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Gao X, Wu M, Zhang W, Li C, Guo RT, Dai Y, Liu W, Mao S, Lu F, Qin HM. Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11616-11625. [PMID: 34553918 DOI: 10.1021/acs.jafc.1c04091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Salicylic acid (SA) decarboxylase from Trichosporon moniliiforme (TmSdc), which reversibly catalyses the decarboxylation of SA to yield phenol, is of significant interest because of its potential for the production of benzoic acid derivatives under environmentally friendly reaction conditions. TmSdc showed a preference for C2 hydroxybenzoate derivatives, with kcat/Km of SA being 3.2 × 103 M-1 s-1. Here, we presented the first crystal structures of TmSdc, including a complex with SA. The three conserved residues of Glu8, His169, and Asp298 are the catalytic residues within the TIM-barrel domain of TmSdc. Trp239 forms a unique hydrophobic recognition site by interacting with the phenyl ring of SA, while Arg235 is responsible for recognizing the hydroxyl group at the C2 of SA via hydrogen bond interactions. Using a semi-rational combinatorial active-site saturation test, we obtained the TmSdc mutant MT3 (Y64T/P191G/F195V/E302D), which exhibited a 26.4-fold increase in kcat/Km with SA, reaching 8.4 × 104 M-1 s-1. Steered molecular dynamics simulations suggested that the structural changes in MT3 relieved the steric hindrance within the substrate access channel and enlarged the substrate-binding pocket, leading to the increased activity by improving substrate access. Our data elucidate the unique substrate recognition mode and the substrate entrance tunnel of SA decarboxylase.
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Affiliation(s)
- Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Mian Wu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, P. R. China
| | - Yujie Dai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
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Tomei MC, Mosca Angelucci D, Clagnan E, Brusetti L. Anaerobic biodegradation of phenol in wastewater treatment: achievements and limits. Appl Microbiol Biotechnol 2021; 105:2195-2224. [PMID: 33630152 DOI: 10.1007/s00253-021-11182-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 11/30/2022]
Abstract
Anaerobic biodegradation of toxic compounds found in industrial wastewater is an attractive solution allowing the recovery of energy and resources but it is still challenging due to the low kinetics making the anaerobic process not competitive against the aerobic one. In this review, we summarise the present state of knowledge on the anaerobic biodegradation process for phenol, a typical target compound employed in toxicity studies on industrial wastewater treatment. The objective of this article is to provide an overview on the microbiological and technological aspects of anaerobic phenol degradation and on the research needs to fill the gaps still hindering the diffusion of the anaerobic process. The first part is focused on the microbiology and extensively presents and characterises phenol-degrading bacteria and biodegradation pathways. In the second part, dedicated to process feasibility, anaerobic and aerobic biodegradation kinetics are analysed and compared, and strategies to enhance process performance, i.e. advanced technologies, bioaugmentation, and biostimulation, are critically analysed and discussed. The final section provides a summary of the research needs. Literature data analysis shows the feasibility of anaerobic phenol biodegradation at laboratory and pilot scale, but there is still a consistent gap between achieved aerobic and anaerobic performance. This is why current research demand is mainly related to the development and optimisation of powerful technologies and effective operation strategies able to enhance the competitiveness of the anaerobic process. Research efforts are strongly justified because the anaerobic process is a step forward to a more sustainable approach in wastewater treatment.Key points• Review of phenol-degraders bacteria and biodegradation pathways.• Anaerobic phenol biodegradation kinetics for metabolic and co-metabolic processes.• Microbial and technological strategies to enhance process performance.
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Affiliation(s)
- M Concetta Tomei
- Water Research Institute, C.N.R., Via Salaria km 29.300, CP 10, 00015, Monterotondo Stazione Rome, Italy.
| | - Domenica Mosca Angelucci
- Water Research Institute, C.N.R., Via Salaria km 29.300, CP 10, 00015, Monterotondo Stazione Rome, Italy
| | - Elisa Clagnan
- Ricicla Group - DiSAA, University of Milan, Via Celoria 2, 20133, Milano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen - Bolzano, Piazza Università 5, 39100, Bolzano, Italy
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Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
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Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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Meier AK, Worch S, Böer E, Hartmann A, Mascher M, Marzec M, Scholz U, Riechen J, Baronian K, Schauer F, Bode R, Kunze G. Agdc1p - a Gallic Acid Decarboxylase Involved in the Degradation of Tannic Acid in the Yeast Blastobotrys (Arxula) adeninivorans. Front Microbiol 2017; 8:1777. [PMID: 28966611 PMCID: PMC5605622 DOI: 10.3389/fmicb.2017.01777] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/31/2017] [Indexed: 11/23/2022] Open
Abstract
Tannins and hydroxylated aromatic acids, such as gallic acid (3,4,5-trihydroxybenzoic acid), are plant secondary metabolites which protect plants against herbivores and plant-associated microorganisms. Some microbes, such as the yeast Arxula adeninivorans are resistant to these antimicrobial substances and are able to use tannins and gallic acid as carbon sources. In this study, the Arxula gallic acid decarboxylase (Agdc1p) which degrades gallic acid to pyrogallol was characterized and its function in tannin catabolism analyzed. The enzyme has a higher affinity for gallic acid (Km -0.7 ± 0.2 mM, kcat -42.0 ± 8.2 s-1) than to protocatechuic acid (3,4-dihydroxybenzoic acid) (Km -3.2 ± 0.2 mM, kcat -44.0 ± 3.2 s-1). Other hydroxylated aromatic acids, such as 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 2,4-dihydroxybenzoic acid and 2,5-dihydroxybenzoic acid are not gallic acid decarboxylase substrates. A. adeninivorans G1212/YRC102-AYNI1-AGDC1, which expresses the AGDC1 gene under the control of the strong nitrate inducible AYNI1 promoter achieved a maximum gallic acid decarboxylase activity of 1064.4 U/l and 97.5 U/g of dry cell weight in yeast grown in minimal medium with nitrate as nitrogen source and glucose as carbon source. In the same medium, gallic acid decarboxylase activity was not detected for the control strain G1212/YRC102 with AGDC1 expression under the control of the endogenous promoter. Gene expression analysis showed that AGDC1 is induced by gallic acid and protocatechuic acid. In contrast to G1212/YRC102-AYNI1-AGDC1 and G1212/YRC102, A. adeninivorans G1234 [Δagdc1] is not able to grow on medium with gallic acid as carbon source but can grow in presence of protocatechuic acid. This confirms that Agdc1p plays an essential role in the tannic acid catabolism and could be useful in the production of catechol and cis,cis-muconic acid. However, the protocatechuic acid catabolism via Agdc1p to catechol seems to be not the only degradation pathway.
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Affiliation(s)
- Anna K. Meier
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Sebastian Worch
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Erik Böer
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Marek Marzec
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Jan Riechen
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Kim Baronian
- Department of Microbiology, School of Biological Sciences, University of CanterburyChristchurch, New Zealand
| | - Frieder Schauer
- Institute of Microbiology, University of GreifswaldGreifswald, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of GreifswaldGreifswald, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
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Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
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Aparicio-Ruiz R, García-González DL, Oliver-Pozo C, Tena N, Morales MT, Aparicio R. Phenolic profile of virgin olive oils with and without sensory defects: Oils with non-oxidative defects exhibit a considerable concentration of phenols. EUR J LIPID SCI TECH 2015. [DOI: 10.1002/ejlt.201400337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | | | - Celia Oliver-Pozo
- Instituto De La Grasa (CSIC); Campus Universidad Pablo de Olavide; Sevilla Spain
| | - Noelia Tena
- Instituto De La Grasa (CSIC); Campus Universidad Pablo de Olavide; Sevilla Spain
| | - María T. Morales
- Department of Analytical Chemistry; Universidad De Sevilla; Sevilla Spain
| | - Ramón Aparicio
- Instituto De La Grasa (CSIC); Campus Universidad Pablo de Olavide; Sevilla Spain
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Sietmann R, Uebe R, Böer E, Bode R, Kunze G, Schauer F. Novel metabolic routes during the oxidation of hydroxylated aromatic acids by the yeast Arxula adeninivorans. J Appl Microbiol 2009; 108:789-799. [PMID: 19702859 DOI: 10.1111/j.1365-2672.2009.04474.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To complete our study on tannin degradation via gallic acid by the biotechnologically interesting yeast Arxula adeninivorans as well as to characterize new degradation pathways of hydroxylated aromatic acids. METHODS AND RESULTS With glucose-grown cells of A. adeninivorans, transformation experiments with hydroxylated derivatives of benzoic acid were carried out. The 12 metabolites were analysed and identified by high performance liquid chromatography and GC/MS. The yeast is able to transform the derivatives by oxidative and nonoxidative decarboxylation as well as by methoxylation. The products of nonoxidative decarboxylation of protocatechuate and gallic acid are substrates for further ring fission. CONCLUSION Whereas other organisms use only one route of transformation, A. adeninivorans is able to carry out three different pathways (oxidative, nonoxidative decarboxylation and methoxylation) on one hydroxylated aromatic acid. The determination of the KM-values for protocatechuate and gallic acid in crude extracts of cells of A. adeninivorans cultivated with protocatechuate and gallic acid, respectively, suggests that the decarboxylation of protocatechuate and gallic acid may be catalysed by the same enzyme. SIGNIFICANCE AND IMPACT OF THE STUDY This transformation pathway of protocatechuate and gallic acid via nonoxidative decarboxylation up to ring fission is novel and has not been described so far. This is also the first report of nonoxidative decarboxylation of gallic acid by a eukaryotic micro-organism.
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Affiliation(s)
- R Sietmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - R Uebe
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - E Böer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - R Bode
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
| | - G Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - F Schauer
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
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