: 26872041 DOI: 10.1038/ismej.2015.255] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/30/2015] [Accepted: 12/04/2015] [Indexed: 02/03/2023]
Abstract
Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative 'omics' approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available.
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Abstract
Water is omnipresent and unreactive. How to speed up water addition and even make it selective are highlighted in this perspective.
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Affiliation(s)
- Verena Resch
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
| | - Ulf Hanefeld
- Gebouw voor Scheikunde
- Biokatalyse
- Afdeling Biotechnologie
- Technische Universiteit Delft
- 2628BL Delft
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Anoxic androgen degradation by the denitrifying bacterium Sterolibacterium denitrificans via the 2,3-seco pathway. Appl Environ Microbiol 2014; 80:3442-52. [PMID: 24657867 DOI: 10.1128/aem.03880-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biodegradation of steroids is a crucial biochemical process mediated exclusively by bacteria. So far, information concerning the anoxic catabolic pathways of androgens is largely unknown, which has prevented many environmental investigations. In this work, we show that Sterolibacterium denitrificans DSMZ 13999 can anaerobically mineralize testosterone and some C19 androgens. By using a (13)C-metabolomics approach and monitoring the sequential appearance of the intermediates, we demonstrated that S. denitrificans uses the 2,3-seco pathway to degrade testosterone under anoxic conditions. Furthermore, based on the identification of a C17 intermediate, we propose that the A-ring cleavage may be followed by the removal of a C2 side chain at C-5 of 17-hydroxy-1-oxo-2,3-seco-androstan-3-oic acid (the A-ring cleavage product) via retro-aldol reaction. The androgenic activities of the bacterial culture and the identified intermediates were assessed using the lacZ-based yeast androgen assay. The androgenic activity in the testosterone-grown S. denitrificans culture decreased significantly over time, indicating its ability to eliminate androgens. The A-ring cleavage intermediate (≤ 500 μM) did not exhibit androgenic activity, whereas the sterane-containing intermediates did. So far, only two androgen-degrading anaerobes (Sterolibacterium denitrificans DSMZ 13999 [a betaproteobacterium] and Steroidobacter denitrificans DSMZ 18526 [a gammaproteobacterium]) have been isolated and characterized, and both of them use the 2,3-seco pathway to anaerobically degrade androgens. The key intermediate 2,3-seco-androstan-3-oic acid can be used as a signature intermediate for culture-independent environmental investigations of anaerobic degradation of C19 androgens.
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Resch V, Jin J, Chen BS, Hanefeld U. Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase? AMB Express 2014; 4:30. [PMID: 24949265 PMCID: PMC4052635 DOI: 10.1186/s13568-014-0030-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
The Michael hydratase – alcohol dehydrogenase (MhyADH) from Alicycliphilus denitrificans was previously identified as a bi-functional enzyme performing a hydration of α,β-unsaturated ketones and subsequent oxidation of the formed alcohols. The investigations of the bi-functionality were based on a spectrophotometric assay and an activity staining in a native gel of the dehydrogenase. New insights in the recently discovered organocatalytic Michael addition of water led to the conclusion that the previously performed experiments to identify MhyADH as a bi-functional enzyme and their results need to be reconsidered and the reliability of the methodology used needs to be critically evaluated.
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Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SAB, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AAM, Gerritse J, van Berkel WJH, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJM. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.). PLoS One 2013; 8:e66971. [PMID: 23825601 PMCID: PMC3692508 DOI: 10.1371/journal.pone.0066971] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/14/2013] [Indexed: 12/04/2022] Open
Abstract
The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.
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Affiliation(s)
| | - Teun Veuskens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Hajnalka E. Daligault
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - David C. Bruce
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Roxanne Tapia
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Cliff S. Han
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Miriam L. Land
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Loren J. Hauser
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | | | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholz Centre for Infection Research, Braunschweig, Germany
| | - Howard Junca
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Bogotá, Colombia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Gosse Schraa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- * E-mail:
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Wang PH, Leu YL, Ismail W, Tang SL, Tsai CY, Chen HJ, Kao AT, Chiang YR. Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans. J Lipid Res 2013; 54:1493-504. [PMID: 23458847 DOI: 10.1194/jlr.m034223] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aerobic degradation of steroids by bacteria has been studied in some detail. In contrast, only little is known about the anaerobic steroid catabolism. Steroidobacter denitrificans can utilize testosterone under both oxic and anoxic conditions. By conducting metabolomic investigations, we demonstrated that S. denitrificans adopts the 9,10-seco-pathway to degrade testosterone under oxic conditions. This pathway depends on the use of oxygenases for oxygenolytic ring fission. Conversely, the detected degradation intermediates under anoxic conditions suggest a novel, oxygenase-independent testosterone catabolic pathway, the 2,3-seco-pathway, which differs significantly from the aerobic route. In this anaerobic pathway, testosterone is first transformed to 1-dehydrotestosterone, which is then reduced to produce 1-testosterone followed by water addition to the C-1/C-2 double bond of 1-testosterone. Subsequently, the C-1 hydroxyl group is oxidized to produce 17-hydroxy-androstan-1,3-dione. The A-ring of this compound is cleaved by hydrolysis as evidenced by H2(18)O-incorporation experiments. Regardless of the growth conditions, testosterone is initially transformed to 1-dehydrotestosterone. This intermediate is a divergence point at which the downstream degradation pathway is governed by oxygen availability. Our results shed light into the previously unknown cleavage of the sterane ring structure without oxygen. We show that, under anoxic conditions, the microbial cleavage of steroidal core ring system begins at the A-ring.
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Affiliation(s)
- Po-Hsiang Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Wuensch C, Gross J, Steinkellner G, Gruber K, Glueck SM, Faber K. Asymmetric enzymatic hydration of hydroxystyrene derivatives. Angew Chem Int Ed Engl 2013; 52:2293-7. [PMID: 23335002 DOI: 10.1002/anie.201207916] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/10/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Christiane Wuensch
- ACIB GmbH c/o Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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Wuensch C, Gross J, Steinkellner G, Gruber K, Glueck SM, Faber K. Asymmetric Enzymatic Hydration of Hydroxystyrene Derivatives. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207916] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Chen BS, Hanefeld U. Enantioselective preparation of (R) and (S)-3-hydroxycyclopentanone by kinetic resolution. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Alicycliphilus denitrificans strain BC and A. denitrificans strain K601(T) degrade cyclic hydrocarbons. These strains have been isolated from a mixture of wastewater treatment plant material and benzene-polluted soil and from a wastewater treatment plant, respectively, suggesting their role in bioremediation of soil and water. Although the strains are phylogenetically closely related, there are some clear physiological differences. The hydrocarbon cyclohexanol, for example, can be degraded by strain K601(T) but not by strain BC. Furthermore, both strains can use nitrate and oxygen as an electron acceptor, but only strain BC can use chlorate as electron acceptor. To better understand the nitrate and chlorate reduction mechanisms coupled to the oxidation of cyclic compounds, the genomes of A. denitrificans strains BC and K601(T) were sequenced. Here, we report the complete genome sequences of A. denitrificans strains BC and K601(T).
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Jin J, Hanefeld U. The selective addition of water to CC bonds; enzymes are the best chemists. Chem Commun (Camb) 2011; 47:2502-10. [DOI: 10.1039/c0cc04153j] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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