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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yang G, Pećanac O, Wijma HJ, Rozeboom HJ, de Gonzalo G, Fraaije MW, Mascotti ML. Evolution of the catalytic mechanism at the dawn of the Baeyer-Villiger monooxygenases. Cell Rep 2024; 43:114130. [PMID: 38640062 DOI: 10.1016/j.celrep.2024.114130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
Enzymes are crucial for the emergence and sustenance of life on earth. How they became catalytically active during their evolution is still an open question. Two opposite explanations are plausible: acquiring a mechanism in a series of discrete steps or all at once in a single evolutionary event. Here, we use molecular phylogeny, ancestral sequence reconstruction, and biochemical characterization to follow the evolution of a specialized group of flavoprotein monooxygenases, the bacterial Baeyer-Villiger monooxygenases (BVMOs). These enzymes catalyze an intricate chemical reaction relying on three different elements: a reduced nicotinamide cofactor, dioxygen, and a substrate. Characterization of ancestral BVMOs shows that the catalytic mechanism evolved in a series of steps starting from a FAD-binding protein and further acquiring reactivity and specificity toward each of the elements participating in the reaction. Together, the results of our work portray how an intrinsically complex catalytic mechanism emerged during evolution.
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Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ognjen Pećanac
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Gonzalo de Gonzalo
- Departamento de Química Orgánica, Universidad de Sevilla, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), 41012 Sevilla, Spain
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
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3
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Russo S, Luján AP, Fraaije MW, Poelarends GJ. Synthesis of Pharmaceutically Relevant Arylamines Enabled by a Nitroreductase from Bacillus tequilensis. Chembiochem 2024:e202300846. [PMID: 38502784 DOI: 10.1002/cbic.202300846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Arylamines are essential building blocks for the manufacture of valuable pharmaceuticals, pigments and dyes. However, their current industrial production involves the use of chemocatalytic procedures with a significant environmental impact. As a result, flavin-dependent nitroreductases (NRs) have received increasing attention as sustainable catalysts for more ecofriendly synthesis of arylamines. In this study, we assessed a novel NR from Bacillus tequilensis, named BtNR, for the synthesis of pharmaceutically relevant arylamines, including valuable synthons used in the manufacture of blockbuster drugs such as vismodegib, sonidegib, linezolid and sildenafil. After optimizing the enzymatic reaction conditions, high conversion of nitroaromatics to arylamines (up to 97 %) and good product yields (up to 56 %) were achieved. Our results indicate that BtNR has a broad substrate scope, including bulky nitro benzenes, nitro pyrazoles and nitro pyridines. Hence, BtNR is an interesting biocatalyst for the synthesis of pharmaceutically relevant amine-functionalized aromatics, providing an attractive alternative to traditional chemical synthesis methodologies.
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Affiliation(s)
- Sara Russo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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4
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Lee M, Fraaije MW. Equipping Saccharomyces cerevisiae with an Additional Redox Cofactor Allows F 420-Dependent Bioconversions in Yeast. ACS Synth Biol 2024; 13:921-929. [PMID: 38346396 PMCID: PMC10949242 DOI: 10.1021/acssynbio.3c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 03/16/2024]
Abstract
Industrial application of the natural deazaflavin cofactor F420 has high potential for the enzymatic synthesis of high value compounds. It can offer an additional range of chemistry to the use of well-explored redox cofactors such as FAD and their respective enzymes. Its limited access through organisms that are rather difficult to grow has urged research on the heterologous production of F420 using more industrially relevant microorganisms such as Escherichia coli. In this study, we demonstrate the possibility of producing this cofactor in a robust and widely used industrial organism, Saccharomyces cerevisiae, by the heterologous expression of the F420 pathway. Through careful selection of involved enzymes and some optimization, we achieved an F420 yield of ∼1.3 μmol/L, which is comparable to the yield of natural F420 producers. Furthermore, we showed the potential use of F420-producing S. cerevisiae for F420-dependent bioconversions by carrying out the whole-cell conversion of tetracycline. As the first demonstration of F420 synthesis and use for bioconversion in a eukaryotic organism, this study contributes to the development of versatile bioconversion platforms.
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Affiliation(s)
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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5
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Santema LL, Basile L, Binda C, Fraaije MW. Discovery and structural characterization of a thermostable bacterial monoamine oxidase. FEBS J 2024; 291:849-864. [PMID: 37814408 DOI: 10.1111/febs.16973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/01/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Monoamine oxidases (MAOs) are pivotal regulators of neurotransmitters in mammals, while microbial MAOs have been shown to be valuable biocatalysts for enantioselective synthesis of pharmaceutical compounds or precursors thereof. To extend the knowledge of how MAOs function at the molecular level and in order to provide more biocatalytic tools, we set out to identify and study a robust bacterial variant: a MAO from the thermophile Thermoanaerobacterales bacterium (MAOTb ). MAOTb is highly thermostable with melting temperatures above 73 °C and is well expressed in Escherichia coli. Substrate screening revealed that the oxidase is most efficient with n-alkylamines with n-heptylamine being the best substrate. Presteady-state kinetic analysis shows that reduced MAOTb rapidly reacts with molecular oxygen, confirming that it is a bona fide oxidase. The crystal structure of MAOTb was resolved at 1.5 Å and showed an exceptionally high similarity with the two human MAOs, MAO A and MAO B. The active site of MAOTb resembles mostly the architecture of human MAO A, including the cysteinyl protein-FAD linkage. Yet, the bacterial MAO lacks a C-terminal extension found in human MAOs, which explains why it is expressed and purified as a soluble protein, while the mammalian counterparts are anchored to the membrane through an α-helix. MAOTb also displays a slightly different active site access tunnel, which may explain the specificity toward long aliphatic amines. Being an easy-to-express, thermostable enzyme, for which a high-resolution structure was elucidated, this bacterial MAO may develop into a valuable biocatalyst for synthetic chemistry or biosensing.
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Affiliation(s)
- Lars L Santema
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Lorenzo Basile
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
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6
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Tjallinks G, Boverio A, Jager AW, Kaya SG, Mattevi A, Fraaije MW. Efficient Oxidation of 5-Hydroxymethylfurfural Using a Flavoprotein Oxidase from the Honeybee Apis mellifera. Chembiochem 2023; 24:e202300588. [PMID: 37800383 DOI: 10.1002/cbic.202300588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/07/2023]
Abstract
The chemical 5-hydroxymethylfurfural (HMF) can be derived from lignocellulose and is an interesting bio-based platform chemical as it has the potential to be transformed into numerous valuable building blocks such as the polymer-precursor 2,5-diformylfuran (DFF). To date, only a few oxidases acting on HMF are known and by sampling atypical species, we discovered a novel flavin-dependent oxidoreductase from the honeybee Apis mellifera (beeHMFO). The enzyme can perform the chemoselective oxidation of HMF to DFF but can also readily accept other aromatic alcohols as substrates. The function of the enzyme may well be the antimicrobial generation of hydrogen peroxide using HMF, which is very abundant in honey. The discovery of this insect-derived flavoprotein oxidase holds promising potential in the synthesis of renewable products and demonstrates that insects can be an interesting source of novel biocatalysts.
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Affiliation(s)
- Gwen Tjallinks
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen (The, Netherlands
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, Pavia, Italy
| | - Alessandro Boverio
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen (The, Netherlands
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, Pavia, Italy
| | - Amarins W Jager
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen (The, Netherlands
| | - Saniye G Kaya
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen (The, Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen (The, Netherlands
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7
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Tong Y, Kaya SG, Russo S, Rozeboom HJ, Wijma HJ, Fraaije MW. Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor. J Am Chem Soc 2023; 145:27140-27148. [PMID: 38048072 PMCID: PMC10722498 DOI: 10.1021/jacs.3c12009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Most flavin-dependent enzymes contain a dissociable flavin cofactor. We present a new approach for installing in vivo a covalent bond between a flavin cofactor and its host protein. By using a flavin transferase and carving a flavinylation motif in target proteins, we demonstrate that "dissociable" flavoproteins can be turned into covalent flavoproteins. Specifically, four different flavin mononucleotide-containing proteins were engineered to undergo covalent flavinylation: a light-oxygen-voltage domain protein, a mini singlet oxygen generator, a nitroreductase, and an old yellow enzyme-type ene reductase. Optimizing the flavinylation motif and expression conditions led to the covalent flavinylation of all four flavoproteins. The engineered covalent flavoproteins retained function and often exhibited improved performance, such as higher thermostability or catalytic performance. The crystal structures of the designed covalent flavoproteins confirmed the designed threonyl-phosphate linkage. The targeted flavoproteins differ in fold and function, indicating that this method of introducing a covalent flavin-protein bond is a powerful new method to create flavoproteins that cannot lose their cofactor, boosting their performance.
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Affiliation(s)
- Yapei Tong
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Saniye G. Kaya
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Sara Russo
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Henriette J. Rozeboom
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Hein J. Wijma
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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8
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Guo Y, Alvigini L, Saifuddin M, Ashley B, Trajkovic M, Alonso-Cotchico L, Mattevi A, Fraaije MW. One-Pot Biocatalytic Synthesis of rac-Syringaresinol from a Lignin-Derived Phenol. ACS Catal 2023; 13:14639-14649. [PMID: 38026814 PMCID: PMC10660655 DOI: 10.1021/acscatal.3c04399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
The drive for a circular bioeconomy has resulted in a great demand for renewable, biobased chemicals. We present a one-pot biocatalytic cascade reaction for the production of racemic syringaresinol, a lignan with applications as a nutraceutical and in polymer chemistry. The process consumes dihydrosinapyl alcohol, which can be produced renewably from the lignocellulosic material. To achieve this, a variant of eugenol oxidase was engineered for the oxidation of dihydrosinapyl alcohol into sinapyl alcohol with good conversion and chemoselectivity. The crystal structure of the engineered oxidase revealed the molecular basis of the influence of the mutations on the chemoselectivity of the oxidation of dihydrosinapyl alcohol. By using horseradish peroxidase, the subsequent oxidative dimerization of sinapyl alcohol into syringaresinol was achieved. Conditions for the one-pot, two-enzyme synthesis were optimized, and a high yield of syringaresinol was achieved by cascading the oxidase and peroxidase steps in a stepwise fashion. This study demonstrates the efficient production of syringaresinol from a compound that can be renewed by reductive catalytic fractionation of lignocellulose, providing a biocatalytic route for generating a valuable compound from lignin.
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Affiliation(s)
- Yiming Guo
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands
| | - Laura Alvigini
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, Pavia 27100, Italy
| | - Mohammad Saifuddin
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands
| | - Ben Ashley
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands
| | - Milos Trajkovic
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands
| | | | - Andrea Mattevi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, Pavia 27100, Italy
| | - Marco W. Fraaije
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands
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9
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Tjallinks G, Boverio A, Maric I, Rozeboom H, Arentshorst M, Visser J, Ram AFJ, Mattevi A, Fraaije MW. Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin. FEBS J 2023; 290:5114-5126. [PMID: 37366079 DOI: 10.1111/febs.16804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Patulin synthase (PatE) from Penicillium expansum is a flavin-dependent enzyme that catalyses the last step in the biosynthesis of the mycotoxin patulin. This secondary metabolite is often present in fruit and fruit-derived products, causing postharvest losses. The patE gene was expressed in Aspergillus niger allowing purification and characterization of PatE. This confirmed that PatE is active not only on the proposed patulin precursor ascladiol but also on several aromatic alcohols including 5-hydroxymethylfurfural. By elucidating its crystal structure, details on its catalytic mechanism were revealed. Several aspects of the active site architecture are reminiscent of that of fungal aryl-alcohol oxidases. Yet, PatE is most efficient with ascladiol as substrate confirming its dedicated role in biosynthesis of patulin.
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Affiliation(s)
- Gwen Tjallinks
- Molecular Enzymology, University of Groningen, The Netherlands
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Alessandro Boverio
- Molecular Enzymology, University of Groningen, The Netherlands
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Ivana Maric
- Molecular Enzymology, University of Groningen, The Netherlands
| | | | | | - Jaap Visser
- Institute of Biology Leiden, Leiden University, The Netherlands
| | - Arthur F J Ram
- Institute of Biology Leiden, Leiden University, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
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10
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Arentshorst M, Kooloth Valappil P, Mózsik L, Regensburg-Tuïnk TJG, Seekles SJ, Tjallinks G, Fraaije MW, Visser J, Ram AFJ. A CRISPR/Cas9-based multicopy integration system for protein production in Aspergillus niger. FEBS J 2023; 290:5127-5140. [PMID: 37335926 DOI: 10.1111/febs.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The filamentous fungus Aspergillus niger is well known for its high protein secretion capacity and a preferred host for homologous and heterologous protein production. To improve the protein production capacity of A. niger even further, a set of dedicated protein production strains was made containing up to 10 glucoamylase landing sites (GLSs) at predetermined sites in the genome. These GLSs replace genes encoding enzymes abundantly present or encoding unwanted functions. Each GLS contains the promotor and terminator region of the glucoamylase gene (glaA), one of the highest expressed genes in A. niger. Integrating multiple gene copies, often realized by random integration, is known to boost protein production yields. In our approach the GLSs allow for rapid targeted gene replacement using CRISPR/Cas9-mediated genome editing. By introducing the same or different unique DNA sequences (dubbed KORE sequences) in each GLS and designing Cas9-compatible single guide RNAs, one is able to select at which GLS integration of a target gene occurs. In this way a set of identical strains with different copy numbers of the gene of interest can be easily and rapidly made to compare protein production levels. As an illustration of its potential, we successfully used the expression platform to generate multicopy A. niger strains producing the Penicillium expansum PatE::6xHis protein catalysing the final step in patulin biosynthesis. The A. niger strain expressing 10 copies of the patE::6xHis expression cassette produced about 70 μg·mL-1 PatE protein in the culture medium with a purity just under 90%.
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Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Prajeesh Kooloth Valappil
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - László Mózsik
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Tonny J G Regensburg-Tuïnk
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Sjoerd J Seekles
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Gwen Tjallinks
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Jaap Visser
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Arthur F J Ram
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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11
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Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023; 82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Ancestral sequence reconstruction (ASR) provides insight into the changes within a protein sequence across evolution. More specifically, it can illustrate how specific amino acid changes give rise to different phenotypes within a protein family. Over the last few decades it has established itself as a powerful technique for revealing molecular common denominators that govern enzyme function. Here, we describe the strength of ASR in unveiling catalytic mechanisms and emerging phenotypes for a range of different proteins, also highlighting biotechnological applications the methodology can provide.
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Affiliation(s)
- Callum R Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marta Massari
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands. https://twitter.com/fraaije1
| | - Maria Laura Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
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12
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Yang G, Wijma HJ, Rozeboom HJ, Mascotti ML, Fraaije MW. Identification and characterization of archaeal and bacterial F 420 -dependent thioredoxin reductases. FEBS J 2023; 290:4777-4791. [PMID: 37403630 DOI: 10.1111/febs.16896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
The thioredoxin pathway is an antioxidant system present in most organisms. Electrons flow from a thioredoxin reductase to thioredoxin at the expense of a specific electron donor. Most known thioredoxin reductases rely on NADPH as a reducing cofactor. Yet, in 2016, a new type of thioredoxin reductase was discovered in Archaea which utilize instead a reduced deazaflavin cofactor (F420 H2 ). For this reason, the respective enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). To have a broader understanding of the biochemistry of DFTRs, we identified and characterized two other archaeal representatives. A detailed kinetic study, which included pre-steady state kinetic analyses, revealed that these two DFTRs are highly specific for F420 H2 while displaying marginal activity with NADPH. Nevertheless, they share mechanistic features with the canonical thioredoxin reductases that are dependent on NADPH (NTRs). A detailed structural analysis led to the identification of two key residues that tune cofactor specificity of DFTRs. This allowed us to propose a DFTR-specific sequence motif that enabled for the first time the identification and experimental characterization of a bacterial DFTR.
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Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | | | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, The Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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13
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Tong Y, Rozeboom HJ, Loonstra MR, Wijma HJ, Fraaije MW. Characterization of two bacterial multi-flavinylated proteins harboring multiple covalent flavin cofactors. BBA Adv 2023; 4:100097. [PMID: 37455753 PMCID: PMC10339131 DOI: 10.1016/j.bbadva.2023.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
In recent years, studies have shown that a large number of bacteria secrete multi-flavinylated proteins. The exact roles and properties, of these extracellular flavoproteins that contain multiple covalently anchored FMN cofactors, are still largely unknown. Herein, we describe the biochemical and structural characterization of two multi-FMN-containing covalent flavoproteins, SaFMN3 from Streptomyces azureus and CbFMN4 from Clostridiaceae bacterium. Based on their primary structure, these proteins were predicted to contain three and four covalently tethered FMN cofactors, respectively. The genes encoding SaFMN3 and CbFMN4 were heterologously coexpressed with a flavin transferase (ApbE) in Escherichia coli, and could be purified by affinity chromatography in good yields. Both proteins were found to be soluble and to contain covalently bound FMN molecules. The SaFMN3 protein was studied in more detail and found to display a single redox potential (-184 mV) while harboring three covalently attached flavins. This is in line with the high sequence similarity when the domains of each flavoprotein are compared. The fully reduced form of SaFMN3 is able to use dioxygen as electron acceptor. Single domains from both proteins were expressed, purified and crystallized. The crystal structures were elucidated, which confirmed that the flavin cofactor is covalently attached to a threonine. Comparison of both crystal structures revealed a high similarity, even in the flavin binding pocket. Based on the crystal structure, mutants of the SaFMN3-D2 domain were designed to improve its fluorescence quantum yield by changing the microenvironment of the isoalloxazine moiety of the flavin cofactor. Residues that quench the flavin fluorescence were successfully identified. Our study reveals biochemical details of multi-FMN-containing proteins, contributing to a better understanding of their role in bacteria and providing leads to future utilization of these flavoprotein in biotechnology.
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14
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Rotilio L, Boverio A, Nguyen QT, Mannucci B, Fraaije MW, Mattevi A. A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center. J Biol Chem 2023; 299:104904. [PMID: 37302552 PMCID: PMC10404684 DOI: 10.1016/j.jbc.2023.104904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023] Open
Abstract
Nitrosuccinate is a biosynthetic building block in many microbial pathways. The metabolite is produced by dedicated L-aspartate hydroxylases that use NADPH and molecular oxygen as co-substrates. Here, we investigate the mechanism underlying the unusual ability of these enzymes to perform successive rounds of oxidative modifications. The crystal structure of Streptomyces sp. V2 L-aspartate N-hydroxylase outlines a characteristic helical domain wedged between two dinucleotide-binding domains. Together with NADPH and FAD, a cluster of conserved arginine residues forms the catalytic core at the domain interface. Aspartate is found to bind in an entry chamber that is close to but not in direct contact with the flavin. It is recognized by an extensive H-bond network that explains the enzyme's strict substrate-selectivity. A mutant designed to create steric and electrostatic hindrance to substrate binding disables hydroxylation without perturbing the NADPH oxidase side-activity. Critically, the distance between the FAD and the substrate is far too long to afford N-hydroxylation by the C4a-hydroperoxyflavin intermediate whose formation is confirmed by our work. We conclude that the enzyme functions through a catch-and-release mechanism. L-aspartate slides into the catalytic center only when the hydroxylating apparatus is formed. It is then re-captured by the entry chamber where it waits for the next round of hydroxylation. By iterating these steps, the enzyme minimizes the leakage of incompletely oxygenated products and ensures that the reaction carries on until nitrosuccinate is formed. This unstable product can then be engaged by a successive biosynthetic enzyme or undergoes spontaneous decarboxylation to produce 3-nitropropionate, a mycotoxin.
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Affiliation(s)
- Laura Rotilio
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Alessandro Boverio
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy; Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Quoc-Thai Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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15
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Eggerichs D, Weindorf N, Mascotti ML, Welzel N, Fraaije MW, Tischler D. Vanillyl alcohol oxidase from Diplodia corticola: Residues Ala420 and Glu466 allow for efficient catalysis of syringyl derivatives. J Biol Chem 2023; 299:104898. [PMID: 37295774 PMCID: PMC10404669 DOI: 10.1016/j.jbc.2023.104898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Vanillyl alcohol oxidases (VAOs) belong to the 4-phenol oxidases family and are found predominantly in lignin-degrading ascomycetes. Systematical investigation of the enzyme family at the sequence level resulted in discovery and characterization of the second recombinantly produced VAO member, DcVAO, from Diplodia corticola. Remarkably high activities for 2,6-substituted substrates like 4-allyl-2,6-dimethoxy-phenol (3.5 ± 0.02 U mg-1) or 4-(hydroxymethyl)-2,6-dimethoxyphenol (6.3 ± 0.5 U mg-1) were observed, which could be attributed to a Phe to Ala exchange in the catalytic center. In order to rationalize this rare substrate preference among VAOs, we resurrected and characterized three ancestral enzymes and performed mutagenesis analyses. The results indicate that a Cys/Glu exchange was required to retain activity for ɣ-hydroxylations and shifted the acceptance towards benzyl ethers (up to 4.0 ± 0.1 U mg-1). Our findings contribute to the understanding of the functionality of VAO enzyme group, and with DcVAO, we add a new enzyme to the repertoire of ether cleaving biocatalysts.
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Affiliation(s)
- Daniel Eggerichs
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Nils Weindorf
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Maria Laura Mascotti
- Department of Molecular Enzymology, University of Groningen, Groningen, The Netherlands; Facultad de Química Bioquímica y Farmacia, IMIBIO-SL CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Natalie Welzel
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Marco W Fraaije
- Department of Molecular Enzymology, University of Groningen, Groningen, The Netherlands
| | - Dirk Tischler
- Department of Microbial Biotechnology, Ruhr-University Bochum, Bochum, Germany.
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Partipilo M, Yang G, Mascotti ML, Wijma HJ, Slotboom DJ, Fraaije MW. A conserved sequence motif in the E. coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. J Biol Chem 2022; 298:102304. [PMID: 35933012 PMCID: PMC9460512 DOI: 10.1016/j.jbc.2022.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/06/2022] Open
Abstract
Soluble pyridine nucleotide transhydrogenases (STHs) are flavoenzymes involved in the redox homeostasis of the essential cofactors NAD(H) and NADP(H). They catalyze the reversible transfer of reducing equivalents between the two nicotinamide cofactors. The soluble transhydrogenase from Escherichia coli (SthA) has found wide use in both in vivo and in vitro applications to steer reducing equivalents toward NADPH-requiring reactions. However, mechanistic insight into SthA function is still lacking. In this work, we present a biochemical characterization of SthA, focusing for the first time on the reactivity of the flavoenzyme with molecular oxygen. We report on oxidase activity of SthA that takes place both during transhydrogenation and in the absence of an oxidized nicotinamide cofactor as an electron acceptor. We find that this reaction produces the reactive oxygen species hydrogen peroxide and superoxide anion. Furthermore, we explore the evolutionary significance of the well-conserved CXXXXT motif that distinguishes STHs from the related family of flavoprotein disulfide reductases in which a CXXXXC motif is conserved. Our mutational analysis revealed the cysteine and threonine combination in SthA leads to better coupling efficiency of transhydrogenation and reduced reactive oxygen species release compared to enzyme variants with mutated motifs. These results expand our mechanistic understanding of SthA by highlighting reactivity with molecular oxygen and the importance of the evolutionarily conserved sequence motif.
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Affiliation(s)
- Michele Partipilo
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guang Yang
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de los Andes 950, D5700HHW, San Luis, Argentina
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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18
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Boverio A, Widodo WS, Santema LL, Rozeboom H, Xiang R, Guallar V, Mattevi A, Fraaije MW. Structural Elucidation and Engineering of a Bacterial Carbohydrate Oxidase. Biochemistry 2022; 62:429-436. [PMID: 35881507 PMCID: PMC9850908 DOI: 10.1021/acs.biochem.2c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Flavin-dependent carbohydrate oxidases are valuable tools in biotechnological applications due to their high selectivity in the oxidation of carbohydrates. In this study, we report the biochemical and structural characterization of a recently discovered carbohydrate oxidase from the bacterium Ralstonia solanacearum, which is a member of the vanillyl alcohol oxidase flavoprotein family. Due to its exceptionally high activity toward N-acetyl-d-galactosamine and N-acetyl-d-glucosamine, the enzyme was named N-acetyl-glucosamine oxidase (NagOx). In contrast to most known (fungal) carbohydrate oxidases, NagOx could be overexpressed in a bacterial host, which facilitated detailed biochemical and enzyme engineering studies. Steady state kinetic analyses revealed that non-acetylated hexoses were also accepted as substrates albeit with lower efficiency. Upon determination of the crystal structure, structural insights into NagOx were obtained. A large cavity containing a bicovalently bound FAD, tethered via histidyl and cysteinyl linkages, was observed. Substrate docking highlighted how a single residue (Leu251) plays a key role in the accommodation of N-acetylated sugars in the active site. Upon replacement of Leu251 (L251R mutant), an enzyme variant was generated with a drastically modified substrate acceptance profile, tuned toward non-N-acetylated monosaccharides and disaccharides. Furthermore, the activity toward bulkier substrates such as the trisaccharide maltotriose was introduced by this mutation. Due to its advantage of being overexpressed in a bacterial host, NagOx can be considered a promising alternative engineerable biocatalyst for selective oxidation of monosaccharides and oligosaccharides.
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Affiliation(s)
- Alessandro Boverio
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands,Department
of Biology and Biotechnology, University
of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Wahyu S. Widodo
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Lars L. Santema
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Henriëtte
J. Rozeboom
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Ruite Xiang
- Electronic
and Atomic Protein Modelling Group, Barcelona
Supercomputing Center, E-08034 Barcelona, Spain
| | - Víctor Guallar
- Electronic
and Atomic Protein Modelling Group, Barcelona
Supercomputing Center, E-08034 Barcelona, Spain
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University
of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Marco W. Fraaije
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands,
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19
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Venturi S, Trajkovic M, Colombo D, Brenna E, Fraaije MW, Gatti FG, Macchi P, Zamboni E. Chemoenzymatic Synthesis of the Most Pleasant Stereoisomer of Jessemal. J Org Chem 2022; 87:6499-6503. [PMID: 35442680 PMCID: PMC9087343 DOI: 10.1021/acs.joc.2c00427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
We describe the asymmetric
synthesis of the most pleasant enantiomer
of Jessemal fragrance. The key steps are (i) the one-pot reduction
of an α-chloro-tetrasubstituted cyclohexenone to give the chlorohydrin,
catalyzed by two stereoselective redox enzymes (an ene-reductase and
an alcohol dehydrogenase); (ii) the regioselective epoxide ring-opening
with organocuprate or organolithium nucleophiles. Density functional
theory calculations together with the Curtin–Hammett principle
allowed the rationalization of the regioselectivity.
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Affiliation(s)
- Silvia Venturi
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Danilo Colombo
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Francesco G Gatti
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Piero Macchi
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Emilio Zamboni
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
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20
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Abstract
![]()
Deazaflavin-dependent
whole-cell conversions in well-studied and
industrially relevant microorganisms such as Escherichia coli and Saccharomyces cerevisiae have high potential
for the biocatalytic production of valuable compounds. The artificial
deazaflavin FOP (FO-5′-phosphate) can functionally substitute
the natural deazaflavin F420 and can be synthesized in
fewer steps, offering a solution to the limited availability of the
latter due to its complex (bio)synthesis. Herein we set out to produce
FOP in vivo as a scalable FOP production method and as a means for
FOP-mediated whole-cell conversions. Heterologous expression of the
riboflavin kinase from Schizosaccharomyces pombe enabled
in vivo phosphorylation of FO, which was supplied by either organic
synthesis ex vivo, or by a coexpressed FO synthase in vivo, producing
FOP in E. coli as well as in S. cerevisiae. Through combined approaches of enzyme engineering as well as optimization
of expression systems and growth media, we further improved the in
vivo FOP production in both organisms. The improved FOP production
yield in E. coli is comparable to the F420 yield of native F420-producing organisms such
as Mycobacterium smegmatis, but the former can be
achieved in a significantly shorter time frame. Our E. coli expression system has an estimated production rate of 0.078 μmol
L–1 h–1 and results in an intracellular
FOP concentration of about 40 μM, which is high enough to support
catalysis. In fact, we demonstrate the successful FOP-mediated whole-cell
conversion of ketoisophorone using E. coli cells.
In S. cerevisiae, in vivo FOP production by SpRFK using supplied FO was improved through media optimization
and enzyme engineering. Through structure-guided enzyme engineering,
a SpRFK variant with 7-fold increased catalytic efficiency
compared to the wild type was discovered. By using this variant in
optimized media conditions, FOP production yield in S. cerevisiae was 20-fold increased compared to the very low initial yield of
0.24 ± 0.04 nmol per g dry biomass. The results show that bacterial
and eukaryotic hosts can be engineered to produce the functional deazaflavin
cofactor mimic FOP.
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Affiliation(s)
- Misun Lee
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - René M. de Jong
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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21
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Alvigini L, Gran-Scheuch A, Guo Y, Trajkovic M, Saifuddin M, Fraaije MW, Mattevi A. Discovery, Biocatalytic Exploration and Structural Analysis of a 4-Ethylphenol Oxidase from Gulosibacter chungangensis. Chembiochem 2021; 22:3225-3233. [PMID: 34523783 PMCID: PMC9293466 DOI: 10.1002/cbic.202100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/14/2021] [Indexed: 11/21/2022]
Abstract
The vanillyl‐alcohol oxidase (VAO) family is a rich source of biocatalysts for the oxidative bioconversion of phenolic compounds. Through genome mining and sequence comparisons, we found that several family members lack a generally conserved catalytic aspartate. This finding led us to study a VAO‐homolog featuring a glutamate residue in place of the common aspartate. This 4‐ethylphenol oxidase from Gulosibacter chungangensis (Gc4EO) shares 42 % sequence identity with VAO from Penicillium simplicissimum, contains the same 8α‐N3‐histidyl‐bound FAD and uses oxygen as electron acceptor. However, Gc4EO features a distinct substrate scope and product specificity as it is primarily effective in the dehydrogenation of para‐substituted phenols with little generation of hydroxylated products. The three‐dimensional structure shows that the characteristic glutamate side chain creates a closely packed environment that may limit water accessibility and thereby protect from hydroxylation. With its high thermal stability, well defined structural properties and high expression yields, Gc4EO may become a catalyst of choice for the specific dehydrogenation of phenolic compounds bearing small substituents.
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Affiliation(s)
- Laura Alvigini
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Alejandro Gran-Scheuch
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Yiming Guo
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Mohammad Saifuddin
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
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22
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Rembeza E, Boverio A, Fraaije MW, Engqvist MKM. Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen. Chembiochem 2021; 23:e202100510. [PMID: 34709726 PMCID: PMC9299179 DOI: 10.1002/cbic.202100510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Indexed: 12/17/2022]
Abstract
Discovery of novel enzymes is a challenging task, yet a crucial one, due to their increasing relevance as chemical catalysts and biotechnological tools. In our work we present a high-throughput screening approach to discovering novel activities. A screen of 96 putative oxidases with 23 substrates led to the discovery of two new enzymes. The first enzyme, N-acetyl-D-hexosamine oxidase (EC 1.1.3.29) from Ralstonia solanacearum, is a vanillyl alcohol oxidase-like flavoprotein displaying the highest activity with N-acetylglucosamine and N-acetylgalactosamine. Before our discovery of the enzyme, its activity was an orphan one - experimentally characterized but lacking the link to amino acid sequence. The second enzyme, from an uncultured marine euryarchaeota, is a long-chain alcohol oxidase (LCAO, EC 1.1.3.20) active with a range of fatty alcohols, with 1-dodecanol being the preferred substrate. The enzyme displays no sequence similarity to previously characterised LCAOs, and thus is a completely novel representative of a protein with such activity.
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Affiliation(s)
- Elzbieta Rembeza
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Alessandro Boverio
- 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
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
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23
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Drenth J, Yang G, Paul CE, Fraaije MW. A Tailor-Made Deazaflavin-Mediated Recycling System for Artificial Nicotinamide Cofactor Biomimetics. ACS Catal 2021; 11:11561-11569. [PMID: 34557329 PMCID: PMC8453485 DOI: 10.1021/acscatal.1c03033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/22/2021] [Indexed: 12/13/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) and its 2'-phosphorylated form NADP are crucial cofactors for a large array of biocatalytically important redox enzymes. Their high cost and relatively poor stability, however, make them less attractive electron mediators for industrial processes. Nicotinamide cofactor biomimetics (NCBs) are easily synthesized, are inexpensive, and are also generally more stable than their natural counterparts. A bottleneck for the application of these artificial hydride carriers is the lack of efficient cofactor recycling methods. Therefore, we engineered the thermostable F420:NADPH oxidoreductase from Thermobifida fusca (Tfu-FNO), by structure-inspired site-directed mutagenesis, to accommodate the unnatural N1 substituents of eight NCBs. The extraordinarily low redox potential of the natural cofactor F420H2 was then exploited to reduce these NCBs. Wild-type enzyme had detectable activity toward all selected NCBs, with K m values in the millimolar range and k cat values ranging from 0.09 to 1.4 min-1. Saturation mutagenesis at positions Gly-29 and Pro-89 resulted in mutants with up to 139 times higher catalytic efficiencies. Mutant G29W showed a k cat value of 4.2 s-1 toward 1-benzyl-3-acetylpyridine (BAP+), which is similar to the k cat value for the natural substrate NADP+. The best Tfu-FNO variants for a specific NCB were then used for the recycling of catalytic amounts of these nicotinamides in conversion experiments with the thermostable ene-reductase from Thermus scotoductus (TsOYE). We were able to fully convert 10 mM ketoisophorone with BAP+ within 16 h, using F420 or its artificial biomimetic FOP (FO-2'-phosphate) as an efficient electron mediator and glucose-6-phosphate as an electron donor. The generated toolbox of thermostable and NCB-dependent Tfu-FNO variants offers powerful cofactor regeneration biocatalysts for the reduction of several artificial nicotinamide biomimetics at both ambient and high temperatures. In fact, to our knowledge, this enzymatic method seems to be the best-performing NCB-recycling system for BNAH and BAPH thus far.
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Affiliation(s)
- Jeroen Drenth
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Guang Yang
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Caroline E. Paul
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Marco W. Fraaije
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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24
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Zuccarello L, Barbosa C, Galdino E, Lončar N, Silveira CM, Fraaije MW, Todorovic S. SERR Spectroelectrochemistry as a Guide for Rational Design of DyP-Based Bioelectronics Devices. Int J Mol Sci 2021; 22:7998. [PMID: 34360763 PMCID: PMC8348443 DOI: 10.3390/ijms22157998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Immobilised dye-decolorizing peroxidases (DyPs) are promising biocatalysts for the development of biotechnological devices such as biosensors for the detection of H2O2. To this end, these enzymes have to preserve native, solution properties upon immobilisation on the electrode surface. In this work, DyPs from Cellulomonas bogoriensis (CboDyP), Streptomyces coelicolor (ScoDyP) and Thermobifida fusca (TfuDyP) are immobilised on biocompatible silver electrodes functionalized with alkanethiols. Their structural, redox and catalytic properties upon immobilisation are evaluated by surface-enhanced resonance Raman (SERR) spectroelectrochemistry and cyclic voltammetry. Among the studied electrode/DyP constructs, only CboDyP shows preserved native structure upon attachment to the electrode. However, a comparison of the redox potentials of the enzyme in solution and immobilised states reveals a large discrepancy, and the enzyme shows no electrocatalytic activity in the presence of H2O2. While some immobilised DyPs outperform existing peroxidase-based biosensors, others fail to fulfil the essential requirements that guarantee their applicability in the immobilised state. The capacity of SERR spectroelectrochemistry for fast screening of the performance of immobilised heme enzymes places it in the front-line of experimental approaches that can advance the search for promising DyP candidates.
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Affiliation(s)
- Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Edilson Galdino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Nikola Lončar
- Gecco Biotech, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Marco W. Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
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25
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Tong Y, Lee M, Drenth J, Fraaije MW. Flavin-tag: A Facile Method for Site-Specific Labeling of Proteins with a Flavin Fluorophore. Bioconjug Chem 2021; 32:1559-1563. [PMID: 34304568 DOI: 10.1021/acs.bioconjchem.1c00306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific protein labeling methods are highly valuable tools for research and applications. We present a new protein labeling method that allows covalent attachment of a chromo- and fluorogenic flavin (FMN) to any targeted protein using a short flavinylation peptide-tag. We show that this peptide can be as short as 7 residues and can be located at the N-terminus, C-terminus, or in internal regions of the target protein. Analogous to kinase-catalyzed phosphorylation, the flavin is covalently attached via a stable phosphothreonyl linkage. The site-specific covalent tethering of FMN is accomplished by using a bacterial flavin transferase. The covalent coupling of FMN was shown to work in Escherichia coli and Saccharomyces cerevisiae cells and could be performed in vitro, rendering the "Flavin-tag" method a powerful tool for the selective decoration of proteins with a biocompatible redox-active fluorescent chromophore.
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Affiliation(s)
- Yapei Tong
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Misun Lee
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
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26
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Mascotti ML, Juri Ayub M, Fraaije MW. On the diversity of F 420 -dependent oxidoreductases: A sequence- and structure-based classification. Proteins 2021; 89:1497-1507. [PMID: 34216160 PMCID: PMC8518648 DOI: 10.1002/prot.26170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/30/2021] [Accepted: 06/26/2021] [Indexed: 11/05/2022]
Abstract
The F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although behaves as a nicotinamide cofactor due to its obligate hydride-transfer reactivity and similar low redox potential. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit great structural variability. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of the F420 -dependent oxidoreductases. Five different deazaflavoenzyme Classes (I-V) are described according to their structural folds as follows: Class I encompassing the TIM-barrel F420 -dependent enzymes; Class II including the Rossmann fold F420 -dependent enzymes; Class III comprising the β-roll F420 -dependent enzymes; Class IV which exclusively gathers the SH3 barrel F420 -dependent enzymes and Class V including the three layer ββα sandwich F420 -dependent enzymes. This classification provides a framework for the identification and biochemical characterization of novel deazaflavoenzymes.
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Affiliation(s)
- María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.,IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Maximiliano Juri Ayub
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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27
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Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW. Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase. FEBS J 2021; 288:3602-3618. [PMID: 33369202 PMCID: PMC8248431 DOI: 10.1111/febs.15687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
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Affiliation(s)
- Ulises A. Zitare
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE)Departamento de Química Inorgánica, Analítica y Química FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and CONICETArgentina
| | - Mohamed H. Habib
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Department of Microbiology and ImmunologyFaculty of PharmacyCairo UniversityEgypt
| | | | - Maria L. Mascotti
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- IMIBIO‐SL CONICETFacultad de Química Bioquímica y FarmaciaUniversidad Nacional de San LuisArgentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
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28
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Tjallinks G, Martin C, Fraaije MW. Enantioselective oxidation of secondary alcohols by the flavoprotein alcohol oxidase from Phanerochaete chrysosporium. Arch Biochem Biophys 2021; 704:108888. [PMID: 33910055 DOI: 10.1016/j.abb.2021.108888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
The enantioselective oxidation of secondary alcohols represents a valuable approach for the synthesis of optically pure compounds. Flavoprotein oxidases can catalyse such selective transformations by merely using oxygen as electron acceptor. While many flavoprotein oxidases preferably act on primary alcohols, the FAD-containing alcohol oxidase from Phanerochaete chrysosporium was found to be able to perform kinetic resolutions of several secondary alcohols. By selective oxidation of the (S)-alcohols, the (R)-alcohols were obtained in high enantiopurity. In silico docking studies were carried out in order to substantiate the observed (S)-selectivity. Several hydrophobic and aromatic residues in the substrate binding site create a cavity in which the substrates can comfortably undergo van der Waals and pi-stacking interactions. Consequently, oxidation of the secondary alcohols is restricted to one of the two enantiomers. This study has uncovered the ability of an FAD-containing alcohol oxidase, that is known for oxidizing small primary alcohols, to perform enantioselective oxidations of various secondary alcohols.
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Affiliation(s)
- Gwen Tjallinks
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, the Netherlands
| | - Caterina Martin
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, the Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, the Netherlands.
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29
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Martin C, Tjallinks G, Trajkovic M, Fraaije MW. Facile Stereoselective Reduction of Prochiral Ketones by using an F 420 -dependent Alcohol Dehydrogenase. Chembiochem 2021; 22:156-159. [PMID: 32935896 PMCID: PMC7820951 DOI: 10.1002/cbic.202000651] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/18/2022]
Abstract
Effective procedures for the synthesis of optically pure alcohols are highly valuable. A commonly employed method involves the biocatalytic reduction of prochiral ketones. This is typically achieved by using nicotinamide cofactor-dependent reductases. In this work, we demonstrate that a rather unexplored class of enzymes can also be used for this. We used an F420 -dependent alcohol dehydrogenase (ADF) from Methanoculleus thermophilicus that was found to reduce various ketones to enantiopure alcohols. The respective (S) alcohols were obtained in excellent enantiopurity (>99 % ee). Furthermore, we discovered that the deazaflavoenzyme can be used as a self-sufficient system by merely using a sacrificial cosubstrate (isopropanol) and a catalytic amount of cofactor F420 or the unnatural cofactor FOP to achieve full conversion. This study reveals that deazaflavoenzymes complement the biocatalytic toolbox for enantioselective ketone reductions.
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Affiliation(s)
- Caterina Martin
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
| | - Gwen Tjallinks
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
| | - Milos Trajkovic
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
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30
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Bailleul G, Nicoll CR, Mascotti ML, Mattevi A, Fraaije MW. Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties. J Biol Chem 2020; 296:100221. [PMID: 33759784 PMCID: PMC7948450 DOI: 10.1074/jbc.ra120.016297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/09/2022] Open
Abstract
Mammals rely on the oxidative flavin-containing monooxygenases (FMOs) to detoxify numerous and potentially deleterious xenobiotics; this activity extends to many drugs, giving FMOs high pharmacological relevance. However, our knowledge regarding these membrane-bound enzymes has been greatly impeded by the lack of structural information. We anticipated that ancestral-sequence reconstruction could help us identify protein sequences that are more amenable to structural analysis. As such, we hereby reconstructed the mammalian ancestral protein sequences of both FMO1 and FMO4, denoted as ancestral flavin-containing monooxygenase (AncFMO)1 and AncFMO4, respectively. AncFMO1, sharing 89.5% sequence identity with human FMO1, was successfully expressed as a functional enzyme. It displayed typical FMO activities as demonstrated by oxygenating benzydamine, tamoxifen, and thioanisole, drug-related compounds known to be also accepted by human FMO1, and both NADH and NADPH cofactors could act as electron donors, a feature only described for the FMO1 paralogs. AncFMO1 crystallized as a dimer and was structurally resolved at 3.0 Å resolution. The structure harbors typical FMO aspects with the flavin adenine dinucleotide and NAD(P)H binding domains and a C-terminal transmembrane helix. Intriguingly, AncFMO1 also contains some unique features, including a significantly porous and exposed active site, and NADPH adopting a new conformation with the 2’-phosphate being pushed inside the NADP+ binding domain instead of being stretched out in the solvent. Overall, the ancestrally reconstructed mammalian AncFMO1 serves as the first structural model to corroborate and rationalize the catalytic properties of FMO1.
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Affiliation(s)
- Gautier Bailleul
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Callum R Nicoll
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands.
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31
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Venturi S, Brenna E, Colombo D, Fraaije MW, Gatti FG, Macchi P, Monti D, Trajkovic M, Zamboni E. Multienzymatic Stereoselective Reduction of Tetrasubstituted Cyclic Enones to Halohydrins with Three Contiguous Stereogenic Centers. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Silvia Venturi
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
| | - Danilo Colombo
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Francesco G. Gatti
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
| | - Piero Macchi
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), C.N.R., Via Mario Bianco, 9, Milano 20131, Italy
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Emilio Zamboni
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica ”G. Natta”, Politecnico di Milano, P.zza Leonardo da Vinci 32, Milano 20133, Italy
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32
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Fabara AN, Fraaije MW. Production of indigo through the use of a dual-function substrate and a bifunctional fusion enzyme. Enzyme Microb Technol 2020; 142:109692. [PMID: 33220871 DOI: 10.1016/j.enzmictec.2020.109692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
The current chemical process for industrial indigo production puts a heavy burden on the environment. An attractive option would be to develop an alternative biotechnological process which does not rely on a petrochemical. This study describes a new biotransformation approach in which l-tryptophan is used as starting material. Its conversion to indigo can be achieved through recombinant overexpression of a bifunctional fusion enzyme, flavin-containing monooxygenase (FMO) fused to tryptophanase (TRP). First, TRP converts l-tryptophan into pyruvate, ammonia and indole. The formed indole serves as substrate for FMO, resulting in indigo formation, while pyruvate fuels the cells for regenerating the required NADPH. To optimize this bioconversion, different fusion constructs were tested. Fusing TRP to FMO at either the N-terminus (TRP-FMO) or the C-terminus (FMO-TRP) resulted in similar high expression levels of bifunctional fusion enzymes. Using whole cells and l-tryptophan as a precursor, high production levels of indigo could be obtained, significantly higher when compared with cells containing only overexpressed FMO. The TRP-FMO containing cells gave the highest yield of indigo resulting in full conversion of 2.0 g l-tryptophan into 1.7 g indigo per liter of culture. The process developed in this study provides an alternative biotransformation approach for the production of indigo starting from biobased starting material.
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Affiliation(s)
- Andrea N Fabara
- 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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33
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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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Tong Y, Trajkovic M, Savino S, van Berkel WJH, Fraaije MW. Substrate binding tunes the reactivity of hispidin 3-hydroxylase, a flavoprotein monooxygenase involved in fungal bioluminescence. J Biol Chem 2020; 295:16013-16022. [PMID: 32917724 DOI: 10.1074/jbc.ra120.014996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/10/2020] [Indexed: 11/06/2022] Open
Abstract
Fungal bioluminescence was recently shown to depend on a unique oxygen-dependent system of several enzymes. However, the identities of the enzymes did not reveal the full biochemical details of this process, as the enzymes do not bear resemblance to those of other luminescence systems, and thus the properties of the enzymes involved in this fascinating process are still unknown. Here, we describe the characterization of the penultimate enzyme in the pathway, hispidin 3-hydroxylase, from the luminescent fungus Mycena chlorophos (McH3H), which catalyzes the conversion of hispidin to 3-hydroxyhispidin. 3-Hydroxyhispidin acts as a luciferin substrate in luminescent fungi. McH3H was heterologously expressed in Escherichia coli and purified by affinity chromatography with a yield of 100 mg/liter. McH3H was found to be a single component monomeric NAD(P)H-dependent FAD-containing monooxygenase having a preference for NADPH. Through site-directed mutagenesis, based on a modeled structure, mutant enzymes were created that are more efficient with NADH. Except for identifying the residues that tune cofactor specificity, these engineered variants may also help in developing new hispidin-based bioluminescence applications. We confirmed that addition of hispidin to McH3H led to the formation of 3-hydroxyhispidin as sole aromatic product. Rapid kinetic analysis revealed that reduction of the flavin cofactor by NADPH is boosted by hispidin binding by nearly 100-fold. Similar to other class A flavoprotein hydroxylases, McH3H did not form a stable hydroperoxyflavin intermediate. These data suggest a mechanism by which the hydroxylase is tuned for converting hispidin into the fungal luciferin.
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Affiliation(s)
- Yapei Tong
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Simone Savino
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.
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Lončar N, Rozeboom HJ, Franken LE, Stuart MC, Fraaije MW. Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation. Biochem Biophys Res Commun 2020; 529:548-553. [DOI: 10.1016/j.bbrc.2020.06.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 01/15/2023]
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Abstract
This review presents a historical outline of the research on vanillyl alcohol oxidase (VAO) from Penicillium simplicissimum, one of the canonical members of the VAO/PCMH flavoprotein family. After describing its discovery and initial biochemical characterization, we discuss the physiological role, substrate scope, and catalytic mechanism of VAO, and review its three-dimensional structure and mechanism of covalent flavinylation. We also explain how protein engineering provided a deeper insight into the role of certain amino acid residues in determining the substrate specificity and enantioselectivity of the enzyme. Finally, we summarize recent computational studies about the migration of substrates and products through the enzyme's structure and the phylogenetic distribution of VAO and related enzymes.
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Affiliation(s)
- Tom A Ewing
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Gudrun Gygli
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands.
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37
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Abstract
This chapter represents a journey through flavoprotein oxidases. The purpose is to excite the reader curiosity regarding this class of enzymes by showing their diverse applications. We start with a brief overview on oxidases to then introduce flavoprotein oxidases and elaborate on the flavin cofactors, their redox and spectroscopic characteristics, and their role in the catalytic mechanism. The six major flavoprotein oxidase families will be described, giving examples of their importance in biology and their biotechnological uses. Specific attention will be given to a few selected flavoprotein oxidases that are not extensively discussed in other chapters of this book. Glucose oxidase, cholesterol oxidase, 5-(hydroxymethyl)furfural (HMF) oxidase and methanol oxidase are four examples of oxidases belonging to the GMC-like flavoprotein oxidase family and that have been shown to be valuable biocatalysts. Their structural and mechanistic features and recent enzyme engineering will be discussed in details. Finally we give a look at the current trend in research and conclude with a future outlook.
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Affiliation(s)
- Caterina Martin
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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38
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Corrigendum: Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020; 59:11698. [DOI: 10.1002/anie.202007393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Berichtigung: Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Savino S, Jensen S, Terwisscha van Scheltinga A, Fraaije MW. Analysis of the structure and substrate scope of chitooligosaccharide oxidase reveals high affinity for C2-modified glucosamines. FEBS Lett 2020; 594:2819-2828. [PMID: 32491191 DOI: 10.1002/1873-3468.13854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023]
Abstract
Chitooligosaccharide oxidase (ChitO) is a fungal carbohydrate oxidase containing a bicovalently bound FAD cofactor. The enzyme is known to catalyse the oxidation of chitooligosaccharides, oligomers of N-acetylated glucosamines derived from chitin degradation. In this study, the unique substrate acceptance was explored by testing a range of N-acetyl-d-glucosamine derivatives, revealing that ChitO preferentially accepts carbohydrates with a hydrophobic group attached to C2. The enzyme also accepts streptozotocin, a natural product used to treat tumours. Elucidation of the crystal structure provides an explanation for the high affinity towards C2-decorated glucosamines: the active site has a secondary binding pocket that accommodates groups attached at C2. Docking simulations are fully in line with the observed substrate preference. This work expands the knowledge on this versatile enzyme.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Sonja Jensen
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | | | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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41
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Roy A. Meoded
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Chemical and Bioprocesses Engineering Pontificia Universidad Católica de Chile Avenida Vicuña Mackenna 4860 7820436 Santiago Chile
| | - Agneya Bhushan
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco W. Fraaije
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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42
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020; 59:7761-7765. [PMID: 32040255 PMCID: PMC7586987 DOI: 10.1002/anie.201916005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/22/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are multimodular megaenzymes that biosynthesize many bioactive natural products. They contain a remarkable range of domains and module types that introduce different substituents into growing polyketide chains. As one such modification, we recently reported Baeyer-Villiger-type oxygen insertion into nascent polyketide backbones, thereby generating malonyl thioester intermediates. In this work, genome mining focusing on architecturally diverse oxidation modules in trans-AT PKSs led us to the culturable plant symbiont Gynuella sunshinyii, which harbors two distinct modules in one orphan PKS. The PKS product was revealed to be lobatamide A, a potent cytotoxin previously only known from a marine tunicate. Biochemical studies show that one module generates glycolyl thioester intermediates, while the other is proposed to be involved in oxime formation. The data suggest varied roles of oxygenation modules in the biosynthesis of polyketide scaffolds and support the importance of trans-AT PKSs in the specialized metabolism of symbiotic bacteria.
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Affiliation(s)
- Reiko Ueoka
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Roy A. Meoded
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- Department of Chemical and Bioprocesses EngineeringPontificia Universidad Católica de ChileAvenida Vicuña Mackenna 48607820436SantiagoChile
| | - Agneya Bhushan
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jörn Piel
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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43
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Román R, Lončar N, Casablancas A, Fraaije MW, Gonzalez G. High-level production of industrially relevant oxidases by a two-stage fed-batch approach: overcoming catabolite repression in arabinose-inducible Escherichia coli systems. Appl Microbiol Biotechnol 2020; 104:5337-5345. [PMID: 32322946 DOI: 10.1007/s00253-020-10622-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/03/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
With the growing interest in enzyme applications, there is an urgent demand for economic, affordable, and flexible enzyme production processes. In the present paper, we developed a high cell density fed-batch process for the production of two cofactor-containing oxidase, 5-hydroxymethylfurfural oxidase (HMFO) and eugenol oxidase (EUGO). The approach involved the arabinose-inducible system to drive the expression while using mineral media. In order to overcome a major drawback of arabinose-inducible promoters, carbon catabolite repression, (CCR) by glucose, we developed a high cell density culture (HCDC), two-stage fed-batch protocol allowing us to reach cell densities exceeding 70 g/L of dry cell weight (DCW) using glucose as carbon source. Then, induction was achieved by adding arabinose, while changing the carbon source to glycerol. This strategy allowed us to obtain an eightfold increase in recombinant HMFO titer when compared with a reference batch fermentation in Erlenmeyer flasks using terrific broth (TB), typically used with arabinose-inducible strains. The optimized protocol was also tested for expression of a structurally unrelated oxidase, EUGO, where a similar yield was achieved. Clearly, this two-step protocol in which a relatively cheap medium (when compared to TB) can be used reduces costs and provides a way to obtain protein production levels similar to those of IPTG-based systems. KEY POINTS: • Arabinose promoters are not well suited for HCDC production due to CCR effect. • This drawback has been overcome by using a two-stage Fed-batch protocol. • Protein yield has been increased by an eightfold factor, improving process economics.
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Affiliation(s)
- Ramón Román
- Fermentation Pilot Plant, Department of Chemical, Biological and Enviromental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | | | - Antoni Casablancas
- Fermentation Pilot Plant, Department of Chemical, Biological and Enviromental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marco W Fraaije
- Molecular Enzymology group, University of Groningen, Groningen, The Netherlands
| | - Glòria Gonzalez
- Fermentation Pilot Plant, Department of Chemical, Biological and Enviromental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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44
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Aalbers FS, Fürst MJ, Rovida S, Trajkovic M, Gómez Castellanos JR, Bartsch S, Vogel A, Mattevi A, Fraaije MW. Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering. eLife 2020; 9:e54639. [PMID: 32228861 PMCID: PMC7164962 DOI: 10.7554/elife.54639] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Enzyme instability is an important limitation for the investigation and application of enzymes. Therefore, methods to rapidly and effectively improve enzyme stability are highly appealing. In this study we applied a computational method (FRESCO) to guide the engineering of an alcohol dehydrogenase. Of the 177 selected mutations, 25 mutations brought about a significant increase in apparent melting temperature (ΔTm ≥ +3 °C). By combining mutations, a 10-fold mutant was generated with a Tm of 94 °C (+51 °C relative to wild type), almost reaching water's boiling point, and the highest increase with FRESCO to date. The 10-fold mutant's structure was elucidated, which enabled the identification of an activity-impairing mutation. After reverting this mutation, the enzyme showed no loss in activity compared to wild type, while displaying a Tm of 88 °C (+45 °C relative to wild type). This work demonstrates the value of enzyme stabilization through computational library design.
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Affiliation(s)
- Friso S Aalbers
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Maximilian Jlj Fürst
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stefano Rovida
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| | | | | | | | - Andrea Mattevi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
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45
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Martin C, Trajkovic M, Fraaije MW. Production of Hydroxy Acids: Selective Double Oxidation of Diols by Flavoprotein Alcohol Oxidase. Angew Chem Int Ed Engl 2020; 59:4869-4872. [PMID: 31912947 PMCID: PMC7079103 DOI: 10.1002/anie.201914877] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/18/2019] [Indexed: 11/10/2022]
Abstract
Flavoprotein oxidases can catalyze oxidations of alcohols and amines by merely using molecular oxygen as the oxidant, making this class of enzymes appealing for biocatalysis. The FAD-containing (FAD=flavin adenine dinucleotide) alcohol oxidase from P. chrysosporium facilitated double and triple oxidations for a range of aliphatic diols. Interestingly, depending on the diol substrate, these reactions result in formation of either lactones or hydroxy acids. For example, diethylene glycol could be selectively and fully converted into 2-(2-hydroxyethoxy)acetic acid. Such a facile cofactor-independent biocatalytic route towards hydroxy acids opens up new avenues for the preparation of polyester building blocks.
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Affiliation(s)
- Caterina Martin
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
| | - Milos Trajkovic
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 4GroningenThe Netherlands
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46
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Maenpuen S, Pongsupasa V, Pensook W, Anuwan P, Kraivisitkul N, Pinthong C, Phonbuppha J, Luanloet T, Wijma HJ, Fraaije MW, Lawan N, Chaiyen P, Wongnate T. Creating Flavin Reductase Variants with Thermostable and Solvent-Tolerant Properties by Rational-Design Engineering. Chembiochem 2020; 21:1481-1491. [PMID: 31886941 DOI: 10.1002/cbic.201900737] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 02/06/2023]
Abstract
We have employed computational approaches-FireProt and FRESCO-to predict thermostable variants of the reductase component (C1 ) of (4-hydroxyphenyl)acetate 3-hydroxylase. With the additional aid of experimental results, two C1 variants, A166L and A58P, were identified as thermotolerant enzymes, with thermostability improvements of 2.6-5.6 °C and increased catalytic efficiency of 2- to 3.5-fold. After heat treatment at 45 °C, both of the thermostable C1 variants remain active and generate reduced flavin mononucleotide (FMNH- ) for reactions catalyzed by bacterial luciferase and by the monooxygenase C2 more efficiently than the wild type (WT). In addition to thermotolerance, the A166L and A58P variants also exhibited solvent tolerance. Molecular dynamics (MD) simulations (6 ns) at 300-500 K indicated that mutation of A166 to L and of A58 to P resulted in structural changes with increased stabilization of hydrophobic interactions, and thus in improved thermostability. Our findings demonstrated that improvements in the thermostability of C1 enzyme can lead to broad-spectrum uses of C1 as a redox biocatalyst for future industrial applications.
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Affiliation(s)
- Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Wiranee Pensook
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Piyanuch Anuwan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | | | - Chatchadaporn Pinthong
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23 Road, Bangkok, 10110, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Thikumporn Luanloet
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huaykaew Road, Suthep, Chiang Mai, 50200, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
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47
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Romero E, Savino S, Fraaije MW, Lončar N. Mechanistic and Crystallographic Studies of Azoreductase AzoA from Bacillus wakoensis A01. ACS Chem Biol 2020; 15:504-512. [PMID: 31967777 PMCID: PMC7040913 DOI: 10.1021/acschembio.9b00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 01/26/2023]
Abstract
The azoreductase AzoA from the alkali-tolerant Bacillus wakoensis A01 has been studied to reveal its structural and mechanistic details. For this, a recombinant expression system was developed which yields impressive amounts of fully active enzyme. The purified holo enzyme is remarkably solvent-tolerant and thermostable with an apparent melting temperature of 71 °C. The dimeric enzyme contains FMN as a prosthetic group and is strictly NADH dependent. While AzoA shows a negligible ability to use molecular oxygen as an electron acceptor, it is efficient in reducing various azo dyes and quinones. The kinetic and catalytic mechanism has been studied in detail using steady state kinetic analyses and stopped-flow studies. The data show that AzoA performs quinone and azo dye reductions via a two-electron transfer. Moreover, quinones were shown to be much better substrates (kcat values of 100-400 s-1 for several naphtoquinones) when compared with azo dyes. This suggests that the physiological role of AzoA and sequence-related microbial reductases is linked to quinone reductions and that they can better be annotated as quinone reductases. The structure of AzoA has been determined in complex with FMN at 1.8 Å resolution. AzoA displays unique features in the active site providing clues for explaining its catalytic and thermostability features. An uncommon loop, when compared with sequence-related reductases, forms an active site lid with Trp60 acting as an anchor. Several Trp60 mutants have been analyzed disclosing an important role of this residue in the stability of AzoA, while they retained activity. Structural details are discussed in relation to other azo and quinone reductases. This study provides new insights into the molecular functioning of AzoA and sequence-related reductases.
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Affiliation(s)
- Elvira Romero
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - 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
| | - Nikola Lončar
- GECCO
Biotech, Nijenborgh 4, 9747AG Groningen, The Netherlands
- Molecular
Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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48
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Martin C, Trajkovic M, Fraaije MW. Production of Hydroxy Acids: Selective Double Oxidation of Diols by Flavoprotein Alcohol Oxidase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914877] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Caterina Martin
- Molecular Enzymology GroupUniversity of Groningen Nijenborgh 4 Groningen The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology GroupUniversity of Groningen Nijenborgh 4 Groningen The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of Groningen Nijenborgh 4 Groningen The Netherlands
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49
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Abstract
Indigo is one of the oldest textile dyes and was originally prepared from plant material. Nowadays, indigo is chemically synthesized at a large scale to satisfy the demand for dyeing jeans. The current indigo production processes are based on fossil feedstocks; therefore, it is highly attractive to develop a more sustainable and environmentally friendly biotechnological process for the production of this popular dye. In the past decades, a number of natural and engineered enzymes have been identified that can be used for the synthesis of indigo. This mini-review provides an overview of the various microbial enzymes which are able to produce indigo and discusses the advantages and disadvantages of each biocatalytic system.
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Affiliation(s)
- Andrea N Fabara
- Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology group, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Lončar N, van Beek HL, Fraaije MW. Structure-Based Redesign of a Self-Sufficient Flavin-Containing Monooxygenase towards Indigo Production. Int J Mol Sci 2019; 20:ijms20246148. [PMID: 31817552 PMCID: PMC6940849 DOI: 10.3390/ijms20246148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Indigo is currently produced by a century-old petrochemical-based process, therefore it is highly attractive to develop a more environmentally benign and efficient biotechnological process to produce this timeless dye. Flavin-containing monooxygenases (FMOs) are able to oxidize a wide variety of substrates. In this paper we show that the bacterial mFMO can be adapted to improve its ability to convert indole into indigo. The improvement was achieved by a combination of computational and structure-inspired enzyme redesign. We showed that the thermostability and the kcat for indole could be improved 1.5-fold by screening a relatively small number of enzyme mutants. This project not only resulted in an improved biocatalyst but also provided an improved understanding of the structural elements that determine the activity of mFMO and provides hints for further improvement of the monooxygenase as biocatalyst.
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Affiliation(s)
| | - Hugo L. van Beek
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
| | - Marco W. Fraaije
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: ; Tel.: +31-50-3634345
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