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Jian X, Li C, Feng X. Strategies for modulating transglycosylation activity, substrate specificity, and product polymerization degree of engineered transglycosylases. Crit Rev Biotechnol 2023; 43:1284-1298. [PMID: 36154438 DOI: 10.1080/07388551.2022.2105687] [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: 12/23/2021] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
Abstract
Glycosides are widely used in many fields due to their favorable biological activity. The traditional plant extractions and chemical methods for glycosides production are limited by environmentally unfriendly, laborious protecting group strategies and low yields. Alternatively, enzymatic glycosylation has drawn special attention due to its mild reaction conditions, high catalytic efficiency, and specific stereo-/regioselectivity. Glycosyltransferases (GTs) and retaining glycoside hydrolases (rGHs) are two major enzymes for the formation of glycosidic linkages. Therein GTs generally use nucleotide phosphate activated donors. In contrast, GHs can use broader simple and affordable glycosyl donors, showing great potential in industrial applications. However, most rGHs mainly show hydrolysis activity and only a few rGHs, namely non-Leloir transglycosylases (TGs), innately present strong transglycosylation activities. To address this problem, various strategies have recently been developed to successfully tailor rGHs to alleviate their hydrolysis activity and obtain the engineered TGs. This review summarizes the current modification strategies in TGs engineering, with a special focus on transglycosylation activity enhancement, substrate specificity modulation, and product polymerization degree distribution, which provides a reference for exploiting the transglycosylation potentials of rGHs.
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Affiliation(s)
- Xing Jian
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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2
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Llopiz A, Ramírez-Martínez MA, Olvera L, Xolalpa-Villanueva W, Pastor N, Saab-Rincon G. The Role of a Loop in the Non-catalytic Domain B on the Hydrolysis/Transglycosylation Specificity of the 4-α-Glucanotransferase from Thermotoga maritima. Protein J 2023; 42:502-518. [PMID: 37464145 PMCID: PMC10480278 DOI: 10.1007/s10930-023-10136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
The mechanism by which glycoside hydrolases control the reaction specificity through hydrolysis or transglycosylation is a key element embedded in their chemical structures. The determinants of reaction specificity seem to be complex. We looked for structural differences in domain B between the 4-α-glucanotransferase from Thermotoga maritima (TmGTase) and the α-amylase from Thermotoga petrophila (TpAmylase) and found a longer loop in the former that extends towards the active site carrying a W residue at its tip. Based on these differences we constructed the variants W131G and the partial deletion of the loop at residues 120-124/128-131, which showed a 11.6 and 11.4-fold increased hydrolysis/transglycosylation (H/T) ratio relative to WT protein, respectively. These variants had a reduction in the maximum velocity of the transglycosylation reaction, while their affinity for maltose as the acceptor was not substantially affected. Molecular dynamics simulations allow us to rationalize the increase in H/T ratio in terms of the flexibility near the active site and the conformations of the catalytic acid residues and their associated pKas.
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Affiliation(s)
- Alexey Llopiz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Marco A Ramírez-Martínez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Morelos, Mexico
| | - Leticia Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Wendy Xolalpa-Villanueva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Morelos, Mexico
| | - Gloria Saab-Rincon
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico.
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3
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Wang R, Pu Z, Janke JJ, Zheng YC, Kong XD, Niu T, Zhao S, Yang L, Wang Z, Xu JH. Engineered Glycosidase for Significantly Improved Production of Naturally Rare Vina-Ginsenoside R7. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3852-3861. [PMID: 36790033 DOI: 10.1021/acs.jafc.2c09115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ginsenosides are the main bioactive ingredients in plants of the genus Panax. Vina-ginsenoside R7 (VG-R7) is one of the rare high-value ginsenosides with health benefits. The only reported method for preparing VG-R7 involves inefficient and low-yield isolation from highly valuable natural resources. Notoginsenoside Fc (NG-Fc) isolated in the leaves and stems of Panax notoginseng is a suitable substrate for the preparation of VG-R7 via specific hydrolysis of the outside xylose at the C-20 position. Here, we first screened putative enzymes belonging to the glycoside hydrolase (GH) families 1, 3, and 43 and found that KfGH01 can specifically hydrolyze the β-d-xylopyranosyl-(1 → 6)-β-d-glucopyranoside linkage of NG-Fc to form VG-R7. The I248F/Y410R variant of KfGH01 obtained by protein engineering displayed a kcat/KM value (305.3 min-1 mM-1) for the reaction enhanced by approximately 270-fold compared with wild-type KfGH01. A change in the shape of the substrate binding pockets in the mutant allows the substrate to sit closer to the catalytic residues which may explain the enhanced catalytic efficiency of the engineered enzyme. This study identifies the first glycosidase for bioconversion of a ginsenoside with more than four sugar units, and it will inspire efforts to investigate other promising enzymes to obtain valuable natural products.
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Affiliation(s)
- Rufeng Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhongji Pu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jonathan Joel Janke
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Xu-Dong Kong
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Tengfei Niu
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Li Yang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
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Chen F, Cocaign-Bousquet M, Girbal L, Nouaille S. 5'UTR sequences influence protein levels in Escherichia coli by regulating translation initiation and mRNA stability. Front Microbiol 2022; 13:1088941. [PMID: 36620028 PMCID: PMC9810816 DOI: 10.3389/fmicb.2022.1088941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
A set of 41 synthetic 5'UTRs with different theoretical translation initiation rates were generated to explore the role of 5'UTRs in the regulation of protein levels in Escherichia coli. The roles of the synthetic 5'UTRs in regulating the expression of different reporter genes were analyzed in vivo. Protein levels varied substantially between the different constructs but for most of the 5'UTRs, protein levels were not correlated with theoretical translation initiation rates. Large variations in mRNA concentrations were measured with the different 5'UTRs even though the same concentration of transcription inducer was used in each case. 5'UTRs were also found to strongly affect mRNA stability, and these changes in mRNA stability often contributed to observed differences in mRNA concentration. Unexpectedly, the effect of the 5'UTRs on mRNA half-lives was found to vary depending on the downstream reporter gene. These results clearly demonstrate that 5'UTRs contribute to gene expression regulation at the level of translation initiation and of mRNA stability, to an extent that depends on the nature of the downstream gene.
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β-Alanine production by L-aspartate-α-decarboxylase from Corynebacterium glutamicum and variants with reduced substrate inhibition. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhao J, Esque J, André I, O'Donohue MJ, Fauré R. Synthesis of α-l-Araf and β-d-Galf series furanobiosides using mutants of a GH51 α-l-arabinofuranosidase. Bioorg Chem 2021; 116:105245. [PMID: 34482168 DOI: 10.1016/j.bioorg.2021.105245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
The GH-51 α-l-arabinofuranosidase from Thermobacillus xylanilyticus (TxAbf) possesses versatile catalytic properties, displaying not only the ability to hydrolyze glycosidic linkages but also to synthesize furanobiosides in α-l-Araf and β-d-Galf series. Herein, mutants are investigated to evaluate their ability to perform self-condensation, assessing both yield improvements and changes in regioselectivity. Overall yields of oligo-α-l-arabino- and oligo-β-d-galactofuranosides were increased up to 4.8-fold compared to the wild-type enzyme. In depth characterization revealed that the mutants exhibit increased transfer rates and thus a hydrolysis/self-condensation ratio in favor of synthesis. The consequence of the substitution N216W is the creation of an additional binding subsite that provides the basis for an alternative acceptor substrate binding mode. As a result, mutants bearing N216W synthesize not only (1,2)-linked furanobiosides, but also (1,3)- and even (1,5)-linked furanobiosides. Since the self-condensation is under kinetic control, the yield of homo-disaccharides was maximized using higher substrate concentrations. In this way, the mutant R69H-N216W produced oligo-β-d-galactofuranosides in > 70% yield. Overall, this study further demonstrates the potential usefulness of TxAbf mutants for glycosynthesis and shows how these might be used to synthesize biologically-relevant glycoconjugates.
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Affiliation(s)
- Jiao Zhao
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Isabelle André
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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Teze D, Zhao J, Wiemann M, Kazi ZGA, Lupo R, Zeuner B, Vuillemin M, Rønne ME, Carlström G, Duus JØ, Sanejouand YH, O'Donohue MJ, Nordberg Karlsson E, Fauré R, Stålbrand H, Svensson B. Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases. Chemistry 2021; 27:10323-10334. [PMID: 33914359 DOI: 10.1002/chem.202100110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.
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Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Jiao Zhao
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Mathias Wiemann
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Zubaida G A Kazi
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Rossana Lupo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Mette E Rønne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Göran Carlström
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Jens Ø Duus
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bulding 207, DK-2800, Kongens Lyngby, Denmark
| | - Yves-Henri Sanejouand
- UFIP, UMR 6286, Université de Nantes, CNRS, 2, chemin de la Houssiniere, Nantes, France
| | - Michael J O'Donohue
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | | | - Régis Fauré
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
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Rational protein engineering of α-L-arabinofuranosidase from Aspergillus niger for improved catalytic hydrolysis efficiency on kenaf hemicellulose. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Collet L, Vander Wauven C, Oudjama Y, Galleni M, Dutoit R. Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis. Acta Crystallogr D Struct Biol 2021; 77:205-216. [PMID: 33559609 DOI: 10.1107/s2059798320015557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
The ability of retaining glycoside hydrolases (GHs) to transglycosylate is inherent to the double-displacement mechanism. Studying reaction intermediates, such as the glycosyl-enzyme intermediate (GEI) and the Michaelis complex, could provide valuable information to better understand the molecular factors governing the catalytic mechanism. Here, the GEI structure of RBcel1, an endo-1,4-β-glucanase of the GH5 family endowed with transglycosylase activity, is reported. It is the first structure of a GH5 enzyme covalently bound to a natural oligosaccharide with the two catalytic glutamate residues present. The structure of the variant RBcel1_E135A in complex with cellotriose is also reported, allowing a description of the entire binding cleft of RBcel1. Taken together, the structures deliver different snapshots of the double-displacement mechanism. The structural analysis revealed a significant movement of the nucleophilic glutamate residue during the reaction. Enzymatic assays indicated that, as expected, the acid/base glutamate residue is crucial for the glycosylation step and partly contributes to deglycosylation. Moreover, a conserved tyrosine residue in the -1 subsite, Tyr201, plays a determinant role in both the glycosylation and deglycosylation steps, since the GEI was trapped in the RBcel1_Y201F variant. The approach used to obtain the GEI presented here could easily be transposed to other retaining GHs in clan GH-A.
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Affiliation(s)
| | | | | | - Moreno Galleni
- Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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Zhao J, Tandrup T, Bissaro B, Barbe S, Poulsen JCN, André I, Dumon C, Lo Leggio L, O'Donohue MJ, Fauré R. Probing the determinants of the transglycosylation/hydrolysis partition in a retaining α-l-arabinofuranosidase. N Biotechnol 2021; 62:68-78. [PMID: 33524585 DOI: 10.1016/j.nbt.2021.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/08/2021] [Accepted: 01/23/2021] [Indexed: 12/15/2022]
Abstract
The use of retaining glycoside hydrolases as synthetic tools for glycochemistry is highly topical and the focus of considerable research. However, due to the incomplete identification of the molecular determinants of the transglycosylation/hydrolysis partition (t/h), rational engineering of retaining glycoside hydrolases to create transglycosylases remains challenging. Therefore, to understand better the factors that underpin transglycosylation in a GH51 retaining α-l-arabinofuranosidase from Thermobacillus xylanilyticus, the investigation of this enzyme's active site was pursued. Specifically, the properties of two mutants, F26L and L352M, located in the vicinity of the active site are described, using kinetic and 3D structural analyses and molecular dynamics simulations. The results reveal that the presence of L352M in the context of a triple mutant (also containing R69H and N216W) generates changes both in the donor and acceptor subsites, the latter being the result of a domino-like effect. Overall, the mutant R69H-N216W-L352M displays excellent transglycosylation activity (70 % yield, 78 % transfer rate and reduced secondary hydrolysis of the product). In the course of this study, the central role played by the conserved R69 residue was also reaffirmed. The mutation R69H affects both the catalytic nucleophile and the acid/base, including their flexibility, and has a determinant effect on the t/h partition. Finally, the results reveal that increased loop flexibility in the acceptor subsites creates new interactions with the acceptor, in particular with a hydrophobic binding platform composed of N216W, W248 and W302.
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Affiliation(s)
- Jiao Zhao
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Bastien Bissaro
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Sophie Barbe
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Isabelle André
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Claire Dumon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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Faijes M, Castejón-Vilatersana M, Val-Cid C, Planas A. Enzymatic and cell factory approaches to the production of human milk oligosaccharides. Biotechnol Adv 2019; 37:667-697. [DOI: 10.1016/j.biotechadv.2019.03.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/22/2019] [Accepted: 03/23/2019] [Indexed: 12/15/2022]
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12
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Dutoit R, Delsaute M, Collet L, Vander Wauven C, Van Elder D, Berlemont R, Richel A, Galleni M, Bauvois C. Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes. Acta Crystallogr D Struct Biol 2019; 75:605-615. [PMID: 31205022 DOI: 10.1107/s2059798319007113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/16/2019] [Indexed: 01/23/2023] Open
Abstract
The discovery of new glycoside hydrolases that can be utilized in the chemoenzymatic synthesis of carbohydrates has emerged as a promising approach for various biotechnological processes. In this study, recombinant Ps_Cel5A from Pseudomonas stutzeri A1501, a novel member of the GH5_5 subfamily, was expressed, purified and crystallized. Preliminary experiments confirmed the ability of Ps_Cel5A to catalyze transglycosylation with cellotriose as a substrate. The crystal structure revealed several structural determinants in and around the positive subsites, providing a molecular basis for a better understanding of the mechanisms that promote and favour synthesis rather than hydrolysis. In the positive subsites, two nonconserved positively charged residues (Arg178 and Lys216) were found to interact with cellobiose. This adaptation has also been reported for transglycosylating β-mannanases of the GH5_7 subfamily.
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Affiliation(s)
| | - Maud Delsaute
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
| | | | | | - Dany Van Elder
- Laboratory of Microbiology, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Renaud Berlemont
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9502, USA
| | - Aurore Richel
- Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, 5030 Gembloux, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, 13 Allée du 6 Août, 4000 Liège, Belgium
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13
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β-Mannanase-catalyzed synthesis of alkyl mannooligosides. Appl Microbiol Biotechnol 2018; 102:5149-5163. [PMID: 29680901 PMCID: PMC5959982 DOI: 10.1007/s00253-018-8997-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 12/28/2022]
Abstract
β-Mannanases catalyze the conversion and modification of β-mannans and may, in addition to hydrolysis, also be capable of transglycosylation which can result in enzymatic synthesis of novel glycoconjugates. Using alcohols as glycosyl acceptors (alcoholysis), β-mannanases can potentially be used to synthesize alkyl glycosides, biodegradable surfactants, from renewable β-mannans. In this paper, we investigate the synthesis of alkyl mannooligosides using glycoside hydrolase family 5 β-mannanases from the fungi Trichoderma reesei (TrMan5A and TrMan5A-R171K) and Aspergillus nidulans (AnMan5C). To evaluate β-mannanase alcoholysis capacity, a novel mass spectrometry-based method was developed that allows for relative comparison of the formation of alcoholysis products using different enzymes or reaction conditions. Differences in alcoholysis capacity and potential secondary hydrolysis of alkyl mannooligosides were observed when comparing alcoholysis catalyzed by the three β-mannanases using methanol or 1-hexanol as acceptor. Among the three β-mannanases studied, TrMan5A was the most efficient in producing hexyl mannooligosides with 1-hexanol as acceptor. Hexyl mannooligosides were synthesized using TrMan5A and purified using high-performance liquid chromatography. The data suggests a high selectivity of TrMan5A for 1-hexanol as acceptor over water. The synthesized hexyl mannooligosides were structurally characterized using nuclear magnetic resonance, with results in agreement with their predicted β-conformation. The surfactant properties of the synthesized hexyl mannooligosides were evaluated using tensiometry, showing that they have similar micelle-forming properties as commercially available hexyl glucosides. The present paper demonstrates the possibility of using β-mannanases for alkyl glycoside synthesis and increases the potential utilization of renewable β-mannans.
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Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 2017; 22:1-12. [PMID: 29110088 DOI: 10.1007/s00792-017-0974-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.
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Yang J, Wang Q, Zhou Y, Li J, Gao R, Guo Z. Engineering T. naphthophila β-glucosidase for enhanced synthesis of galactooligosaccharides by site-directed mutagenesis. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Abdul Manas NH, Md Illias R, Mahadi NM. Strategy in manipulating transglycosylation activity of glycosyl hydrolase for oligosaccharide production. Crit Rev Biotechnol 2017; 38:272-293. [PMID: 28683572 DOI: 10.1080/07388551.2017.1339664] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The increasing market demand for oligosaccharides has intensified the need for efficient biocatalysts. Glycosyl hydrolases (GHs) are still gaining popularity as biocatalyst for oligosaccharides synthesis owing to its simple reaction and high selectivity. PURPOSE Over the years, research has advanced mainly directing to one goal; to reduce hydrolysis activity of GHs for increased transglycosylation activity in achieving high production of oligosaccharides. DESIGN AND METHODS This review concisely presents the strategies to increase transglycosylation activity of GHs for oligosaccharides synthesis, focusing on controlling the reaction equilibrium, and protein engineering. Various modifications of the subsites of GHs have been demonstrated to significantly modulate the hydrolysis and transglycosylation activity of the enzymes. The clear insight of the roles of each amino acid in these sites provides a platform for designing an enzyme that could synthesize a specific oligosaccharide product. CONCLUSIONS The key strategies presented here are important for future improvement of GHs as a biocatalyst for oligosaccharide synthesis.
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Affiliation(s)
- Nor Hasmaliana Abdul Manas
- a Department of Chemical Engineering and Energy Sustainability, Faculty of Engineering , Universiti Malaysia Sarawak , Kota Samarahan , Malaysia.,b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia
| | - Rosli Md Illias
- b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia.,c Department of Bioprocess Engineering, Faculty of Chemical and Energy Engineering , Universiti Teknologi Malaysia , Skudai , Malaysia
| | - Nor Muhammad Mahadi
- d Comparative Genomics and Genetics Research Centre , Malaysia Genome Institute , Kajang , Malaysia
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Chlubnová I, Králová B, Dvořáková H, Spiwok V, Filipp D, Nugier-Chauvin C, Daniellou R, Ferrières V. Biocatalyzed synthesis of difuranosides and their ability to trigger production of TNF-α. Bioorg Med Chem Lett 2016; 26:1550-1553. [PMID: 26876932 DOI: 10.1016/j.bmcl.2016.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 10/22/2022]
Abstract
Transglycosylation reactions biocatalyzed by the native arabinofuranosidase Araf51 and using d-galactosyl, d-fucosyl and 6-deoxy-6-fluoro-D-galactosyl derivatives as donors and acceptors provided di-to pentahexofuranosides. The immunostimulatory potency of these compounds, and more especially their ability to induce production of TNF-α, was evaluated on the murine macrophage cell line, Raw 264.7. The results obtained showed concentration-dependent and most importantly, structure-dependent responses. Interestingly, oligoarabinofuranosides belonging to the oligopentafuranoside family displayed concentration-, chain length and aglycon-dependent bioactivities irrespective of their fine chemical variations. Thus, neo-oligofuranosides in D-Galf series, as well as their D-Fucf and 6-fluorinated counterparts are indeed potential sources of immunostimulating agents.
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Affiliation(s)
- Ilona Chlubnová
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France; Université européenne de Bretagne, France; Department of Biochemistry and Microbiology, Institute of Chemical Technology of Prague, Techniká 3, 166 28 Prague 6, Czech Republic; Laboratory of Immunobiology, Institute of Molecular Genetics AS CR, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Blanka Králová
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France; Department of Biochemistry and Microbiology, Institute of Chemical Technology of Prague, Techniká 3, 166 28 Prague 6, Czech Republic
| | - Hana Dvořáková
- Department of Biochemistry and Microbiology, Institute of Chemical Technology of Prague, Techniká 3, 166 28 Prague 6, Czech Republic; Laboratory of NMR Spectroscopy, Institute of Chemical Technology of Prague, Techniká 5, 166 28 Prague 6, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, Institute of Chemical Technology of Prague, Techniká 3, 166 28 Prague 6, Czech Republic
| | - Dominik Filipp
- Laboratory of Immunobiology, Institute of Molecular Genetics AS CR, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Caroline Nugier-Chauvin
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France; Université européenne de Bretagne, France
| | - Richard Daniellou
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France; Université européenne de Bretagne, France
| | - Vincent Ferrières
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France; Université européenne de Bretagne, France.
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18
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Trincone A. Uncommon Glycosidases for the Enzymatic Preparation of Glycosides. Biomolecules 2015; 5:2160-83. [PMID: 26404386 PMCID: PMC4693232 DOI: 10.3390/biom5042160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 01/11/2023] Open
Abstract
Most of the reports in literature dedicated to the use of glycosyl hydrolases for the preparation of glycosides are about gluco- (α- and β-form) and galacto-sidase (β-form), reflecting the high-availability of both anomers of glucosides and of β-galactosides and their wide-ranging applications. Hence, the idea of this review was to analyze the literature focusing on hardly-mentioned natural and engineered glycosyl hydrolases. Their performances in the synthetic mode and natural hydrolytic potential are examined. Both the choice of articles and their discussion are from a biomolecular and a biotechnological perspective of the biocatalytic process, shedding light on new applicative ideas and on the assortment of biomolecular diversity. The hope is to elicit new interest for the development of biocatalysis and to gather attention of biocatalyst practitioners for glycosynthesis.
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Affiliation(s)
- Antonio Trincone
- Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, Pozzuoli 80078, Naples, Italy.
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19
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Bissaro B, Durand J, Biarnés X, Planas A, Monsan P, O’Donohue MJ, Fauré R. Molecular Design of Non-Leloir Furanose-Transferring Enzymes from an α-l-Arabinofuranosidase: A Rationale for the Engineering of Evolved Transglycosylases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00949] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bastien Bissaro
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Julien Durand
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Xevi Biarnés
- Laboratory
of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory
of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 08017 Barcelona, Spain
| | - Pierre Monsan
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- Toulouse White
Biotechnology, UMS INRA/INSA 1337, UMS CNRS/INSA 3582, 3 Rue des Satellites, 31400 Toulouse, France
| | - Michael J. O’Donohue
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Régis Fauré
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
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20
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Arab-Jaziri F, Bissaro B, Tellier C, Dion M, Fauré R, O’Donohue MJ. Enhancing the chemoenzymatic synthesis of arabinosylated xylo-oligosaccharides by GH51 α-l-arabinofuranosidase. Carbohydr Res 2015; 401:64-72. [DOI: 10.1016/j.carres.2014.10.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 02/04/2023]
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