1
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Santema LL, Rotilio L, Xiang R, Tjallinks G, Guallar V, Mattevi A, Fraaije MW. Discovery and biochemical characterization of thermostable glycerol oxidases. Appl Microbiol Biotechnol 2024; 108:61. [PMID: 38183484 PMCID: PMC10771423 DOI: 10.1007/s00253-023-12883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 01/08/2024]
Abstract
Alditol oxidases are promising tools for the biocatalytic oxidation of glycerol to more valuable chemicals. By integrating in silico bioprospecting with cell-free protein synthesis and activity screening, an effective pipeline was developed to rapidly identify enzymes that are active on glycerol. Three thermostable alditol oxidases from Actinobacteria Bacterium, Streptomyces thermoviolaceus, and Thermostaphylospora chromogena active on glycerol were discovered. The characterization of these three flavoenzymes demonstrated their glycerol oxidation activities, preference for alkaline conditions, and excellent thermostabilities with melting temperatures higher than 75 °C. Structural elucidation of the alditol oxidase from Actinobacteria Bacterium highlighted a constellation of side chains that engage the substrate through several hydrogen bonds, a histidine residue covalently bound to the FAD prosthetic group, and a tunnel leading to the active site. Upon computational simulations of substrate binding, a double mutant targeting a residue pair at the tunnel entrance was created and found to display an improved thermal stability and catalytic efficiency for glycerol oxidation. The hereby described alditol oxidases form a valuable panel of oxidative biocatalysts that can perform regioselective oxidation of glycerol and other polyols. KEY POINTS: • Rapid pipeline designed to identify putative oxidases • Biochemical and structural characterization of alditol oxidases • Glycerol oxidation to more valuable derivatives.
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Affiliation(s)
- Lars L Santema
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Laura Rotilio
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08034, Spain
| | - Gwen Tjallinks
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08034, Spain.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
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2
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Allaert Y, Leyder A, Franceus J, Desmet T. Strategies for the synthesis of the osmolyte glucosylglycerate and its precursor glycerate. Appl Microbiol Biotechnol 2024; 108:297. [PMID: 38607564 PMCID: PMC11009771 DOI: 10.1007/s00253-024-13139-w] [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: 02/20/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Glycosidic osmolytes are widespread natural compounds that protect microorganisms and their macromolecules from the deleterious effects of various environmental stresses. Their protective properties have attracted considerable interest for industrial applications, especially as active ingredients in cosmetics and healthcare products. In that regard, the osmolyte glucosylglycerate is somewhat overlooked. Glucosylglycerate is typically accumulated by certain organisms when they are exposed to high salinity and nitrogen starvation, and its potent stabilizing effects have been demonstrated in vitro. However, the applications of this osmolyte have not been thoroughly explored due to the lack of a cost-efficient production process. Here, we present an overview of the progress that has been made in developing promising strategies for the synthesis of glucosylglycerate and its precursor glycerate, and discuss the remaining challenges. KEY POINTS: • Bacterial milking could be explored for fermentative production of glucosylglycerate • Glycoside phosphorylases of GH13_18 represent attractive alternatives for biocatalytic production • Conversion of glycerol with alditol oxidase is a promising strategy for generating the precursor glycerate.
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Affiliation(s)
- Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Arthur Leyder
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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3
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Guo Y, Alvigini L, Trajkovic M, Alonso-Cotchico L, Monza E, Savino S, Marić I, Mattevi A, Fraaije MW. Structure- and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound. Nat Commun 2022; 13:7195. [PMID: 36418310 PMCID: PMC9684555 DOI: 10.1038/s41467-022-34912-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022] Open
Abstract
Various 4-alkylphenols can be easily obtained through reductive catalytic fractionation of lignocellulosic biomass. Selective dehydrogenation of 4-n-propylguaiacol results in the formation of isoeugenol, a valuable flavor and fragrance molecule and versatile precursor compound. Here we present the engineering of a bacterial eugenol oxidase to catalyze this reaction. Five mutations, identified from computational predictions, are first introduced to render the enzyme more thermostable. Other mutations are then added and analyzed to enhance chemoselectivity and activity. Structural insight demonstrates that the slow catalytic activity of an otherwise promising enzyme variant is due the formation of a slowly-decaying covalent substrate-flavin cofactor adduct that can be remedied by targeted residue changes. The final engineered variant comprises eight mutations, is thermostable, displays good activity and acts as a highly chemoselective 4-n-propylguaiacol oxidase. We lastly use our engineered biocatalyst in an illustrative preparative reaction at gram-scale. Our findings show that a natural enzyme can be redesigned into a tailored biocatalyst capable of valorizing lignin-based monophenols.
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Affiliation(s)
- Yiming Guo
- grid.4830.f0000 0004 0407 1981Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Laura Alvigini
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Milos Trajkovic
- grid.4830.f0000 0004 0407 1981Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | | | | | - Simone Savino
- grid.4830.f0000 0004 0407 1981Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Ivana Marić
- grid.4830.f0000 0004 0407 1981Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Andrea Mattevi
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Marco W. Fraaije
- grid.4830.f0000 0004 0407 1981Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
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4
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Lima LMS, Okamoto DN, Passarini MRZ, Gonçalves SS, Goldman GH, Silveira MAV, Ramos PL, Cruz JB, Juliano M, Marcondes MFM, Vasconcellos SP. Enzymatic diversity of filamentous fungi isolated from forest soil incremented by sugar cane solid waste. ENVIRONMENTAL TECHNOLOGY 2022; 43:3037-3046. [PMID: 33826477 DOI: 10.1080/09593330.2021.1914179] [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: 08/06/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Fungi are natural degraders of organic matter which can produce enzymes for many industrial and biotechnological applications. In this context, crude enzymatic extracts of fungal isolates were evaluated regarding their hydrolytic and ligninolytic abilities. The fungal strains were isolated from soil samples from Atlantic Rain Forest Park incremented with sugar cane biomass (filter cake), which allowed the selection of efficient lignocellulolytic enzymes. A total of 190 fungi were isolated and evaluated by endocellulase screenings. Thirteen fungi were selected about their hydrolytic and ligninolytic abilities. Among them, three isolates showed xylanolytic activity. Eleven of the isolates were selected by their cellulolytic abilities. Proteolytic enzymes were also detected for three fungi, allowing the classification as metalloprotease and serine protease. The isolates SPZPF3_47 (Mucor sp.), SPZPF1_129 (Byssochlamys nivea) and SPZPF1_141 (Paecilomyces saturatus) were selected for further investigation on their lignin peroxidase abilities. KM, Vmax and kcat apparent for lignin peroxidases were also determined. The strain of Mucor sp. (SPZPF3_47) was highlighted since this fungal genus was not well described about its isolation in the adopted conditions in our study, and showing ligninolytic abilities.
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Affiliation(s)
- Lidiane M S Lima
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Debora N Okamoto
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michel R Z Passarini
- Latin American Institute of Life and Natural Sciences, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Brazil
| | - Sarah S Gonçalves
- Health Science Center, Universidade Federal do Espírito Santo, Espírito Santo, Brazil
| | - Gustavo H Goldman
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Marghuel A V Silveira
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - João B Cruz
- São Paulo Zoo Park Foundation, São Paulo, Brazil
| | - Maria Juliano
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo F M Marcondes
- Department of Biophysics, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Suzan P Vasconcellos
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Universidade Federal de São Paulo, São Paulo, Brazil
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5
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Wang Z, Li X, Li Z. Engineering of cascade reactions and alditol oxidase for high‐yielding synthesis of (R)‐phenylethanolamine from styrene, ʟ‐phenylalanine, glycerol or glucose. ChemCatChem 2022. [DOI: 10.1002/cctc.202200418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zilong Wang
- National University of Singapore Department of Chemical and Biomolecular Engineering SINGAPORE
| | - Xirui Li
- National University of Singapore Department of Chemical and Biomolecular Engineering SINGAPORE
| | - Zhi Li
- National University of Singapore Department of Chemical and Biomolecular Engineering 4 Engineering Drive 4, #03-03 117576 Singapore SINGAPORE
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6
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Chen Z, Fei K, Hu Y, Xu X, Gao XD, Li Z. Identification of a Novel Alditol Oxidase from Thermopolyspora flexuosa with Potential Application in D-Glyceric Acid Production. Mol Biotechnol 2022; 64:804-813. [PMID: 35129810 DOI: 10.1007/s12033-022-00459-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
Abstract
Glycerol is a potential sustainable feedstock, and biorefining processes to convert glycerol into value-added chemicals have been developed over the past decade. Alditol oxidase (AldO) is capable of selectively oxidizing the primary hydroxyl groups of alditols such as glycerol. In this study, a new FAD-binding protein from Thermopolyspora flexuosa was expressed and identified as a novel alditol oxidase (AldOT. fle). AldOT. fle displayed the optimal activity at pH 8.0 and 25 °C. AldOT. fle was not metal-dependent, but the activity was completely inhibited by Fe3+. AldOT. fle had a wide substrate specificity and high catalytic efficiency for glycerol. Furthermore, the recombinant AldOT. fle could produce D-glyceric acid from glycerol with a conversion rate ranging from 86.6% (5 mM glycerol) to 20.5% (500 mM glycerol). The recombinant E. coli with AldOT. fle could also produce 23.8 mM D-glyceric acid from 100 mM glycerol. The recombinant AldOT. fle had the potential to produce other aldehyde products by selectively oxidizing the hydroxyl groups of alditols and many other commodity chemicals by redesigning glycerol metabolism.
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Affiliation(s)
- Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Kangqing Fei
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yangfan Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiangyang Xu
- Zaozhuang Jienuo Enzyme Co., Ltd, Zaozhuang, 277100, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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7
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Biochemical synthesis of the medicinal sugar l-gulose using fungal alditol oxidase. Biochem Biophys Res Commun 2021; 575:85-89. [PMID: 34461440 DOI: 10.1016/j.bbrc.2021.08.061] [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: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/23/2022]
Abstract
Some rare sugars can be potently medicinal, such as l-gulose. In this study, we present a novel alditol oxidase (fAldOx) from the soil fungus Penicillium sp. KU-1, and its application for the effective production of l-gulose. To the best of our knowledge, this is the first report of a successful direct conversion of d-sorbitol to l-gulose. We further purified it to homogeneity with a ∼108-fold purification and an overall yield of 3.26%, and also determined the effectors of fAldOx. The enzyme possessed broad substrate specificity for alditols such as erythritol (kcat/KM, 355 m-1 s-1), thus implying that the effective production of multiple rare sugars for medicinal applications may be possible.
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8
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Zhou Y, Wu S, Bornscheuer UT. Recent advances in (chemo)enzymatic cascades for upgrading bio-based resources. Chem Commun (Camb) 2021; 57:10661-10674. [PMID: 34585190 DOI: 10.1039/d1cc04243b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Developing (chemo)enzymatic cascades is very attractive for green synthesis, because they streamline multistep synthetic processes. In this Feature Article, we have summarized the recent advances in in vitro or whole-cell cascade reactions with a focus on the use of renewable bio-based resources as starting materials. This includes the synthesis of rare sugars (such as ketoses, L-ribulose, D-tagatose, myo-inositol or aminosugars) from readily available carbohydrate sources (cellulose, hemi-cellulose, starch), in vitro enzyme pathways to convert glucose to various biochemicals, cascades to convert 5-hydroxymethylfurfural and furfural obtained from lignin or xylose into novel precursors for polymer synthesis, the syntheses of phenolic compounds, cascade syntheses of aliphatic and highly reduced chemicals from plant oils and fatty acids, upgrading of glycerol or ethanol as well as cascades to transform natural L-amino acids into high-value (chiral) compounds. In several examples these processes have demonstrated their efficiency with respect to high space-time yields and low E-factors enabling mature green chemistry processes. Also, the strengths and limitations are discussed and an outlook is provided for improving the existing and developing new cascades.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China.
| | - Shuke Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China. .,Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
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9
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Zhang C, Chen Q, Fan F, Tang J, Zhan T, Wang H, Zhang X. Directed evolution of alditol oxidase for the production of optically pure D-glycerate from glycerol in the engineered Escherichia coli. J Ind Microbiol Biotechnol 2021; 48:6312499. [PMID: 34196357 PMCID: PMC8788829 DOI: 10.1093/jimb/kuab041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022]
Abstract
D-glycerate is an attractive chemical for a wide variety of pharmaceutical, cosmetic, biodegradable polymers, and other applications. Now several studies have been reported about the synthesis of glycerate by different biotechnological and chemical routes from glycerol or other feedstock. Here, we present the construction of an Escherichia coli engineered strain to produce optically pure D-glycerate by oxidizing glycerol with an evolved variant of alditol oxidase (AldO) from Streptomyces coelicolor. This is achieved by starting from a previously reported variant mAldO and employing three rounds of directed evolution, as well as the combination of growth-coupled high throughput selection with colorimetric screening. The variant eAldO3-24 displays a higher substrate affinity toward glycerol with 5.23-fold than the wild-type AldO, and a 1.85-fold increase of catalytic efficiency (kcat/KM). Then we introduced an isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible T7 expression system in E. coli to overexpress the variant eAldO3-24, and deleted glucosylglycerate phosphorylase encoding gene ycjM to block the consumption of D-glycerate. Finally, the resulting strain TZ-170 produced 30.1 g/l D-glycerate at 70 h with a yield of 0.376 mol/mol in 5-l fed-batch fermentation.
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Affiliation(s)
- Chao Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China.,College of Chemistry and Life Science, Changchun University of Technology, Jilin, Changchun 130012, China
| | - Qian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Feiyu Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Jinlei Tang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Tao Zhan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Honglei Wang
- College of Chemistry and Life Science, Changchun University of Technology, Jilin, Changchun 130012, China
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
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10
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Lukito BR, Wang Z, Sundara Sekar B, Li Z. Production of (R)-mandelic acid from styrene, L-phenylalanine, glycerol, or glucose via cascade biotransformations. BIORESOUR BIOPROCESS 2021; 8:22. [PMID: 38650227 PMCID: PMC10992357 DOI: 10.1186/s40643-021-00374-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
(R)-mandelic acid is an industrially important chemical, especially used for producing antibiotics. Its chemical synthesis often uses highly toxic cyanide to produce its racemic form, followed by kinetic resolution with 50% maximum yield. Here we report a green and sustainable biocatalytic method for producing (R)-mandelic acid from easily available styrene, biobased L-phenylalanine, and renewable feedstocks such as glycerol and glucose, respectively. An epoxidation-hydrolysis-double oxidation artificial enzyme cascade was developed to produce (R)-mandelic acid at 1.52 g/L from styrene with > 99% ee. Incorporation of deamination and decarboxylation into the above cascade enables direct conversion of L-phenylalanine to (R)-mandelic acid at 913 mg/L and > 99% ee. Expressing the five-enzyme cascade in an L-phenylalanine-overproducing E. coli NST74 strain led to the direct synthesis of (R)-mandelic acid from glycerol or glucose, affording 228 or 152 mg/L product via fermentation. Moreover, coupling of E. coli cells expressing L-phenylalanine biosynthesis pathway with E. coli cells expressing the artificial enzyme cascade enabled the production of 760 or 455 mg/L (R)-mandelic acid from glycerol or glucose. These simple, safe, and green methods show great potential in producing (R)-mandelic acid from renewable feedstocks.
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Affiliation(s)
- Benedict Ryan Lukito
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Zilong Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Balaji Sundara Sekar
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore.
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.
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11
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Abstract
Glycerol is a readily available and inexpensive substance that is mostly generated during biofuel production processes. In order to ensure the viability of the biofuel industry, it is essential to develop complementing technologies for the resource utilization of glycerol. Ethylene glycol is a two-carbon organic chemical with multiple applications and a huge market. In this study, an artificial enzymatic cascade comprised alditol oxidase, catalase, glyoxylate/hydroxypyruvate reductase, pyruvate decarboxylase and lactaldehyde:propanediol oxidoreductase was developed for the production of ethylene glycol from glycerol. The reduced nicotinamide adenine dinucleotide (NADH) generated during the dehydrogenation of the glycerol oxidation product d-glycerate can be as the reductant to support the ethylene glycol production. Using this in vitro synthetic system with self-sufficient NADH recycling, 7.64 ± 0.15 mM ethylene glycol was produced from 10 mM glycerol in 10 h, with a high yield of 0.515 ± 0.1 g/g. The in vitro enzymatic cascade is not only a promising alternative for the generation of ethylene glycol but also a successful example of the value-added utilization of glycerol.
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12
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Savino S, Fraaije MW. The vast repertoire of carbohydrate oxidases: An overview. Biotechnol Adv 2020; 51:107634. [PMID: 32961251 DOI: 10.1016/j.biotechadv.2020.107634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/06/2020] [Indexed: 01/01/2023]
Abstract
Carbohydrates are widely abundant molecules present in a variety of forms. For their biosynthesis and modification, nature has evolved a plethora of carbohydrate-acting enzymes. Many of these enzymes are of particular interest for biotechnological applications, where they can be used as biocatalysts or biosensors. Among the enzymes catalysing conversions of carbohydrates are the carbohydrate oxidases. These oxidative enzymes belong to different structural families and use different cofactors to perform the oxidation reaction of CH-OH bonds in carbohydrates. The variety of carbohydrate oxidases available in nature reflects their specificity towards different sugars and selectivity of the oxidation site. Thanks to their properties, carbohydrate oxidases have received a lot of attention in basic and applied research, such that nowadays their role in biotechnological processes is of paramount importance. In this review we provide an overview of the available knowledge concerning the known carbohydrate oxidases. The oxidases are first classified according to their structural features. After a description on their mechanism of action, substrate acceptance and characterisation, we report on the engineering of the different carbohydrate oxidases to enhance their employment in biocatalysis and biotechnology. In the last part of the review we highlight some practical applications for which such enzymes have been exploited.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands.
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13
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Jiang Y, Li Z, Zheng S, Xu H, Zhou YJ, Gao Z, Meng C, Li S. Establishing an enzyme cascade for one-pot production of α-olefins from low-cost triglycerides and oils without exogenous H 2O 2 addition. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:52. [PMID: 32190117 PMCID: PMC7075034 DOI: 10.1186/s13068-020-01684-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/21/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biological α-olefins can be used as both biofuels and high value-added chemical precursors to lubricants, polymers, and detergents. The prototypic CYP152 peroxygenase family member OleTJE from Jeotgalicoccus sp. ATCC 8456 catalyzes a single-step decarboxylation of free fatty acids (FFAs) to form α-olefins using H2O2 as a cofactor, thus attracting much attention since its discovery. To improve the productivity of α-olefins, significant efforts on protein engineering, electron donor engineering, and metabolic engineering of OleTJE have been made. However, little success has been achieved in obtaining α-olefin high-producer microorganisms due to multiple reasons such as the tight regulation of FFA biosynthesis, the difficulty of manipulating multi-enzyme metabolic network, and the poor catalytic performance of OleTJE. RESULTS In this study, a novel enzyme cascade was developed for one-pot production of α-olefins from low-cost triacylglycerols (TAGs) and natural oils without exogenous H2O2 addition. This artificial biocatalytic route consists of a lipase (CRL, AOL or Lip2) for TAG hydrolysis to produce glycerol and free fatty acids (FFAs), an alditol oxidase (AldO) for H2O2 generation upon glycerol oxidation, and the P450 fatty acid decarboxylase OleTJE for FFA decarboxylation using H2O2 generated in situ. The multi-enzyme system was systematically optimized leading to the production of α-olefins with the conversion rates ranging from 37.2 to 68.5%. Furthermore, a reaction using lyophilized CRL/OleTJE/AldO enzymes at an optimized ratio (5 U/6 μM/30 μM) gave a promising α-olefin yield of 0.53 g/L from 1500 μM (~1 g/L) coconut oil. CONCLUSIONS The one-pot enzyme cascade was successfully established and applied to prepare high value-added α-olefins from low-cost and renewable TAGs/natural oils. This system is independent of exogenous addition of H2O2, thus not only circumventing the detrimental effect of H2O2 on the stability and activity of involved enzymes, but also lower the overall costs on the TAG-to-olefin transformation. It is anticipated that this biotransformation system will become industrially relevant in the future upon more engineering efforts based on this proof-of-concept work.
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Affiliation(s)
- Yuanyuan Jiang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Huifang Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 Liaoning China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Chunxiao Meng
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 Shandong China
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14
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Martinho V, dos Santos Lima LM, Barros CA, Ferrari VB, Passarini MRZ, Santos LA, de Souza Sebastianes FL, Lacava PT, de Vasconcellos SP. Enzymatic potential and biosurfactant production by endophytic fungi from mangrove forest in Southeastern Brazil. AMB Express 2019; 9:130. [PMID: 31428885 PMCID: PMC6702500 DOI: 10.1186/s13568-019-0850-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/02/2019] [Indexed: 11/17/2022] Open
Abstract
Microbial activity is the main route for cycling mangrove nutrients. In general, microorganisms have abilities to degrade lignocellulosic compounds. Among the biotechnological potential of the microbiota from mangroves, it is noteworthy about endophytic fungi, which can be considered as effective sources of different bioactive compounds. In this sense, thirty (30) endophytic fungi were isolated from mangrove forest sampling Cananeia, SP, Brazil. These microorganisms were analyzed about their enzymatic activities including: lignin peroxidase EC 1.11.1.14, manganese peroxidase EC 1.11.1.13 and laccase EC 1.10.3.2, as well endo-cellulase EC 3.2.1.4 and endo-xylanase EC 3.2.1.8. Besides that, production of bioactive secondary metabolites like biosurfactant and/or bioemulsifier was also investigated. As results, nineteen (19) isolates were selected about their ligninolytic abilities, nine (9) of them about cellulase activity and thirteen (13) showed xylanase abilities. The fungal isolate named as 3(3), characterized as Fusarium sambucinum, showed a prominent lignin peroxidase (42.4 U L-1) and manganese peroxidase (23.6 U L-1) activities. The isolate 63.1, also related to Fusarium sp. genera, was selected about its laccase activity (41.5 U L-1). From all the investigated fungi, the isolate 47(4) Trichoderma camerunense was selected about its cellulolytic and xylanolytic activities, showing 45.23 and 26.09 U mL-1, respectively. The same fungi also showed biosurfactant ability demonstrated by superficial tension decreasing to 38 mN/m. In addition, fifteen (15) fungi exhibited bioemulsifier activity, with E24 values up to 62.8%.
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Affiliation(s)
- Vivian Martinho
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
| | - Lidiane Maria dos Santos Lima
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
| | - Caroline Almeida Barros
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
| | - Vitor Baptista Ferrari
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
| | - Michel Rodrigo Zambrano Passarini
- Latin American Institute of Life Sciences and Nature, Federal University of Latin American Integration, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR Zip Code 85870-901 Brazil
| | - Leonardo André Santos
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
| | - Fernanda Luisa de Souza Sebastianes
- Laboratory of Microbiology and Biomolecules - LaMiB, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, Via Washington Luís km 235, PO BOX 676, São Carlos, SP 13565‑905 Brazil
| | - Paulo Teixeira Lacava
- Laboratory of Microbiology and Biomolecules - LaMiB, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, Via Washington Luís km 235, PO BOX 676, São Carlos, SP 13565‑905 Brazil
| | - Suzan Pantaroto de Vasconcellos
- Department of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), R. São Nicolau, 210, Diadema, SP Zip Code 09913-030 Brazil
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15
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16
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Fernandes AC, Petersen B, Møller L, Gernaey KV, Krühne U. Caught in-between: System for in-flow inactivation of enzymes as an intermediary step in "plug-and-play" microfluidic platforms. N Biotechnol 2018; 47:39-49. [PMID: 29684658 DOI: 10.1016/j.nbt.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 01/16/2023]
Abstract
The need for fast and comprehensive characterization of biocatalysts has pushed the development of new screening platforms based on microfluidics, capable of monitoring several parameters simultaneously, with new configurations of liquid handling, sample treatment and sensing. Modular microfluidics allows the integration of these newly developed approaches in a more flexible way towards increasing applicability of the microfluidic chips to different types of biocatalysts and reactions. A highly relevant operation in such a system is biocatalyst inactivation, which can enable the precise control of reaction time by avoiding the continuation of the reaction in another module or connecting tubes. Such control is important when different modules of reactors and/or sensing units are used and changed frequently. Here we describe the development, characterization and application of a module for rapid enzyme inactivation. The thermal inactivation platform developed is compared with a standard benchtop ThermoMixer in terms of inactivation efficiency for glucose oxidase and catalase. A higher activity loss was observed for enzyme inactivation under flow conditions (inactivation achieved at 120 s residence time at 338 K and 20 s residence time at 353 K) which indicated a high heat transfer to the fluid under dynamic conditions. Moreover, partial deactivation of the enzymes was observed for the continuous thermal inactivation module, when activity measurements were performed after 1 and 2 days following inactivation. The thermal inactivation unit presented can be easily integrated into modular microfluidic platforms and can be a useful addition for enzyme characterization and screening.
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Affiliation(s)
- Ana C Fernandes
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark.
| | - Benjamin Petersen
- Kemiteknik Workshop, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Lars Møller
- Kemiteknik Workshop, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Krist V Gernaey
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Ulrich Krühne
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
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17
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Biocatalyst Screening with a Twist: Application of Oxygen Sensors Integrated in Microchannels for Screening Whole Cell Biocatalyst Variants. Bioengineering (Basel) 2018; 5:bioengineering5020030. [PMID: 29642515 PMCID: PMC6027248 DOI: 10.3390/bioengineering5020030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022] Open
Abstract
Selective oxidative functionalization of molecules is a highly relevant and often demanding reaction in organic chemistry. The use of biocatalysts allows the stereo- and regioselective introduction of oxygen molecules in organic compounds at milder conditions and avoids the use of complex group-protection schemes and toxic compounds usually applied in conventional organic chemistry. The identification of enzymes with the adequate properties for the target reaction and/or substrate requires better and faster screening strategies. In this manuscript, a microchannel with integrated oxygen sensors was applied to the screening of wild-type and site-directed mutated variants of naphthalene dioxygenase (NDO) from Pseudomonas sp. NICB 9816-4. The oxygen sensors were used to measure the oxygen consumption rate of several variants during the conversion of styrene to 1-phenylethanediol. The oxygen consumption rate allowed the distinguishing of endogenous respiration of the cell host from the oxygen consumed in the reaction. Furthermore, it was possible to identify the higher activity and different reaction rate of two variants, relative to the wild-type NDO. The meander microchannel with integrated oxygen sensors can therefore be used as a simple and fast screening platform for the selection of dioxygenase mutants, in terms of their ability to convert styrene, and potentially in terms of substrate specificity.
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18
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Dourado DFAR, Swart M, Carvalho ATP. Why the Flavin Adenine Dinucleotide (FAD) Cofactor Needs To Be Covalently Linked to Complex II of the Electron-Transport Chain for the Conversion of FADH 2 into FAD. Chemistry 2017; 24:5246-5252. [PMID: 29124817 PMCID: PMC5969107 DOI: 10.1002/chem.201704622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/07/2017] [Indexed: 11/10/2022]
Abstract
A covalently bound flavin cofactor is predominant in the succinate‐ubiquinone oxidoreductase (SQR; Complex II), an essential component of aerobic electron transport, and in the menaquinol‐fumarate oxidoreductase (QFR), the anaerobic counterpart, although it is only present in approximately 10 % of the known flavoenzymes. This work investigates the role of this 8α‐N3‐histidyl linkage between the flavin adenine dinucleotide (FAD) cofactor and the respiratory Complex II. After parameterization with DFT calculations, classical molecular‐dynamics simulations and quantum‐mechanics calculations for Complex II:FAD and Complex II:FADH2, with and without the covalent bond, were performed. It was observed that the covalent bond is essential for the active‐center arrangement of the FADH2/FAD cofactor. Removal of this bond causes a displacement of the isoalloxazine group, which influences interactions with the protein, flavin solvation, and possible proton‐transfer pathways. Specifically, for the noncovalently bound FADH2 cofactor, the N1 atom moves away from the His‐A365 and His‐A254 residues and the N5 atom moves away from the glutamine‐62A residue. Both of the histidine and glutamine residues interact with a chain of water molecules that cross the enzyme, which is most likely involved in proton transfer. Breaking this chain of water molecules could thereby compromise proton transfer across the two active sites of Complex II.
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Affiliation(s)
- Daniel F A R Dourado
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.,Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, Northern Ireland, UK
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, 17003, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Alexandra T P Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
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19
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Rational Engineering of a Flavoprotein Oxidase for Improved Direct Oxidation of Alcohols to Carboxylic Acids. Molecules 2017; 22:molecules22122205. [PMID: 29231859 PMCID: PMC6149797 DOI: 10.3390/molecules22122205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 11/25/2022] Open
Abstract
The oxidation of alcohols to the corresponding carbonyl or carboxyl compounds represents a convenient strategy for the selective introduction of electrophilic carbon centres into carbohydrate-based starting materials. The O2-dependent oxidation of prim-alcohols by flavin-containing alcohol oxidases often yields mixtures of aldehyde and carboxylic acid, which is due to “over-oxidation” of the aldehyde hydrate intermediate. In order to directly convert alcohols into carboxylic acids, rational engineering of 5-(hydroxymethyl)furfural oxidase was performed. In an attempt to improve the binding of the aldehyde hydrate in the active site to boost aldehyde-oxidase activity, two active-site residues were exchanged for hydrogen-bond-donating and -accepting amino acids. Enhanced over-oxidation was demonstrated and Michaelis–Menten kinetics were performed to corroborate these findings.
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20
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Ewing TA, Fraaije MW, Mattevi A, van Berkel WJ. The VAO/PCMH flavoprotein family. Arch Biochem Biophys 2017; 632:104-117. [DOI: 10.1016/j.abb.2017.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/26/2017] [Accepted: 06/29/2017] [Indexed: 01/15/2023]
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21
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Matthews S, Tee KL, Rattray NJ, McLean KJ, Leys D, Parker DA, Blankley RT, Munro AW. Production of alkenes and novel secondary products by P450 Ole
T
JE
using novel H
2
O
2
‐generating fusion protein systems. FEBS Lett 2017; 591:737-750. [DOI: 10.1002/1873-3468.12581] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah Matthews
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Kang Lan Tee
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Nicholas J. Rattray
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - David Leys
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | | | | | - Andrew W. Munro
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
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22
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Colpa DI, Fraaije MW. High overexpression of dye decolorizing peroxidase TfuDyP leads to the incorporation of heme precursor protoporphyrin IX. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Aboobucker SI, Lorence A. Recent progress on the characterization of aldonolactone oxidoreductases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 98:171-85. [PMID: 26696130 PMCID: PMC4725720 DOI: 10.1016/j.plaphy.2015.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
L-Ascorbic acid (ascorbate, AsA, vitamin C) is essential for animal and plant health. Despite our dependence on fruits and vegetables to fulfill our requirement for this vitamin, the metabolic network leading to its formation in plants is just being fully elucidated. There is evidence supporting the operation of at least four biosynthetic pathways leading to AsA formation in plants. These routes use D-mannose/L-galactose, L-gulose, D-galacturonate, and myo-inositol as the main precursors. This review focuses on aldonolactone oxidoreductases, a subgroup of the vanillyl alcohol oxidase (VAO; EC 1.1.3.38) superfamily, enzymes that catalyze the terminal step in AsA biosynthesis in bacteria, protozoa, animals, and plants. In this report, we review the properties of well characterized aldonolactone oxidoreductases to date. A shared feature in these proteins is the presence of a flavin cofactor as well as a thiol group. The flavin cofactor in many cases is bound to the N terminus of the enzymes or to a recently discovered HWXK motif in the C terminus. The binding between the flavin moiety and the protein can be either covalent or non-covalent. Substrate specificity and subcellular localization differ among the isozymes of each kingdom. All oxidases among these enzymes possess dehydrogenase activity, however, exclusive dehydrogenases are also found. We also discuss recent evidence indicating that plants have both L-gulono-1,4-lactone oxidases and L-galactono-1,4-lactone dehydrogenases involved in AsA biosynthesis.
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Affiliation(s)
- Siddique I Aboobucker
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA
| | - Argelia Lorence
- Arkansas Biosciences Institute, Arkansas State University, P.O. Box 639, State University, AR 72467, USA; Department of Chemistry and Physics, Arkansas State University, P.O. Box 419, State University, AR 72467, USA.
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24
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Pickl M, Fuchs M, Glueck SM, Faber K. The substrate tolerance of alcohol oxidases. Appl Microbiol Biotechnol 2015; 99:6617-42. [PMID: 26153139 PMCID: PMC4513209 DOI: 10.1007/s00253-015-6699-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/10/2015] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Abstract
Alcohols are a rich source of compounds from renewable sources, but they have to be activated in order to allow the modification of their carbon backbone. The latter can be achieved via oxidation to the corresponding aldehydes or ketones. As an alternative to (thermodynamically disfavoured) nicotinamide-dependent alcohol dehydrogenases, alcohol oxidases make use of molecular oxygen but their application is under-represented in synthetic biotransformations. In this review, the mechanism of copper-containing and flavoprotein alcohol oxidases is discussed in view of their ability to accept electronically activated or non-activated alcohols and their propensity towards over-oxidation of aldehydes yielding carboxylic acids. In order to facilitate the selection of the optimal enzyme for a given biocatalytic application, the substrate tolerance of alcohol oxidases is compiled and discussed: Substrates are classified into groups (non-activated prim- and sec-alcohols; activated allylic, cinnamic and benzylic alcohols; hydroxy acids; sugar alcohols; nucleotide alcohols; sterols) together with suitable alcohol oxidases, their microbial source, relative activities and (stereo)selectivities.
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Affiliation(s)
- Mathias Pickl
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010, Graz, Austria
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25
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Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P. Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. FEBS J 2015; 282:3060-74. [PMID: 25619330 DOI: 10.1111/febs.13212] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
UNLABELLED The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60,000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle. DATABASE Structural data are available in PDB database under the accession numbers 4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC and 4PZF.
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Affiliation(s)
- Domen Zafred
- Institute of Biochemistry, Graz University of Technology, Austria.,Institute of Molecular Biosciences, University of Graz, Austria
| | - Barbara Steiner
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Altijana Hromic
- Institute of Molecular Biosciences, University of Graz, Austria
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | | | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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26
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Huijbers MM, van Berkel WJ. High yields of activeThermus thermophilusproline dehydrogenase are obtained using maltose-binding protein as a solubility tag. Biotechnol J 2015; 10:395-403. [DOI: 10.1002/biot.201400229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 12/19/2022]
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27
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The Oxidation of Thiols by Flavoprotein Oxidases: a Biocatalytic Route to Reactive Thiocarbonyls. Angew Chem Int Ed Engl 2014; 53:13206-9. [DOI: 10.1002/anie.201407520] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/09/2014] [Indexed: 11/07/2022]
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28
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Ewing TA, Dijkman WP, Vervoort JM, Fraaije MW, van Berkel WJH. The Oxidation of Thiols by Flavoprotein Oxidases: a Biocatalytic Route to Reactive Thiocarbonyls. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Kopacz MM, Fraaije MW. Turning a monocovalent flavoprotein into a bicovalent flavoprotein by structure-inspired mutagenesis. Bioorg Med Chem 2014; 22:5621-7. [DOI: 10.1016/j.bmc.2014.05.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
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30
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Characterization of the starvation-induced chitinase CfcA and α-1,3-glucanase AgnB of Aspergillus niger. Appl Microbiol Biotechnol 2014; 99:2209-23. [DOI: 10.1007/s00253-014-6062-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
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31
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Krondorfer I, Brugger D, Paukner R, Scheiblbrandner S, Pirker KF, Hofbauer S, Furtmüller PG, Obinger C, Haltrich D, Peterbauer CK. Agaricus meleagris pyranose dehydrogenase: influence of covalent FAD linkage on catalysis and stability. Arch Biochem Biophys 2014; 558:111-9. [PMID: 25043975 PMCID: PMC4148704 DOI: 10.1016/j.abb.2014.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/04/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Pyranose dehydrogenase (PDH) is a monomeric flavoprotein belonging to the glucose-methanol-choline (GMC) family of oxidoreductases. It catalyzes the oxidation of free, non-phosphorylated sugars to the corresponding keto sugars. The enzyme harbors an FAD cofactor that is covalently attached to histidine 103 via an 8α-N(3) histidyl linkage. Our previous work showed that variant H103Y was still able to bind FAD (non-covalently) and perform catalysis but steady-state kinetic parameters for several substrates were negatively affected. In order to investigate the impact of the covalent FAD attachment in Agaricus meleagris PDH in more detail, pre-steady-state kinetics, reduction potential and stability of the variant H103Y in comparison to the wild-type enzyme were probed. Stopped-flow analysis revealed that the mutation slowed down the reductive half-reaction by around three orders of magnitude whereas the oxidative half-reaction was affected only to a minor degree. This was reflected by a decrease in the standard reduction potential of variant H103Y compared to the wild-type protein. The existence of an anionic semiquinone radical in the resting state of both the wild-type and variant H103Y was demonstrated using electron paramagnetic resonance (EPR) spectroscopy and suggested a higher mobility of the cofactor in the variant H103Y. Unfolding studies showed significant negative effects of the disruption of the covalent bond on thermal and conformational stability. The results are discussed with respect to the role of covalently bound FAD in catalysis and stability.
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Affiliation(s)
- Iris Krondorfer
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Dagmar Brugger
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Regina Paukner
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Stefan Scheiblbrandner
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Katharina F Pirker
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Dietmar Haltrich
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Clemens K Peterbauer
- Department of Food Science and Technology, Food Biotechnology Laboratory, BOKU - University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria.
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Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688. Appl Environ Microbiol 2013; 80:1082-90. [PMID: 24271187 DOI: 10.1128/aem.03740-13] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from Methylovorus sp. strain MP688 in Escherichia coli and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations.
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Kim HJ, Winge DR. Emerging concepts in the flavinylation of succinate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:627-36. [PMID: 23380393 DOI: 10.1016/j.bbabio.2013.01.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/14/2013] [Accepted: 01/18/2013] [Indexed: 12/28/2022]
Abstract
The Succinate Dehydrogenase (SDH) heterotetrameric complex catalyzes the oxidation of succinate to fumarate in the tricarboxylic acid (TCA) cycle and in the aerobic respiratory chains of eukaryotes and bacteria. Essential in this catalysis is the covalently-linked cofactor flavin adenine dinucleotide (FAD) in subunit1 (Sdh1) of the SDH enzyme complex. The mechanism of FAD insertion and covalent attachment to Sdh1 is unknown. Our working concept of this flavinylation process has relied mostly on foundational works from the 1990s and by applying the principles learned from other enzymes containing a similarly linked FAD. The discovery of the flavinylation factor Sdh5, however, has provided new insight into the possible mechanism associated with Sdh1 flavinylation. This review focuses on encapsulating prior and recent advances towards understanding the mechanism associated with flavinylation of Sdh1 and how this flavinylation process affects the overall assembly of SDH. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Hyung J Kim
- Department of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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34
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Scheele S, Oertel D, Bongaerts J, Evers S, Hellmuth H, Maurer KH, Bott M, Freudl R. Secretory production of an FAD cofactor-containing cytosolic enzyme (sorbitol-xylitol oxidase from Streptomyces coelicolor) using the twin-arginine translocation (Tat) pathway of Corynebacterium glutamicum. Microb Biotechnol 2012; 6:202-6. [PMID: 23163932 PMCID: PMC3917463 DOI: 10.1111/1751-7915.12005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/08/2012] [Accepted: 10/13/2012] [Indexed: 12/02/2022] Open
Abstract
Carbohydrate oxidases are biotechnologically interesting enzymes that require a tightly or covalently bound cofactor for activity. Using the industrial workhorse Corynebacterium glutamicum as the expression host, successful secretion of a normally cytosolic FAD cofactor-containing sorbitol–xylitol oxidase from Streptomyces coelicolor was achieved by using the twin-arginine translocation (Tat) protein export machinery for protein translocation across the cytoplasmic membrane. Our results demonstrate for the first time that, also for cofactor-containing proteins, a secretory production strategy is a feasible and promising alternative to conventional intracellular expression strategies.
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Affiliation(s)
- Sandra Scheele
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich, Germany
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35
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van Munster JM, van der Kaaij RM, Dijkhuizen L, van der Maarel MJEC. Biochemical characterization of Aspergillus niger CfcI, a glycoside hydrolase family 18 chitinase that releases monomers during substrate hydrolysis. MICROBIOLOGY-SGM 2012; 158:2168-2179. [PMID: 22575895 DOI: 10.1099/mic.0.054650-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome of the industrially important fungus Aspergillus niger encodes a large number of glycoside hydrolase family 18 members annotated as chitinases. We identified one of these putative chitinases, CfcI, as a representative of a distinct phylogenetic clade of homologous enzymes conserved in all sequenced Aspergillus species. Where the catalytic domain of more distantly related chitinases consists of a triosephosphate isomerase barrel in which a small additional (α+β) domain is inserted, CfcI-like proteins were found to have, in addition, a carbohydrate-binding module (CBM18) that is inserted in the (α+β) domain next to the substrate-binding cleft. This unusual domain structure and sequence dissimilarity to previously characterized chitinases suggest that CfcI has a novel activity or function different from chitinases investigated so far. Following its heterologous expression and purification, its biochemical characterization showed that CfcI displays optimal activity at pH 4 and 55-65 °C and degrades chitin oligosaccharides by releasing N-acetylglucosamine from the reducing end, possibly via a processive mechanism. This is the first fungal family 18 exochitinase described, to our knowledge, that exclusively releases monomers. The cfcI expression profile suggests that its physiological function is important in processes that take place during the late stages of the aspergillus life cycle, such as autolysis or sporulation.
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Affiliation(s)
- Jolanda M van Munster
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Rachel M van der Kaaij
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Marc J E C van der Maarel
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
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36
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Asymmetric synthesis of d-glyceric acid by an alditol oxidase and directed evolution for enhanced oxidative activity towards glycerol. Appl Microbiol Biotechnol 2012; 96:1243-52. [DOI: 10.1007/s00253-012-3885-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/01/2012] [Accepted: 01/02/2012] [Indexed: 10/14/2022]
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37
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Winter RT, Heuts DPHM, Rijpkema EMA, van Bloois E, Wijma HJ, Fraaije MW. Hot or not? Discovery and characterization of a thermostable alditol oxidase from Acidothermus cellulolyticus 11B. Appl Microbiol Biotechnol 2012; 95:389-403. [PMID: 22231860 PMCID: PMC3371188 DOI: 10.1007/s00253-011-3750-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/01/2011] [Accepted: 11/17/2011] [Indexed: 11/26/2022]
Abstract
We describe the discovery, isolation and characterization of a highly thermostable alditol oxidase from Acidothermus cellulolyticus 11B. This protein was identified by searching the genomes of known thermophiles for enzymes homologous to Streptomyces coelicolor A3(2) alditol oxidase (AldO). A gene (sharing 48% protein sequence identity to AldO) was identified, cloned and expressed in Escherichia coli. Following 6xHis tag purification, characterization revealed the protein to be a covalent flavoprotein of 47 kDa with a remarkably similar reactivity and substrate specificity to that of AldO. A steady-state kinetic analysis with a number of different polyol substrates revealed lower catalytic rates but slightly altered substrate specificity when compared to AldO. Thermostability measurements revealed that the novel AldO is a highly thermostable enzyme with an unfolding temperature of 84 °C and an activity half-life at 75 °C of 112 min, prompting the name HotAldO. Inspired by earlier studies, we attempted a straightforward, exploratory approach to improve the thermostability of AldO by replacing residues with high B-factors with corresponding residues from HotAldO. None of these mutations resulted in a more thermostable oxidase; a fact that was corroborated by in silico analysis.
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Affiliation(s)
- Remko T. Winter
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dominic P. H. M. Heuts
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Egon M. A. Rijpkema
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Edwin van Bloois
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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38
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Winter RT, van den Berg TE, Colpa DI, van Bloois E, Fraaije MW. Functionalization of oxidases with peroxidase activity creates oxiperoxidases: a new breed of hybrid enzyme capable of cascade chemistry. Chembiochem 2011; 13:252-8. [PMID: 22213198 DOI: 10.1002/cbic.201100639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 11/09/2022]
Abstract
The covalent flavoprotein alditol oxidase (AldO) from Streptomyces coelicolor A3(2) was endowed with an extra catalytic functionality by fusing it to a microperoxidase. Purification of the construct resulted in the isolation of a synthetic bifunctional enzyme that was both fully covalently flavinylated and heminylated: an oxiperoxidase. Characterization revealed that both oxidase and peroxidase functionalities were active, with the construct functioning as a single-component xylitol biosensor. In an attempt to reduce the size of the oxidase-peroxidase fusion, we replaced portions of the native AldO sequence with the bacterial cytochrome c CXXCH heme-binding motif. By mutating only three residues of the AldO protein we were able to create a functional oxidase-peroxidase hybrid.
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Affiliation(s)
- Remko T Winter
- Laboratory of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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39
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Wongnate T, Sucharitakul J, Chaiyen P. Identification of a Catalytic Base for Sugar Oxidation in the Pyranose 2-Oxidase Reaction. Chembiochem 2011; 12:2577-86. [DOI: 10.1002/cbic.201100564] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Indexed: 11/10/2022]
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Affiliation(s)
- Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K
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41
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Koetsier MJ, Jekel PA, Wijma HJ, Bovenberg RAL, Janssen DB. Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from Penicillium chrysogenum. FEBS Lett 2011; 585:893-8. [PMID: 21334330 DOI: 10.1016/j.febslet.2011.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 02/13/2011] [Accepted: 02/14/2011] [Indexed: 11/19/2022]
Abstract
Coenzyme A ligases play an important role in metabolism by catalyzing the activation of carboxylic acids. In this study we describe the synthesis of aminoacyl-coenzyme As (CoAs) catalyzed by a CoA ligase from Penicillium chrysogenum. The enzyme accepted medium-chain length fatty acids as the best substrates, but the proteinogenic amino acids L-phenylalanine and L-tyrosine, as well as the non-proteinogenic amino acids D-phenylalanine, D-tyrosine and (R)- and (S)-β-phenylalanine were also accepted. Of these amino acids, the highest activity was found for (R)-β-phenylalanine, forming (R)-β-phenylalanyl-CoA. Homology modeling suggested that alanine 312 is part of the active site cavity, and mutagenesis (A312G) yielded a variant that has an enhanced catalytic efficiency with β-phenylalanines and D-α-phenylalanine.
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Affiliation(s)
- Martijn J Koetsier
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen NL-9747 AG, The Netherlands
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42
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Characterization of cytochrome P450 monooxygenase CYP154H1 from the thermophilic soil bacterium Thermobifida fusca. Appl Microbiol Biotechnol 2010; 89:1475-85. [PMID: 21057946 PMCID: PMC3036808 DOI: 10.1007/s00253-010-2965-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/13/2010] [Accepted: 10/14/2010] [Indexed: 10/25/2022]
Abstract
Cytochrome P450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. We have cloned the gene for a new cytochrome P450 monooxygenase, named CYP154H1, from the moderately thermophilic soil bacterium Thermobifida fusca. The enzyme was overexpressed in Escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. CYP154H1 activity was reconstituted using putidaredoxin reductase and putidaredoxin from Pseudomonas putida DSM 50198 as surrogate electron transfer partners. In biocatalytic reactions with different aliphatic and aromatic substrates of varying size, the enzyme converted small aromatic and arylaliphatic compounds like ethylbenzene, styrene, and indole. Furthermore, CYP154H1 also accepted different arylaliphatic sulfides as substrates chemoselectively forming the corresponding sulfoxides and sulfones. The enzyme is moderately thermostable with an apparent melting temperature of 67°C and exhibited still 90% of initial activity after incubation at 50°C.
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43
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Jorns MS, Chen ZW, Mathews FS. Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase . Biochemistry 2010; 49:3631-9. [PMID: 20353187 DOI: 10.1021/bi100160j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygen reduction and sarcosine oxidation in monomeric sarcosine oxidase (MSOX) occur at separate sites above the si- and re-faces, respectively, of the flavin ring. Mutagenesis studies implicate Lys265 as the oxygen activation site. Substitution of Lys265 with a neutral (Met, Gln, or Ala) or basic (Arg) residue results in an approximately 10(4)- or 250-fold decrease, respectively, in the reaction rate. The overall structure of MSOX and residue conformation in the sarcosine binding cavity are unaffected by replacement of Lys265 with Met or Arg. The side chain of Met265 exhibits the same configuration in each molecule of Lys265Met crystals and is nearly congruent with Lys265 in wild-type MSOX. The side chain of Arg265 is, however, dramatically shifted ( approximately 4-5 A) compared with Lys265, points in the opposite direction, and exhibits significant conformational variability between molecules of the same crystal. The major species in solutions of Lys265Arg is likely to contain a "flipped-out" Arg265 and exhibit negligible oxygen activation, similar to Lys265Met. The 400-fold higher oxygen reactivity observed with Lys265Arg is attributed to a minor (<1%) "flipped-in" Arg265 conformer whose oxygen reactivity is similar to that of wild-type MSOX. A structural water (WAT1), found above the si-face of the flavin ring in all previously determined MSOX structures, is part of an apparent proton relay system that extends from FAD N(5) to bulk solvent. WAT1 is strikingly absent in Lys265Met and Lys265Arg, a feature that may account for the apparent kinetic stabilization of a reductive half-reaction intermediate that is detectable with the mutants but not wild-type MSOX.
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Affiliation(s)
- Marilyn Schuman Jorns
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.
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44
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Baron R, McCammon JA, Mattevi A. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Curr Opin Struct Biol 2009; 19:672-9. [DOI: 10.1016/j.sbi.2009.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 10/07/2009] [Indexed: 11/28/2022]
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45
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Kuipers RKP, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NGH, van Berkel WJH, Vriend G, Schaap PJ. Correlated mutation analyses on super-family alignments reveal functionally important residues. Proteins 2009; 76:608-16. [DOI: 10.1002/prot.22374] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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van Hellemond E, Vermote L, Koolen W, Sonke T, Zandvoort E, Heuts DP, Janssen D, Fraaije M. Exploring the Biocatalytic Scope of Alditol Oxidase fromStreptomyces coelicolor. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900176] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Forneris F, Orru R, Bonivento D, Chiarelli LR, Mattevi A. ThermoFAD, a Thermofluor-adapted flavin ad hoc detection system for protein folding and ligand binding. FEBS J 2009; 276:2833-40. [PMID: 19459938 DOI: 10.1111/j.1742-4658.2009.07006.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In living organisms, genes encoding proteins that contain flavins as a prosthetic group constitute approximately 2-3% of the total. The fluorescence of flavin cofactors in these proteins is a property that is widely employed for biochemical characterisation. Here, we present a modified Thermofluor approach called ThermoFAD (Thermofluor-adapted flavin ad hoc detection system), which simplifies identification of optimal purification and storage conditions as well as high-affinity ligands. In this technique, the flavin cofactor is used as an intrinsic probe to monitor protein folding and stability, taking advantage of the different fluorescent properties of flavin-containing proteins between the folded and denatured state. The main advantage of the method is that it allows a large amount of biochemical data to be obtained using very small amounts of protein sample and standard laboratory equipment. We have explored several cases that demonstrate the reliability and versatility of this technique when applied to globular flavoenzymes, membrane-anchored flavoproteins, and macromolecular complexes. The information gathered from ThermoFAD analysis can be very valuable for any biochemical and biophysical analysis, including crystallisation. The method is likely to be applicable to other classes of proteins that possess endogenous fluorescent cofactors and prosthetic groups.
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Affiliation(s)
- Federico Forneris
- Department of Genetics and Microbiology, University of Pavia, Italy.
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48
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Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A 2009; 106:10603-8. [PMID: 19541622 DOI: 10.1073/pnas.0903809106] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dioxygen (O(2)) and other gas molecules have a fundamental role in a variety of enzymatic reactions. However, it is only poorly understood which O(2) uptake mechanism enzymes employ to promote efficient catalysis and how general this is. We investigated O(2) diffusion pathways into monooxygenase and oxidase flavoenzymes, using an integrated computational and experimental approach. Enhanced-statistics molecular dynamics simulations reveal spontaneous protein-guided O(2) diffusion from the bulk solvent to preorganized protein cavities. The predicted protein-guided diffusion paths and the importance of key cavity residues for oxygen diffusion were verified by combining site-directed mutagenesis, rapid kinetics experiments, and high-resolution X-ray structures. This study indicates that monooxygenase and oxidase flavoenzymes employ multiple funnel-shaped diffusion pathways to absorb O(2) from the solvent and direct it to the reacting C4a atom of the flavin cofactor. The difference in O(2) reactivity among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine modulation of the local environment embedding the reactive locus of the flavin.
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49
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Prongjit M, Sucharitakul J, Wongnate T, Haltrich D, Chaiyen P. Kinetic mechanism of pyranose 2-oxidase from trametes multicolor. Biochemistry 2009; 48:4170-80. [PMID: 19317444 DOI: 10.1021/bi802331r] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoprotein oxidase that catalyzes the oxidation of aldopyranoses by molecular oxygen to yield the corresponding 2-keto-aldoses and hydrogen peroxide. P2O is the first enzyme in the class of flavoprotein oxidases, for which a C4a-hydroperoxy-flavin adenine dinucleotide (FAD) intermediate has been detected during the oxidative half-reaction. In this study, the reduction kinetics of P2O by d-glucose and 2-d-d-glucose at pH 7.0 was investigated using stopped-flow techniques. The results indicate that d-glucose binds to the enzyme with a two-step binding process; the first step is the initial complex formation, while the second step is the isomerization to form an active Michaelis complex (E-Fl(ox):G). Interestingly, the complex (E-Fl(ox):G) showed greater absorbance at 395 nm than the oxidized enzyme, and the isomerization process showed a significant inverse isotope effect, implying that the C2-H bond of d-glucose is more rigid in the E-Fl(ox):G complex than in the free form. A large normal primary isotope effect (k(H)/k(D) = 8.84) was detected in the flavin reduction step. Steady-state kinetics at pH 7.0 shows a series of parallel lines. Kinetics of formation and decay of C-4a-hydroperoxy-FAD is the same in absence and presence of 2-keto-d-glucose, implying that the sugar does not bind to P2O during the oxidative half-reaction. This suggests that the kinetic mechanism of P2O is likely to be the ping-pong-type where the sugar product leaves prior to the oxygen reaction. The movement of the active site loop when oxygen is present is proposed to facilitate the release of the sugar product. Correlation between data from pre-steady-state and steady-state kinetics has shown that the overall turnover of the reaction is limited by the steps of flavin reduction and decay of C4a-hydroperoxy-FAD.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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50
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Heuts DPHM, Scrutton NS, McIntire WS, Fraaije MW. What's in a covalent bond? On the role and formation of covalently bound flavin cofactors. FEBS J 2009; 276:3405-27. [PMID: 19438712 DOI: 10.1111/j.1742-4658.2009.07053.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many enzymes use one or more cofactors, such as biotin, heme, or flavin. These cofactors may be bound to the enzyme in a noncovalent or covalent manner. Although most flavoproteins contain a noncovalently bound flavin cofactor (FMN or FAD), a large number have these cofactors covalently linked to the polypeptide chain. Most covalent flavin-protein linkages involve a single cofactor attachment via a histidyl, tyrosyl, cysteinyl or threonyl linkage. However, some flavoproteins contain a flavin that is tethered to two amino acids. In the last decade, many studies have focused on elucidating the mechanism(s) of covalent flavin incorporation (flavinylation) and the possible role(s) of covalent protein-flavin bonds. These endeavors have revealed that covalent flavinylation is a post-translational and self-catalytic process. This review presents an overview of the known types of covalent flavin bonds and the proposed mechanisms and roles of covalent flavinylation.
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Affiliation(s)
- Dominic P H M Heuts
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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