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Phienluphon A, Kondo K, Mikami B, Nagata T, Katahira M. Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii. Int J Biol Macromol 2023; 253:127188. [PMID: 37783244 DOI: 10.1016/j.ijbiomac.2023.127188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, attractive for biochemical production. Among these, Aspergillus sydowii FAE (AsFaeE), an SF6 FAE, exhibits remarkable activity across various substrates. In this study, we conducted X-ray crystallography and kinetic analysis to unravel the molecular mechanisms governing substrate recognition and catalysis by AsFaeE. AsFaeE exhibits a typical α/β-hydrolase fold, characterized by a catalytic triad of serine, aspartate, and histidine. Comparative analysis of substrate-free, ferulic acid-bound, and sinapic acid-bound forms of AsFaeE suggests a conformational change in the loop covering the substrate-binding pocket upon binding. Notably, Pro158 and Phe159 within this loop cover the phenolic part of the substrate, forming three layers of planar rings. Our structure-based functional mutagenesis clarifies the roles of the residues involved in substrate binding and catalytic activity. Furthermore, distinct substrate-binding mechanisms between AsFaeE and other studied FAEs are identified. This investigation offers the initial structural insights into substrate recognition by SF6 FAEs, equipping us with structural knowledge that might facilitate the design of FAE variants capable of efficiently processing a wider range of substrate sizes.
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Affiliation(s)
- Apisan Phienluphon
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Integrated Research Center for Carbon Negative Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Integrated Research Center for Carbon Negative Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Integrated Research Center for Carbon Negative Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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2
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Khattab IM, Fischer J, Kaźmierczak A, Thines E, Nick P. Ferulic acid is a putative surrender signal to stimulate programmed cell death in grapevines after infection with Neofusicoccum parvum. PLANT, CELL & ENVIRONMENT 2023; 46:339-358. [PMID: 36263963 DOI: 10.1111/pce.14468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
An apoplectic breakdown from grapevine trunk diseases (GTDs) has become a serious challenge to viticulture as a consequence of drought stress. We hypothesize that fungal aggressiveness is controlled by a chemical communication between the host and colonizing fungus. We introduce the new concept of a 'plant surrender signal' accumulating in host plants under stress and facilitating the aggressive behaviour of the strain Neofusicoccum parvum (Bt-67) causing Botryosphaeriaceae-related dieback in grapevines. Using a cell-based experimental system (Vitis cells) and bioactivity-guided fractionation, we identify trans-ferulic acid, a monolignol precursor, as a 'surrender signal'. We show that this signal specifically activates the secretion of the fungal phytotoxin fusicoccin A aglycone. We show further that this phytotoxin, mediated by 14-3-3 proteins, activates programmed cell death in Vitis cells. We arrive at a model showing a chemical communication facilitating fusicoccin A secretion that drives necrotrophic behaviour during Botryosphaeriaceae-Vitis interaction through trans-ferulic acid. We thus hypothesize that channelling the phenylpropanoid pathway from this lignin precursor to the trans-resveratrol phytoalexin could be a target for future therapy.
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Affiliation(s)
- Islam M Khattab
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Jochen Fischer
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH, Kaiserslautern, Germany
| | - Andrzej Kaźmierczak
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH, Kaiserslautern, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
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3
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Lo Verde C, Pepra-Ameyaw NB, Drucker CT, Okumura TLS, Lyon KA, Muniz JC, Sermet CS, Were Senger L, Owens CP. A highly active esterase from Lactobacillus helveticus hydrolyzes chlorogenic acid in sunflower meal to prevent chlorogenic acid induced greening in sunflower protein isolates. Food Res Int 2022; 162:111996. [PMID: 36461298 DOI: 10.1016/j.foodres.2022.111996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Chlorogenic acid (CGA) is an ester between caffeic and quinic acid. It is found in many foods and reacts with free amino groups in proteins at alkaline pH, leading to the formation of an undesirable green pigment in sunflower seed-derived ingredients. This paper presents the biochemical characterization and application of a highly active chlorogenic acid esterase from Lactobacillus helveticus. The enzyme is one of the most active CGA esterases known to date with a Km of 0.090 mM and a kcat of 82.1 s-1. The CGA esterase is easily expressed recombinantly in E. coli in large yields and is stable over a wide range of pH and temperatures. We characterized CGA esterase's kinetic properties in sunflower meal and demonstrated that the enzyme completely hydrolyzes CGA in the meal. Finally, we showed that CGA esterase treatment of sunflower seed meal enables the production of pale brown sunflower protein isolates using alkaline extraction. This work will allow for more widespread use of sunflower-derived products in applications where neutrally-colored food products are desired.
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Affiliation(s)
- Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Nana Baah Pepra-Ameyaw
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Charles T Drucker
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Tracie L S Okumura
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Katherine A Lyon
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Julia C Muniz
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Chloe S Sermet
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Lilian Were Senger
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
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4
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Vega-Rodríguez MAD, Rodríguez-González JA, Armendáriz-Ruiz MA, Asaff-Torres A, Sotelo-Mundo RR, Velasco-Lozano S, Mateos-Díaz JC. Feruloyl Esterases Protein Engineering to Enhance Their Performance as Biocatalysts: A Review. Chembiochem 2022; 23:e202200354. [PMID: 35781918 DOI: 10.1002/cbic.202200354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/01/2022] [Indexed: 02/03/2023]
Abstract
Feruloyl esterases (FAEs) are versatile enzymes able to release hydroxycinnamic acids or synthesize their ester derivatives, both molecules with interesting biological activities such as: antioxidants, antifungals, antivirals, antifibrotic, anti-inflammatory, among others. The importance of these molecules in medicine, food or cosmetic industries provides FAEs with several biotechnological applications as key industrial biocatalysts. However, FAEs have some operational limitations that must be overcome, which can be addressed through different protein engineering approaches to enhance their thermal stability, catalytic efficiencies, and selectivity. This review aims to present a brief historical tour through the mutagenesis strategies employed to improve enzymes performance and analyze the current protein engineering strategies applied to FAEs as interesting biocatalysts. Finally, an outlook of the future of FAEs protein engineering approaches to achieve successful industrial biocatalysts is given.
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Affiliation(s)
- Ms Ana Daniela Vega-Rodríguez
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Jorge Alberto Rodríguez-González
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | | | - Ali Asaff-Torres
- Unidad de Biotecnología Industrial, Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a la Victoria Km 0.6, 83304, Hermosillo, Sonora, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a la Victoria Km 0.6, 83304, Hermosillo, Sonora (Mexico
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Miramon Pasealekua, 182, 20014, Donostia, Spain
| | - Juan Carlos Mateos-Díaz
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
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5
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Liu P, Guo J, Miao L, Liu H. Enhancing the secretion of a feruloyl esterase in Bacillus subtilis by signal peptide screening and rational design. Protein Expr Purif 2022; 200:106165. [PMID: 36038098 DOI: 10.1016/j.pep.2022.106165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Feruloyl esterase is a subclass of α/β hydrolase, which could release ferulic acid from biomass residues for use as an efficient additive in food or pharmaceutical industries. In the present study, a feruloyl esterase with broad substrate specificity was characterised and secreted by Bacillus subtilis WB600. After codon usage optimisation and signal peptide library screening, the secretion amount of feruloyl esterase was enhanced by up to 10.2-fold in comparison with the base strain. The site-specific amino acid substitutions that facilitate protein folding further improved the secretion by about 1.5-fold. The purified rationally designed enzyme exhibited maximal activity against methyl ferulate at pH 6.5 and 65 °C. In the solid-state fermentation, the genetically engineered B. subtilis released about 37% of the total alkali-extractable ferulic acid in maize bran. This study provides a promising candidate for ferulic acid production and demonstrates that the secretion of a heterologous enzyme from B. subtilis can be cumulatively improved by changes in protein sequence features.
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Affiliation(s)
- Pulin Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jingxiao Guo
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Lihong Miao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Hanyan Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
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6
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Hameleers L, Penttinen L, Ikonen M, Jaillot L, Fauré R, Terrapon N, Deuss PJ, Hakulinen N, Master ER, Jurak E. Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:127. [PMID: 34059129 PMCID: PMC8165983 DOI: 10.1186/s13068-021-01976-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/19/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes. RESULTS We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/β-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs. CONCLUSIONS The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Leena Penttinen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Martina Ikonen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Léa Jaillot
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Régis Fauré
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Terrapon
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Peter J Deuss
- Department of Chemical Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Yliopistokatu 7, 80130, Joensuu, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Edita Jurak
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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7
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Silveira RL, Knott BC, Pereira CS, Crowley MF, Skaf MS, Beckham GT. Transition Path Sampling Study of the Feruloyl Esterase Mechanism. J Phys Chem B 2021; 125:2018-2030. [PMID: 33616402 DOI: 10.1021/acs.jpcb.0c09725] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine-histidine-aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the "moving histidine" mechanism, thus calling into question the "ring flip" mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s-1. Overall, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.
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Affiliation(s)
- Rodrigo L Silveira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil.,Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Brandon C Knott
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Caroline S Pereira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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8
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Kmezik C, Mazurkewich S, Meents T, McKee LS, Idström A, Armeni M, Savolainen O, Brändén G, Larsbrink J. A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. J Biol Chem 2021; 296:100500. [PMID: 33667545 PMCID: PMC8040265 DOI: 10.1016/j.jbc.2021.100500] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomke Meents
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden
| | - Alexander Idström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marina Armeni
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden.
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9
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Underlin EN, Frommhagen M, Dilokpimol A, van Erven G, de Vries RP, Kabel MA. Feruloyl Esterases for Biorefineries: Subfamily Classified Specificity for Natural Substrates. Front Bioeng Biotechnol 2020; 8:332. [PMID: 32391342 PMCID: PMC7191039 DOI: 10.3389/fbioe.2020.00332] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/21/2022] Open
Abstract
Feruloyl esterases (FAEs) have an important role in the enzymatic conversion of lignocellulosic biomass by decoupling plant cell wall polysaccharides and lignin. Moreover, FAEs release anti-oxidative hydroxycinnamic acids (HCAs) from biomass. As a plethora of FAE candidates were found in fungal genomes, FAE classification related to substrate specificity is an indispensability for selection of most suitable candidates. Hence, linking distinct substrate specificities to a FAE classification, such as the recently classified FAE subfamilies (SF), is a promising approach to improve the application of these enzymes for a variety of industrial applications. In total, 14 FAEs that are classified members of SF1, 5, 6, 7, 9, and 13 were tested in this research. All FAEs were investigated for their activity toward a variety of substrates: synthetic model substrates, plant cell wall-derived substrates, including lignin, and natural substrates. Released HCAs were determined using reverse phase-ultra high performance liquid chromatography coupled to UV detection and mass spectrometry. Based on this study, FAEs of SF5 and SF7 showed the highest release of FA, pCA, and diFAs over the range of substrates, while FAEs of SF6 were comparable but less pronounced for diFAs release. These results suggest that SF5 and SF7 FAEs are promising enzymes for biorefinery applications, like the production of biofuels, where a complete degradation of the plant cell wall is desired. In contrast, SF6 FAEs might be of interest for industrial applications that require a high release of only FA and pCA, which are needed as precursors for the production of biochemicals. In contrast, FAEs of SF1, 9 and 13 showed an overall low release of HCAs from plant cell wall-derived and natural substrates. The obtained results substantiate the previous SF classification as a useful tool to predict the substrate specificity of FAEs, which eases the selection of FAE candidates for industrial applications.
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Affiliation(s)
- Emilie N. Underlin
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, Netherlands
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, Netherlands
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10
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Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED. The crystal structure of a Fusarium oxysporum feruloyl esterase that belongs to the tannase family. FEBS Lett 2020; 594:1738-1749. [PMID: 32297315 DOI: 10.1002/1873-3468.13776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022]
Abstract
Feruloyl esterases are enzymes of industrial interest that catalyse the hydrolysis of the ester bond between hydroxycinnamic acids such as ferulic acid and sugars present in the plant cell wall. Although there are several structures of biochemically characterized feruloyl esterases available, the structural determinants of their substrate specificity are not yet fully understood. Here, we present the crystal structure of a feruloyl esterase from Fusarium oxysporum (FoFaeC) at 2.3 Å resolution. Similar to the two other tannase-like feruloyl esterases, FoFaeC features a large lid domain covering the active site with potential regulatory role and a disulphide bond that brings together the serine and histidine of the catalytic triad. Differences are mainly observed in the metal coordination site and the substrate binding pocket. ENZYMES: E.C.3.1.1.73. DATABASES: The sequence of FoFaeC has been deposited with UniProt with accession code A0A1D3S5H0_FUSOX and the atomic coordinates of the three-dimensional structure with Protein Data Bank, with PDB code: 6FAT.
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Affiliation(s)
- Maria Dimarogona
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, Greece
| | - Evangelos Topakas
- School of Chemical Engineering, National Technical University of Athens, Greece
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Sweden
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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11
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Kmezik C, Bonzom C, Olsson L, Mazurkewich S, Larsbrink J. Multimodular fused acetyl-feruloyl esterases from soil and gut Bacteroidetes improve xylanase depolymerization of recalcitrant biomass. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:60. [PMID: 32266006 PMCID: PMC7110780 DOI: 10.1186/s13068-020-01698-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/16/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plant biomass is an abundant and renewable carbon source that is recalcitrant towards both chemical and biochemical degradation. Xylan is the second most abundant polysaccharide in biomass after cellulose, and it possesses a variety of carbohydrate substitutions and non-carbohydrate decorations which can impede enzymatic degradation by glycoside hydrolases. Carbohydrate esterases are able to cleave the ester-linked decorations and thereby improve the accessibility of the xylan backbone to glycoside hydrolases, thus improving the degradation process. Enzymes comprising multiple catalytic glycoside hydrolase domains on the same polypeptide have previously been shown to exhibit intramolecular synergism during degradation of biomass. Similarly, natively fused carbohydrate esterase domains are encoded by certain bacteria, but whether these enzymes can result in similar synergistic boosts in biomass degradation has not previously been evaluated. RESULTS Two carbohydrate esterases with similar architectures, each comprising two distinct physically linked catalytic domains from families 1 (CE1) and 6 (CE6), were selected from xylan-targeting polysaccharide utilization loci (PULs) encoded by the Bacteroidetes species Bacteroides ovatus and Flavobacterium johnsoniae. The full-length enzymes as well as the individual catalytic domains showed activity on a range of synthetic model substrates, corn cob biomass, and Japanese beechwood biomass, with predominant acetyl esterase activity for the N-terminal CE6 domains and feruloyl esterase activity for the C-terminal CE1 domains. Moreover, several of the enzyme constructs were able to substantially boost the performance of a commercially available xylanase on corn cob biomass (close to twofold) and Japanese beechwood biomass (up to 20-fold). Interestingly, a significant improvement in xylanase biomass degradation was observed following addition of the full-length multidomain enzyme from B. ovatus versus the addition of its two separated single domains, indicating an intramolecular synergy between the esterase domains. Despite high sequence similarities between the esterase domains from B. ovatus and F. johnsoniae, their addition to the xylanolytic reaction led to different degradation patterns. CONCLUSION We demonstrated that multidomain carbohydrate esterases, targeting the non-carbohydrate decorations on different xylan polysaccharides, can considerably facilitate glycoside hydrolase-mediated hydrolysis of xylan and xylan-rich biomass. Moreover, we demonstrated for the first time a synergistic effect between the two fused catalytic domains of a multidomain carbohydrate esterase.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Cyrielle Bonzom
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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12
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Su R, Ni K, Wang T, Yang X, Zhang J, Liu Y, Shi W, Yan L, Jie C, Zhong J. Effects of ferulic acid esterase-producing Lactobacillus fermentum and cellulase additives on the fermentation quality and microbial community of alfalfa silage. PeerJ 2019; 7:e7712. [PMID: 31608168 PMCID: PMC6788448 DOI: 10.7717/peerj.7712] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/21/2019] [Indexed: 12/02/2022] Open
Abstract
Background Alfalfa (Medicago sativa) is an important forage material widely used for animal feed production. Ensiling is an effective method for preserving alfalfa, but it has shown some limitations in the production of high-quality alfalfa silage due to its low water soluble carbohydrates (WSC) content and high buffering capacity. Lactic acid bacteria (LAB) and cellulase are often used as silage additives to promote the ensiling process and enhance fermentation quality. Methods Experiments were conducted to investigate the effects of ferulic acid esterase (FAE)-producing Lactobacillus fermentum 17SD-2 (LF) and cellulase (CE) on the fermentation quality and microbial community of alfalfa silage. After 60 days of ensiling, analysis of fermentation quality and bacterial diversity in alfalfa silages were conducted using high-performance liquid chromatography and high-throughput sequencing methods. Results Alfalfa was ensiled with additives (LF, CE, and LF+CE) or without additives for 60 days. All additives increased lactic acid and decreased pH values and ammonia-N contents compared to control. Among all treatments, the combined addition of LF and CE showed lowest pH (4.66) and ammonia-N (NH3-N, 0.57% DM) content, highest contents of lactic acid (LA, 10.51% DM), dry matter (DM, 22.54%) and crude protein (CP, 24.60% DM). Combined addition of LF and CE performed better in reducing neutral detergent fiber (NDF, 29.76% DM) and acid detergent fiber (ADF, 22.86% DM) contents than the addition of LF (33.71, 27.39% DM) or CE (32.07, 25.45% DM) alone. Moreover, the microbial analysis indicated that LF+CE treatments increased the abundance of desirable Lactobacillus and inhibited the growth of detrimental Enterobacter and Clostridia in alfalfa silage. Discussion Combined addition of FAE-producing LF and CE is more effective than treatments of LF or CE alone in improving fermentation quality and nutrition values of alfalfa silage. This is likely due to a synergistic effect of CE and FAE produced by LF on plant cell wall degradation, indicating that these additives promote each other to improve fiber degradation and silage fermentation. In conclusion, combined addition of FAE-producing LF and CE could be a feasible way to improve alfalfa silage quality.
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Affiliation(s)
- Rina Su
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianwei Wang
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaopan Yang
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yayong Liu
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weixiong Shi
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liu Yan
- Hebei Zhongyu Zhongke Biotechnology Development Company, Hebei, China
| | - Chen Jie
- Hebei Zhongyu Zhongke Biotechnology Development Company, Hebei, China
| | - Jin Zhong
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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13
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Holck J, Fredslund F, Møller MS, Brask J, Krogh KBRM, Lange L, Welner DH, Svensson B, Meyer AS, Wilkens C. A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan. J Biol Chem 2019; 294:17339-17353. [PMID: 31558605 DOI: 10.1074/jbc.ra119.009523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/17/2019] [Indexed: 12/25/2022] Open
Abstract
Feruloyl esterases (EC 3.1.1.73), belonging to carbohydrate esterase family 1 (CE1), hydrolyze ester bonds between ferulic acid (FA) and arabinose moieties in arabinoxylans. Recently, some CE1 enzymes identified in metagenomics studies have been predicted to contain a family 48 carbohydrate-binding module (CBM48), a CBM family associated with starch binding. Two of these CE1s, wastewater treatment sludge (wts) Fae1A and wtsFae1B isolated from wastewater treatment surplus sludge, have a cognate CBM48 domain and are feruloyl esterases, and wtsFae1A binds arabinoxylan. Here, we show that wtsFae1B also binds to arabinoxylan and that neither binds starch. Surface plasmon resonance analysis revealed that wtsFae1B's Kd for xylohexaose is 14.8 μm and that it does not bind to starch mimics, β-cyclodextrin, or maltohexaose. Interestingly, in the absence of CBM48 domains, the CE1 regions from wtsFae1A and wtsFae1B did not bind arabinoxylan and were also unable to catalyze FA release from arabinoxylan. Pretreatment with a β-d-1,4-xylanase did enable CE1 domain-mediated FA release from arabinoxylan in the absence of CBM48, indicating that CBM48 is essential for the CE1 activity on the polysaccharide. Crystal structures of wtsFae1A (at 1.63 Å resolution) and wtsFae1B (1.98 Å) revealed that both are folded proteins comprising structurally-conserved hydrogen bonds that lock the CBM48 position relative to that of the CE1 domain. wtsFae1A docking indicated that both enzymes accommodate the arabinoxylan backbone in a cleft at the CE1-CBM48 domain interface. Binding at this cleft appears to enable CE1 activities on polymeric arabinoxylan, illustrating an unexpected and crucial role of CBM48 domains for accommodating arabinoxylan.
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Affiliation(s)
- Jesper Holck
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Folmer Fredslund
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK-2800 Kongens Lyngby, Denmark
| | - Marie S Møller
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kongens Lyngby, Denmark
| | | | - Lene Lange
- LLa-Bioeconomy, Research and Advisory, Karensgade 5, DK-2500 Valby, Denmark
| | - Ditte H Welner
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK-2800 Kongens Lyngby, Denmark
| | - Birte Svensson
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Casper Wilkens
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
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14
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Metagenomic discovery of feruloyl esterases from rumen microflora. Appl Microbiol Biotechnol 2019; 103:8449-8457. [PMID: 31511934 DOI: 10.1007/s00253-019-10102-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/31/2019] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
Abstract
Feruloyl esterases (FAEs) are a key group of enzymes that hydrolyze ferulic acids ester-linked to plant polysaccharides. The cow's rumen is a highly evolved ecosystem of complex microbial microflora capable of converting fibrous substances to energy. From direct cloning of the rumen microbial metagenome, we identified seven active phagemids conferring feruloyl esterase activity. The genomic inserts ranged from 1633 to 4143 bp, and the ORFs from 681 to 1359 bp. BLAST search reveals sequence homology to feruloyl esterases and esterases/lipases identified in anaerobes. The seven genes were expressed in Escherichia coli, and the proteins were purified to homogeneity. The FAEs were found to cover types B, C, and D in the feruloyl esterase classification system using model hydroxycinnamic acid esters. The release of ferulic acid (FA) catalyzed by these enzymes was established using natural substrates corn fiber (CF) and wheat insoluble arabinoxylan (WIA). Three of the enzymes were demonstrated to cleave diferulates and hence the capability to break down Araf-FA-FA-Araf cross-links. The wide variation in the sequence, activity, and substrate specificity observed in the FAEs discovered in this study is a confirming evidence that combined actions of a full range of FAE enzymes contribute to the high-efficiency fiber digestion in the rumen microbial ecosystem.
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15
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Karnaouri A, Antonopoulou I, Zerva A, Dimarogona M, Topakas E, Rova U, Christakopoulos P. Thermophilic enzyme systems for efficient conversion of lignocellulose to valuable products: Structural insights and future perspectives for esterases and oxidative catalysts. BIORESOURCE TECHNOLOGY 2019; 279:362-372. [PMID: 30685134 DOI: 10.1016/j.biortech.2019.01.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/12/2019] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Thermophilic enzyme systems are of major importance nowadays in all industrial processes due to their great performance at elevated temperatures. In the present review, an overview of the current knowledge on the properties of thermophilic and thermotolerant carbohydrate esterases and oxidative enzymes with great thermostability is provided, with respect to their potential use in biotechnological applications. A special focus is given to the lytic polysaccharide monooxygenases that are able to oxidatively cleave lignocellulose through the use of oxygen or hydrogen peroxide as co-substrate and a reducing agent as electron donor. Structural characteristics of the enzymes, including active site conformation and surface properties are discussed and correlated with their substrate specificity and thermostability properties.
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Affiliation(s)
- Anthi Karnaouri
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| | - Io Antonopoulou
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Anastasia Zerva
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Maria Dimarogona
- Section of Process and Environmental Engineering, Department of Chemical Engineering, University of Patras, 26504 Rio, Patras, Greece
| | - Evangelos Topakas
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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16
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Oliveira DM, Mota TR, Oliva B, Segato F, Marchiosi R, Ferrarese-Filho O, Faulds CB, Dos Santos WD. Feruloyl esterases: Biocatalysts to overcome biomass recalcitrance and for the production of bioactive compounds. BIORESOURCE TECHNOLOGY 2019; 278:408-423. [PMID: 30704902 DOI: 10.1016/j.biortech.2019.01.064] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 05/25/2023]
Abstract
Ferulic acid and its hydroxycinnamate derivatives represent one of the most abundant forms of low molecular weight phenolic compounds in plant biomass. Feruloyl esterases are part of a microorganism's plant cell wall-degrading enzymatic arsenal responsible for cleaving insoluble wall-bound hydroxycinnamates and soluble cytosolic conjugates. Stimulated by industrial requirements, accelerating scientific discoveries and knowledge transfer, continuous improvement efforts have been made to identify, create and repurposed biocatalysts dedicated to plant biomass conversion and biosynthesis of high-added value molecules. Here we review the basic knowledge and recent advances in biotechnological characteristics and the gene content encoding for feruloyl esterases. Information about several enzymes is systematically organized according to their function, biochemical properties, substrate specificity, and biotechnological applications. This review contributes to further structural, functional, and biotechnological R&D both for obtaining hydroxycinnamates from agricultural by-products as well as for lignocellulose biomass treatments aiming for production of bioethanol and other derivatives of industrial interest.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil.
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Craig B Faulds
- Aix-Marseille Université, INRA UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France
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17
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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18
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Romero-Borbón E, Grajales-Hernández D, Armendáriz-Ruiz M, Ramírez-Velasco L, Rodríguez-González JA, Cira-Chávez LA, Estrada-Alvarado MI, Mateos-Díaz JC. Type C feruloyl esterase from Aspergillus ochraceus: A butanol specific biocatalyst for the synthesis of hydroxycinnamates in a ternary solvent system. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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19
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Mäkelä MR, Dilokpimol A, Koskela SM, Kuuskeri J, de Vries RP, Hildén K. Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database. Microb Biotechnol 2018; 11:869-880. [PMID: 29697197 PMCID: PMC6116738 DOI: 10.1111/1751-7915.13273] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023] Open
Abstract
Feruloyl esterases (FAEs) are accessory enzymes for plant biomass degradation, which catalyse hydrolysis of carboxylic ester linkages between hydroxycinnamic acids and plant cell‐wall carbohydrates. They are a diverse group of enzymes evolved from, e.g. acetyl xylan esterases (AXEs), lipases and tannases, thus complicating their classification and prediction of function by sequence similarity. Recently, an increasing number of fungal FAEs have been biochemically characterized, owing to their potential in various biotechnological applications and multitude of candidate FAEs in fungal genomes. However, only part of the fungal FAEs are included in Carbohydrate Esterase family 1 (CE1) of the carbohydrate‐active enzymes (CAZy) database. In this work, we performed a phylogenetic analysis that divided the fungal members of CE1 into five subfamilies of which three contained characterized enzymes with conserved activities. Conservation within one of the subfamilies was confirmed by characterization of an additional CE1 enzyme from Aspergillus terreus. Recombinant A. terreus FaeD (AtFaeD) showed broad specificity towards synthetic methyl and ethyl esters, and released ferulic acid from plant biomass substrates, demonstrating its true FAE activity and interesting features as potential biocatalyst. The subfamily division of the fungal CE1 members enables more efficient selection of candidate enzymes for biotechnological processes.
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Affiliation(s)
- Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Salla M Koskela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Jaana Kuuskeri
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Kristiina Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Helsinki, Finland
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20
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Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies. N Biotechnol 2018; 41:9-14. [DOI: 10.1016/j.nbt.2017.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 12/21/2022]
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21
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Insights into substrate binding of ferulic acid esterases by arabinose and methyl hydroxycinnamate esters and molecular docking. Sci Rep 2017; 7:17315. [PMID: 29230049 PMCID: PMC5725599 DOI: 10.1038/s41598-017-17260-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/23/2017] [Indexed: 01/24/2023] Open
Abstract
Ferulic acid esterases (FAE, EC 3.1.1.73) cleave the arabinose hydroxycinnamate ester in plant hemicellulose and other related substrates. FAE are commonly categorised as type A-D based on catalytic activities towards model, short alkyl chain esters of hydroxycinnamates. However, this system correlates poorly with sequence and structural features of the enzymes. In this study, we investigated the basis of the type A categorisation of an FAE from Aspergillus niger, AnFaeA, by comparing its activity toward methyl and arabinose hydroxycinnamate esters. kcat/Km ratios revealed that AnFaeA hydrolysed arabinose ferulate 1600-fold, and arabinose caffeate 6.5 times more efficiently than their methyl ester counterparts. Furthermore, small docking studies showed that while all substrates adopted a catalytic orientation with requisite proximity to the catalytic serine, methyl caffeate and methyl p-coumarate preferentially formed alternative non-catalytic conformations that were energetically favoured. Arabinose ferulate was unable to adopt the alternative conformation while arabinose caffeate preferred the catalytic orientation. This study demonstrates that use of short alkyl chain hydroxycinnnamate esters can result in activity misclassification. The findings of this study provide a basis for developing a robust classification system for FAE and form the basis of sequence-function relationships for this class.
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Schär A, Sprecher I, Topakas E, Faulds CB, Nyström L. Hydrolysis of Nonpolar n-Alkyl Ferulates by Feruloyl Esterases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8549-8554. [PMID: 27600375 DOI: 10.1021/acs.jafc.6b02694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ferulic acid is one of the major phenolic acids in plants and can be found esterified to plant cell wall components, but also as long-chain n-alkyl and steryl esters. Microbial feruloyl esterases may play a role in the bioavailability of phenolic acids during human and animal digestion. It is therefore of interest if feruloyl esterases are capable of hydrolyzing nonpolar ferulic acid esters. A series of n-alkyl ferulates with increasing lipophilicity were enzymatically synthesized, and the kinetic constants of their hydrolysis by four feruloyl esterases and a lipase as control were determined. A decrease in Km and kcat could be observed with decreased substrate polarity for all of the feruloyl esterases. Only one feruloyl esterase and the control lipase showed hydrolytic activity toward octadecyl ferulate. These results led to the conclusion that lipophilic ferulates are poor substrates for known feruloyl esterases and more specific esterases/lipases need to be identified.
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Affiliation(s)
- Aline Schär
- Institute of Food, Nutrition and Health, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
| | - Isabel Sprecher
- Institute of Food, Nutrition and Health, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens , 5 Iroon Polytechniou Str., Zografou Campus, 15700 Athens, Greece
| | - Craig B Faulds
- Aix Marseille Université , INRA BBF UMR_A 1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille cedex 02, France
- INRA BBF UMR_A1163, Polytech Marseille , 163 Avenue de Luminy, 13288 Marseille cedex 02, France
| | - Laura Nyström
- Institute of Food, Nutrition and Health, ETH Zurich , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
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Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases. Biochem J 2016; 473:839-49. [PMID: 27026397 DOI: 10.1042/bj20151153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/18/2016] [Indexed: 11/17/2022]
Abstract
Lignocellulosic biomass is a promising renewable resource; however, deconstruction of this material is still the rate-limiting step. Major obstacles in the biocatalytic turnover of lignocellulose are ester-linked decorations that prevent access to primary structural polysaccharides. Enzymes targeting these esters represent promising biotools for increasing bioconversion efficiency. Ruminant livestock are unique in their ability to degrade lignocellulose through the action of their gut microbiome. The anaerobic fungi (phylum Neocallimastigomycota) are key members of this ecosystem that express a large repertoire of carbohydrate-active enzymes (CAZymes) with little sequence identity with characterized CAZymes [Lombard, Golaconda, Drula, Coutinho and Henrissat (2014) Nucleic Acids Res. 42: , D490-D495]. We have identified a carbohydrate esterase family 1 (CE1) ferulic acid esterase (FAE) belonging to Anaeromyces mucronatus(AmCE1/Fae1a), and determined its X-ray structure in both the presence [1.55 Å (1 Å=0.1 nm)] and absence (1.60 Å) of ferulic acid. AmCE1 adopts an α/β-hydrolase fold that is structurally conserved with bacterial FAEs, and possesses a unique loop, termed the β-clamp, that encloses the ligand. Isothermal titration calorimetry reveals that substrate binding is driven by enthalpic contributions, which overcomes a large entropic penalty. A comparative analysis of AmCE1 with related enzymes has uncovered the apparent structural basis for differential FAE activities targeting cross-linking ferulic acid conjugates compared with terminal decorations. Based on comparisons to structurally characterized FAEs, we propose that the β-clamp may define the structural basis of exolytic activities in FAEs. This provides a structure-based tool for predicting exolysis and endolysis in CE1. These insights hold promise for rationally identifying enzymes tailored for bioconversion of biomass with variations in cell wall composition.
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Gherbovet O, Fauré R, Ferreira F, Durand J, Ragon M, Hostyn G, Record E, Bozonnet S, O’Donohue MJ. Design of chromogenic probes for efficient screening and evaluation of feruloyl esterase-like activities. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Dilokpimol A, Mäkelä MR, Aguilar-Pontes MV, Benoit-Gelber I, Hildén KS, de Vries RP. Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:231. [PMID: 27795736 PMCID: PMC5084320 DOI: 10.1186/s13068-016-0651-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
Feruloyl esterases (FAEs) represent a diverse group of carboxyl esterases that specifically catalyze the hydrolysis of ester bonds between ferulic (hydroxycinnamic) acid and plant cell wall polysaccharides. Therefore, FAEs act as accessory enzymes to assist xylanolytic and pectinolytic enzymes in gaining access to their site of action during biomass conversion. Their ability to release ferulic acid and other hydroxycinnamic acids from plant biomass makes FAEs potential biocatalysts in a wide variety of applications such as in biofuel, food and feed, pulp and paper, cosmetics, and pharmaceutical industries. This review provides an updated overview of the knowledge on fungal FAEs, in particular describing their role in plant biomass degradation, diversity of their biochemical properties and substrate specificities, their regulation and conditions needed for their induction. Furthermore, the discovery of new FAEs using genome mining and phylogenetic analysis of current publicly accessible fungal genomes will also be presented. This has led to a new subfamily classification of fungal FAEs that takes into account both phylogeny and substrate specificity.
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Affiliation(s)
- Adiphol Dilokpimol
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Miia R. Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Kristiina S. Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Ronald P. de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
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Acidic–alkaline ferulic acid esterase from Chaetomium thermophilum var. dissitum: Molecular cloning and characterization of recombinant enzyme expressed in Pichia pastoris. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2015.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Probing role of key residues in the divergent evolution of Yarrowia lipolytica lipase 2 and Aspergillus niger eruloyl esterase A. Microbiol Res 2015; 178:27-34. [DOI: 10.1016/j.micres.2015.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/09/2015] [Accepted: 05/16/2015] [Indexed: 11/19/2022]
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Topakas E, Moukouli M, Dimarogona M, Christakopoulos P. Expression, characterization and structural modelling of a feruloyl esterase from the thermophilic fungus Myceliophthora thermophila. Appl Microbiol Biotechnol 2011; 94:399-411. [PMID: 22012339 DOI: 10.1007/s00253-011-3612-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/20/2011] [Accepted: 09/28/2011] [Indexed: 11/25/2022]
Abstract
A ferulic acid esterase (FAE) from the thermophilic fungus Myceliophthora thermophila (synonym Sporotrichum thermophile), belonging to the carbohydrate esterase family 1 (CE-1), was functionally expressed in methylotrophic yeast Pichia pastoris. The putative FAE from the genomic DNA was successfully cloned in P. pastoris X-33 to confirm that the enzyme exhibits FAE activity. The recombinant FAE was purified to its homogeneity (39 kDa) and subsequently characterized using a series of model substrates including methyl esters of hydroxycinnamates, alkyl ferulates and monoferuloylated 4-nitrophenyl glycosides. The substrate specificity profiling reveals that the enzyme shows a preference for the hydrolysis of methyl caffeate and p-coumarate and a strong preference for the hydrolysis of n-butyl and iso-butyl ferulate. The enzyme was active on substrates containing ferulic acid ester linked to the C-5 and C-2 linkages of arabinofuranose, whilst it was found capable of de-esterifying acetylated glucuronoxylans. Ferulic acid (FA) was efficiently released from destarched wheat bran when the esterase was incubated together with an M3 xylanase from Trichoderma longibrachiatum (a maximum of 41% total FA released after 1 h incubation). Prediction of the secondary structure of MtFae1a was performed in the PSIPRED server whilst modelling the 3D structure was accomplished by the use of the HH 3D structure prediction server.
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Affiliation(s)
- Evangelos Topakas
- School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Lai KK, Stogios PJ, Vu C, Xu X, Cui H, Molloy S, Savchenko A, Yakunin A, Gonzalez CF. An inserted α/β subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase. PLoS One 2011; 6:e23269. [PMID: 21876742 PMCID: PMC3158066 DOI: 10.1371/journal.pone.0023269] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 07/14/2011] [Indexed: 11/18/2022] Open
Abstract
Background Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. Methodology/Principal Findings We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical α/β fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser106, His225, and Asp197, while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted α/β subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. Conclusions The binding mechanism characterized (involving the inserted α/β subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases.
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Affiliation(s)
- Kin-Kwan Lai
- Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Peter J. Stogios
- Banting and Best Department of Medical Research, Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario, Canada
| | - Clara Vu
- Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- UF Undergraduate Research Program MCB4905, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Xiaohui Xu
- Banting and Best Department of Medical Research, Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario, Canada
| | - Hong Cui
- Banting and Best Department of Medical Research, Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario, Canada
| | - Sara Molloy
- Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- UF Undergraduate Research Program MCB4905, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Yakunin
- Banting and Best Department of Medical Research, Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario, Canada
| | - Claudio F. Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Faulds CB, Pérez-Boada M, Martínez AT. Influence of organic co-solvents on the activity and substrate specificity of feruloyl esterases. BIORESOURCE TECHNOLOGY 2011; 102:4962-4967. [PMID: 21354789 DOI: 10.1016/j.biortech.2011.01.088] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/27/2011] [Accepted: 01/28/2011] [Indexed: 05/30/2023]
Abstract
Organic co-solvents can expand the use of enzymes in lignocellulose deconstruction through making substrates more soluble and thus more accessible. In choosing the most adequate co-solvent for feruloyl esterases, hydrolysis of methyl p-hydroxycinnamates by three pure enzymes (and a multi-enzyme preparation) was evaluated. Low concentrations of dimethylsulfoxide (DMSO) enhanced hydrolysis by two of the enzymes while at levels >20%, activity was reduced. DMSO also enhanced acetyl esterase-type activity of the enzymes. The co-solvent effect was different for each enzyme-substrate couple, indicating that other factors are also involved. Kinetic studies with a Talaromyces stipitatus feruloyl esterase showed low concentrations of dimethylsulfoxide enhanced the hydrolytic rate while K(m) also increased. Moreover, long-term incubation (96 h) of an Aspergillus niger feruloyl esterase in dimethylsulfoxide:water provided to the enzyme the ability to hydrolyze methyl p-coumarate, suggesting an active-site re-arrangement. Dimethylsulfoxide (10-30%) is proposed as an adequate co-solvent for feruloyl esterase treatment of water-insoluble substrates.
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Affiliation(s)
- Craig B Faulds
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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A thermostable feruloyl-esterase from the hemicellulolytic bacterium Thermobacillus xylanilyticus releases phenolic acids from non-pretreated plant cell walls. Appl Microbiol Biotechnol 2011; 90:541-52. [DOI: 10.1007/s00253-011-3103-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
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The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases. Biotechnol Adv 2011; 29:94-110. [DOI: 10.1016/j.biotechadv.2010.09.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 08/27/2010] [Accepted: 09/06/2010] [Indexed: 11/18/2022]
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Fazary AE, Hamad HA, Lee JC, Koskei T, Lee CK, Ju YH. Expression of feruloyl esterase from Aspergillus awamori in Escherichia coli: Characterization and crystal studies of the recombinant enzyme. Int J Biol Macromol 2010; 46:440-4. [DOI: 10.1016/j.ijbiomac.2010.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 01/24/2010] [Accepted: 01/28/2010] [Indexed: 11/16/2022]
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Buanafina MMDO, Langdon T, Hauck B, Dalton S, Timms-Taravella E, Morris P. Targeting expression of a fungal ferulic acid esterase to the apoplast, endoplasmic reticulum or golgi can disrupt feruloylation of the growing cell wall and increase the biodegradability of tall fescue (Festuca arundinacea). PLANT BIOTECHNOLOGY JOURNAL 2010; 8:316-31. [PMID: 20102533 DOI: 10.1111/j.1467-7652.2009.00485.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the cell walls of grasses, ferulic acid is esterified to arabinoxylans and undergoes oxidative reactions to form ferulates dimers, trimers and oligomers. Feruloylation of arabinoxylan is considered important not only because it leads to cross-linked xylans but also because ferulates may act as a nucleating site for the formation of lignin and hence link arabinoxylans to lignin by forming a lignin-ferulate-arabinoxylan complex. Such cross-linking is among the main factors inhibiting the release of fermentable carbohydrates from grasses either for ruminant nutrition or for biofuel production. We have found that significant reductions in the levels of monomeric and dimeric phenolics can be achieved in the growing cell walls during plant development in leaves of Festuca arundinacea by constitutive intracellular targeted expression of Aspergillus niger ferulic acid esterase (FAEA). We propose that this occurred by directly disrupting ester bonds linking phenolics to cell wall polysaccharides by apoplast targeting or by preventing excessive feruloylation of cell wall carbohydrates prior to their incorporation into the cell wall, by targeting to the Golgi membrane system. Plants with lower cell wall ferulate levels, which showed increased digestibility and increased rates of cellulase-mediated release of fermentable sugars, were identified. Targeting FAE to the Golgi was found to be more effective than targeting to the ER, which supports the current theories of the Golgi as the site of feruloylation of arabinoxylans. It is concluded that targeting FAEA expression to the Golgi or apoplast is likely to be an effective strategy for improving wall digestibility in grass species used for fodder or cellulosic ethanol production.
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Affiliation(s)
- Marcia M de O Buanafina
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth University, Wales, UK.
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Vieites JM, Ghazi A, Beloqui A, Polaina J, Andreu JM, Golyshina OV, Nechitaylo TY, Waliczek A, Yakimov MM, Golyshin PN, Ferrer M. Inter-conversion of catalytic abilities in a bifunctional carboxyl/feruloyl-esterase from earthworm gut metagenome. Microb Biotechnol 2009; 3:48-58. [PMID: 21255305 PMCID: PMC3815946 DOI: 10.1111/j.1751-7915.2009.00135.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Carboxyl esterases (CE) exhibit various reaction specificities despite of their overall structural similarity. In present study we have exploited functional metagenomics, saturation mutagenesis and experimental protein evolution to explore residues that have a significant role in substrate discrimination. We used an enzyme, designated 3A6, derived from the earthworm gut metagenome that exhibits CE and feruloyl esterase (FAE) activities with p‐nitrophenyl and cinnamate esters, respectively, with a [(kcat/Km)]CE/[(kcat/Km)]FAE factor of 17. Modelling‐guided saturation mutagenesis at specific hotspots (Lys281, Asp282, Asn316 and Lys317) situated close to the catalytic core (Ser143/Asp273/His305) and a deletion of a 34‐AA–long peptide fragment yielded mutants with the highest CE activity, while cinnamate ester bond hydrolysis was effectively abolished. Although, single to triple mutants with both improved activities (up to 180‐fold in kcat/Km values) and enzymes with inverted specificity ((kcat/Km)CE/(kcat/Km)FAE ratio of ∼0.4) were identified, no CE inactive variant was found. Screening of a large error‐prone PCR‐generated library yielded by far less mutants for substrate discrimination. We also found that no significant changes in CE activation energy occurs after any mutation (7.3 to −5.6 J mol−1), whereas a direct correlation between loss/gain of FAE function and activation energies (from 33.05 to −13.7 J mol−1) was found. Results suggest that the FAE activity in 3A6 may have evolved via introduction of a limited number of ‘hot spot’ mutations in a common CE ancestor, which may retain the original hydrolytic activity due to lower restrictive energy barriers but conveys a dynamic energetically favourable switch of a second hydrolytic reaction.
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Affiliation(s)
- José María Vieites
- CSIC, Institute of Catalysis, 28049 Madrid, Spain. CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain
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Cloning, characterization and functional expression of an alkalitolerant type C feruloyl esterase from Fusarium oxysporum. Appl Microbiol Biotechnol 2008; 79:245-54. [DOI: 10.1007/s00253-008-1432-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 02/22/2008] [Accepted: 02/24/2008] [Indexed: 11/26/2022]
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Fazary AE, Ju YH. Feruloyl esterases as biotechnological tools: current and future perspectives. Acta Biochim Biophys Sin (Shanghai) 2007; 39:811-28. [PMID: 17989872 DOI: 10.1111/j.1745-7270.2007.00348.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Feruloyl esterases represent a diverse group of hydrolases catalyzing the cleavage and formation of ester bonds between plant cell wall polysaccharide and phenolic acid. They are widely distributed in plants and microorganisms. Besides lipases, a considerable number of microbial feruloyl esterases have also been discovered and overexpressed. This review summarizes the latest research on their classification, production, and biophysicochemical properties. Special emphasis is given to the importance of that type of enzyme and their related phenolic ferulic acid compound in biotechnological processes, and industrial and medicinal applications.
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Affiliation(s)
- Ahmed E Fazary
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106-07, Taiwan, China
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Levasseur A, Gouret P, Lesage-Meessen L, Asther M, Asther M, Record E, Pontarotti P. Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol Biol 2006; 6:92. [PMID: 17092334 PMCID: PMC1660568 DOI: 10.1186/1471-2148-6-92] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 11/08/2006] [Indexed: 11/10/2022] Open
Abstract
Background There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and functional shifts with special emphasis on the role of the environment. For this purpose, we studied the fungal lipase/feruloyl esterase A family, whose functional diversification makes it a very promising candidate. Results The results suggested functional shift following a duplication event where neofunctionalisation of feruloyl esterase A had occurred with conservation of the ancestral lipase function. Evolutionary shift was detected using the branch-site model for testing positive selection on individual codons along specific lineages. Positively selected amino acids were detected. Furthermore, biological data obtained from site-directed mutagenesis experiments clearly demonstrated that certain amino acids under positive selection were involved in the functional shift. We reassessed evolutionary history in terms of environmental response, and hypothesized that environmental changes such as colonisation by terrestrial plants might have driven adaptation by functional diversification in Euascomycetes (Aspergilli), thus conferring a selective advantage on this group. Conclusion The results reported here illustrate a rare example of connection between fundamental events in molecular evolution. We demonstrated an unequivocal connection between evolutionary and functional shifts, which led us to conclude that these events were probably linked to environmental change.
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Affiliation(s)
- Anthony Levasseur
- Phylogenomics Laboratory. EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
| | - Philippe Gouret
- Phylogenomics Laboratory. EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France
| | - Laurence Lesage-Meessen
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
| | - Michèle Asther
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
| | - Marcel Asther
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
| | - Eric Record
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
| | - Pierre Pontarotti
- Phylogenomics Laboratory. EA 3781 Evolution Biologique Université de Provence, Case 19, Pl. V. Hugo, 13331 Marseille Cedex 03, France
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Benoit I, Asther M, Sulzenbacher G, Record E, Marmuse L, Parsiegla G, Gimbert I, Asther M, Bignon C. Respective importance of protein folding and glycosylation in the thermal stability of recombinant feruloyl esterase A. FEBS Lett 2006; 580:5815-21. [PMID: 17027758 DOI: 10.1016/j.febslet.2006.09.039] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 09/07/2006] [Accepted: 09/18/2006] [Indexed: 10/24/2022]
Abstract
The thermal stability of four molecular forms (native, refolded, glycosylated, non-glycosylated) of feruloyl esterase A (FAEA) was studied. From the most to the least thermo-resistant, the four molecular species ranked as follows: (i) glycosylated form produced native, (ii) non-glycosylated form produced native, (iii) non-glycosylated form produced as inclusion bodies and refolded, and (iv) glycosylated form produced native chemically denatured and then refolded. On the basis of these results and of crystal structure data, we discuss the respective importance of protein folding and glycosylation in the thermal stability of recombinant FAEA.
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Affiliation(s)
- Isabelle Benoit
- UMR 1163 INRA/Universités de Provence et de la Méditerranée, Unité de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, ESIL, 163 avenue de Luminy CP 925, 13288 MARSEILLE cedex 09, France
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42
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Gordillo F, Caputo V, Peirano A, Chavez R, Van Beeumen J, Vandenberghe I, Claeyssens M, Bull P, Ravanal MC, Eyzaguirre J. Penicillium purpurogenum produces a family 1 acetyl xylan esterase containing a carbohydrate-binding module: characterization of the protein and its gene. ACTA ACUST UNITED AC 2006; 110:1129-39. [PMID: 17008082 DOI: 10.1016/j.mycres.2006.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 05/22/2006] [Accepted: 07/05/2006] [Indexed: 11/21/2022]
Abstract
At least three acetyl xylan esterases (AXE I, II and III) are secreted by Penicillium purpurogenum. This publication describes more detailed work on AXE I and its gene. AXE I binds cellulose but not xylan; it is glycosylated and inactivated by phenylmethylsulphonyl fluoride, showing that it is a serine esterase. The axe1 gene presents an open reading frame of 1278 bp, including two introns of 68 and 61 bp; it codes for a signal peptide of 31 residues and a mature protein of 351 amino acids (molecular weight 36,693). AXE I has a modular structure: a catalytic module at the amino terminus belonging to family 1 of the carbohydrate esterases, a linker rich in serines and threonines, and a family 1 carboxy terminal carbohydrate binding module (CBM). The CBM is similar to that of AXE from Trichoderma reesei, (with a family 5 catalytic module) indicating that the genes for catalytic modules and CBMs have evolved separately, and that they have been linked by gene fusion. The promoter sequence of axe1 contains several putative sequences for binding of gene expression regulators also found in other family 1 esterase gene promoters. It is proposed that AXE I and II act in succession in xylan degradation; first, xylan is attacked by AXE I and other xylanases possessing CBMs (which facilitate binding to lignocellulose), followed by other enzymes acting mainly on soluble substrates.
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Affiliation(s)
- Felipe Gordillo
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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43
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Vafiadi C, Topakas E, Christakopoulos P, Faulds CB. The feruloyl esterase system of Talaromyces stipitatus: Determining the hydrolytic and synthetic specificity of TsFaeC. J Biotechnol 2006; 125:210-21. [PMID: 16584797 DOI: 10.1016/j.jbiotec.2006.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 02/02/2006] [Accepted: 02/17/2006] [Indexed: 10/24/2022]
Abstract
The active site of the recombinant Talaromyces stipitatus type-C feruloyl esterase (TsFaeC) was probed using a series of C1-C4 alkyl ferulates and methyl esters of phenylalkanoic and cinnamic acids. The enzyme was active on 23 of the 34 substrates tested. Lengthening or shortening the aliphatic side chain while maintaining the same aromatic substitutions completely abolished the enzyme activity. Maintaining the phenylpropenoate structure but altering the substitutions of the aromatic ring demonstrated the importance of hydroxyl groups on meta and/or para position of the benzoic ring. The highest catalytic efficiency of TsFaeC for methyl cinnamates was shown on methyl 3,4-dihydroxy cinnamate and on its hydro form (3,4-dihydroxy-phenyl-propionate). Maintaining the ferulate structure but altering the esterified alkyl group, the comparison of k(cat) and k(cat)/K(m) values showed that the enzyme hydrolysed faster and more efficiently than ethyl ferulate. Alkyl ferulates were applied also for substrate selectivity mapping of feruloyl esterase to catalyze feruloyl group transfer to l-arabinose, using as a reaction system a ternary water-organic mixture consisting of n-hexane, t-butanol and water. The reaction parameters affecting the feruloylation rate and the conversion of the enzymatic synthesis, such as the composition of the reaction media, temperature, substrate and enzyme concentration have been investigated.
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Affiliation(s)
- Christina Vafiadi
- Biotechnology Laboratory, Chemical Engineering Department, National Technical University of Athens, 5 Iroon Polytechniou Str, Zografou Campus, 15700 Athens, Greece
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Benoit I, Navarro D, Marnet N, Rakotomanomana N, Lesage-Meessen L, Sigoillot JC, Asther M, Asther M. Feruloyl esterases as a tool for the release of phenolic compounds from agro-industrial by-products. Carbohydr Res 2006; 341:1820-7. [PMID: 16697997 DOI: 10.1016/j.carres.2006.04.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/07/2006] [Accepted: 04/11/2006] [Indexed: 11/28/2022]
Abstract
Agro-industrial by-products are a potential source of added-value phenolic acids with promising applications in the food and pharmaceutical industries. Here two purified feruloyl esterases from Aspergillus niger, FAEA and FAEB were tested for their ability to release phenolic acids such as caffeic acid, p-coumaric acid and ferulic acid from coffee pulp, apple marc and wheat straw. Their hydrolysis activity was evaluated and compared with their action on maize bran and sugar beet pulp. The specificity of both enzymes against natural and synthetic substrates was evaluated; particular attention was paid to quinic esters and lignin monomers. The efficiency of both enzymes on model substrates was studied. We show the ability of these enzymes to hydrolyze quinic esters and ester linkages between phenolic acids and lignin monomer.
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Affiliation(s)
- Isabelle Benoit
- UMR-1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, Marseille, France
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