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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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2
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Qiao M, Zhang L, Jiao R, Zhang S, Li B, Zhang X. Chemical and enzymatic synthesis of S-linked sugars and glycoconjugates. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131920] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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3
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Li C, Roy JK, Park KC, Cho AE, Lee J, Kim YW. pH-promoted O-α-glucosylation of flavonoids using an engineered α-glucosidase mutant. Bioorg Chem 2020; 107:104581. [PMID: 33383321 DOI: 10.1016/j.bioorg.2020.104581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/26/2022]
Abstract
Retaining glycosidase mutants lacking its general acid/base catalytic residue are originally termed thioglycoligases which synthesize thio-linked disaccharides using sugar acceptor bearing a nucleophilic thiol group. A few thioglycoligases derived from retaining α-glycosidases have been classified into a new class of catalysts, O-glycoligases which transfer sugar moiety to a hydroxy group of sugar acceptors, resulting in the formation of O-linked glycosides or oligosaccharides. In this study, an efficient O-α-glucosylation of flavonoids was developed using an O-α-glycoligase derived from a thermostable α-glucosidase from Sulfolobus solfataricus (MalA-D416A). The O-glycoligase exhibited efficient transglycosylation activity with a broad substrate spectrum for all kinds of tested flavonoids including flavone, flavonol, flavanone, flavanonol, flavanol and isoflavone classes in yields of higher than 90%. The glucosylation by MalA-D416A preferred alkaline conditions, suggesting that pH-promoted deprotonation of hydroxyl groups of the flavonoids would accelerate turnover of covalent enzyme intermediate via transglucosylation. More importantly, the glucosylation of flavonoids by MalA-D416A was exclusively regioselective, resulting in the synthesis of flavonoid 7-O-α-glucosides as the sole product. Kinetic analysis and molecular dynamics simulations provided insights into the acceptor specificity and the regiospecificity of O-α-glucosylation by MalA-D416A. This pH promoted transglycosylation using O-α-glycoligases may prove to be a general synthesis route to flavonoid O-α-glycosides.
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Affiliation(s)
- Chao Li
- Department of Food and Biotechnology, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea
| | - Jetendra Kumar Roy
- Department of Food and Biotechnology, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea
| | - Ki-Cheul Park
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea
| | - Art E Cho
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea
| | - Jaeick Lee
- Department of Food and Biotechnology, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea
| | - Young-Wan Kim
- Department of Food and Biotechnology, Korea University, 2511 Sejong-Ro, Sejong 30019, Republic of Korea.
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Nieto-Domínguez M, Fernández de Toro B, de Eugenio LI, Santana AG, Bejarano-Muñoz L, Armstrong Z, Méndez-Líter JA, Asensio JL, Prieto A, Withers SG, Cañada FJ, Martínez MJ. Thioglycoligase derived from fungal GH3 β-xylosidase is a multi-glycoligase with broad acceptor tolerance. Nat Commun 2020; 11:4864. [PMID: 32978392 PMCID: PMC7519651 DOI: 10.1038/s41467-020-18667-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
The synthesis of customized glycoconjugates constitutes a major goal for biocatalysis. To this end, engineered glycosidases have received great attention and, among them, thioglycoligases have proved useful to connect carbohydrates to non-sugar acceptors. However, hitherto the scope of these biocatalysts was considered limited to strong nucleophilic acceptors. Based on the particularities of the GH3 glycosidase family active site, we hypothesized that converting a suitable member into a thioglycoligase could boost the acceptor range. Herein we show the engineering of an acidophilic fungal β-xylosidase into a thioglycoligase with broad acceptor promiscuity. The mutant enzyme displays the ability to form O-, N-, S- and Se- glycosides together with sugar esters and phosphoesters with conversion yields from moderate to high. Analyses also indicate that the pKa of the target compound was the main factor to determine its suitability as glycosylation acceptor. These results expand on the glycoconjugate portfolio attainable through biocatalysis.
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Affiliation(s)
- Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Beatriz Fernández de Toro
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Lara Bejarano-Muñoz
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Zach Armstrong
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Juan Antonio Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Stephen G Withers
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Francisco Javier Cañada
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Abstract
Glycosylation is one of the most prevalent posttranslational modifications that profoundly affects the structure and functions of proteins in a wide variety of biological recognition events. However, the structural complexity and heterogeneity of glycoproteins, usually resulting from the variations of glycan components and/or the sites of glycosylation, often complicates detailed structure-function relationship studies and hampers the therapeutic applications of glycoproteins. To address these challenges, various chemical and biological strategies have been developed for producing glycan-defined homogeneous glycoproteins. This review highlights recent advances in the development of chemoenzymatic methods for synthesizing homogeneous glycoproteins, including the generation of various glycosynthases for synthetic purposes, endoglycosidase-catalyzed glycoprotein synthesis and glycan remodeling, and direct enzymatic glycosylation of polypeptides and proteins. The scope, limitation, and future directions of each method are discussed.
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Affiliation(s)
- Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Pedersen MJ, Madsen R, Clausen MH. Iridium catalysis: reductive conversion of glucan to xylan. Chem Commun (Camb) 2018; 54:952-955. [DOI: 10.1039/c7cc09260a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iridium catalyzed dehydrogenative decarbonylation is used to convert cellobiosides to xylobiosides, which is used in rapid assembly of oligoxylans.
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Affiliation(s)
- Martin Jæger Pedersen
- Center for Nanomedicine and Theranostics
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - Robert Madsen
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - Mads Hartvig Clausen
- Center for Nanomedicine and Theranostics
- Department of Chemistry
- Technical University of Denmark
- Denmark
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Guillotin L, Richet N, Lafite P, Daniellou R. Is the acid/base catalytic residue mutation in β- d -mannosidase Dt Man from Dictyoglomus thermophilum sufficient enough to provide thioglycoligase activity? Biochimie 2017; 137:190-196. [DOI: 10.1016/j.biochi.2017.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/31/2017] [Indexed: 10/19/2022]
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Abstract
A robust platform for facile defined glycan synthesis does not exist. Yet the need for such technology has never been greater as researchers seek to understand the full scope of carbohydrate function, stretching beyond the classical roles of structure and energy storage to encompass highly nuanced cell signaling events. To comprehensively explore and exploit the full diversity of carbohydrate functions, we must first be able to synthesize them in a controlled manner. Toward this goal, traditional chemical syntheses are inefficient while nature's own synthetic enzymes, the glycosyl transferases, can be challenging to express and expensive to employ on scale. Glycoside hydrolases represent a pool of glycan processing enzymes that can be either used in a transglycosylation mode or, better, engineered to function as "glycosynthases," mutant enzymes capable of assembling glycosides. Glycosynthases grant access to valuable glycans that act as functional and structural probes or indeed as inhibitors and therapeutics in their own right. The remodelling of glycosylation patterns in therapeutic proteins via glycoside hydrolases and their mutants is an exciting frontier in both basic research and industrial scale processes.
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Affiliation(s)
- Phillip M. Danby
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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Marroun S, Montaut S, Marquès S, Lafite P, Coadou G, Rollin P, Jousset G, Schuler M, Tatibouët A, Oulyadi H, Daniellou R. UGT74B1 from Arabidopsis thaliana as a versatile biocatalyst for the synthesis of desulfoglycosinolates. Org Biomol Chem 2016; 14:6252-61. [DOI: 10.1039/c6ob01003b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A glucosyltransferase is able to catalyze the formation of the thioglycosidic bond and lead to desulfoglycosinolates.
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Affiliation(s)
- Sami Marroun
- Normandie Univ
- COBRA
- UMR 6014 et FR 3038; Univ Rouen; INSA Rouen; CNRS
- IRCOF
- 76821 Mont Saint Aignan Cedex
| | - Sabine Montaut
- Department of Chemistry and Biochemistry
- Biomolecular Sciences Programme
- Laurentian University
- Sudbury
- Canada
| | | | | | - Gaël Coadou
- Normandie Univ
- COBRA
- UMR 6014 et FR 3038; Univ Rouen; INSA Rouen; CNRS
- IRCOF
- 76821 Mont Saint Aignan Cedex
| | | | | | | | | | - Hassan Oulyadi
- Normandie Univ
- COBRA
- UMR 6014 et FR 3038; Univ Rouen; INSA Rouen; CNRS
- IRCOF
- 76821 Mont Saint Aignan Cedex
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Ahn HJ, Li C, Cho HB, Park S, Chang PS, Kim YW. Enzymatic synthesis of 3-O-α-maltosyl-l-ascorbate using an engineered cyclodextrin glucanotransferase. Food Chem 2015; 169:366-71. [DOI: 10.1016/j.foodchem.2014.07.110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/17/2014] [Accepted: 07/22/2014] [Indexed: 11/30/2022]
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Li C, Ahn HJ, Kim JH, Kim YW. Transglycosylation of engineered cyclodextrin glucanotransferases as O-glycoligases. Carbohydr Polym 2014; 99:39-46. [DOI: 10.1016/j.carbpol.2013.08.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 11/28/2022]
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12
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Mewis K, Armstrong Z, Song YC, Baldwin SA, Withers SG, Hallam SJ. Biomining active cellulases from a mining bioremediation system. J Biotechnol 2013; 167:462-71. [PMID: 23906845 DOI: 10.1016/j.jbiotec.2013.07.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 11/12/2022]
Abstract
Functional metagenomics has emerged as a powerful method for gene model validation and enzyme discovery from natural and human engineered ecosystems. Here we report development of a high-throughput functional metagenomic screen incorporating bioinformatic and biochemical analyses features. A fosmid library containing 6144 clones sourced from a mining bioremediation system was screened for cellulase activity using 2,4-dinitrophenyl β-cellobioside, a previously proven cellulose model substrate. Fifteen active clones were recovered and fully sequenced revealing 9 unique clones with the ability to hydrolyse 1,4-β-D-glucosidic linkages. Transposon mutagenesis identified genes belonging to glycoside hydrolase (GH) 1, 3, or 5 as necessary for mediating this activity. Reference trees for GH 1, 3, and 5 families were generated from sequences in the CAZy database for automated phylogenetic analysis of fosmid end and active clone sequences revealing known and novel cellulase encoding genes. Active cellulase genes recovered in functional screens were subcloned into inducible high copy plasmids, expressed and purified to determine enzymatic properties including thermostability, pH optima, and substrate specificity. The workflow described here provides a general paradigm for recovery and characterization of microbially derived genes and gene products based on genetic logic and contemporary screening technologies developed for model organismal systems.
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Affiliation(s)
- Keith Mewis
- Genome Science and Technology Program, Canada
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13
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Armstrong Z, Withers SG. Synthesis of Glycans and Glycopolymers Through Engineered Enzymes. Biopolymers 2013; 99:666-74. [DOI: 10.1002/bip.22335] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Zachary Armstrong
- Genome Science and Technology Program; University of British Columbia; Canada
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Chlubnova I, Legentil L, Dureau R, Pennec A, Almendros M, Daniellou R, Nugier-Chauvin C, Ferrières V. Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis. Carbohydr Res 2012; 356:44-61. [PMID: 22554502 DOI: 10.1016/j.carres.2012.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.
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Affiliation(s)
- Ilona Chlubnova
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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Kwan DH, Withers SG. Toward Efficient Enzymatic Glycan Synthesis: Directed Evolution and Enzyme Engineering. J Carbohydr Chem 2011. [DOI: 10.1080/07328303.2011.604457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Gantt RW, Peltier-Pain P, Thorson JS. Enzymatic methods for glyco(diversification/randomization) of drugs and small molecules. Nat Prod Rep 2011; 28:1811-53. [DOI: 10.1039/c1np00045d] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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19
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Almendros M, Danalev D, François-Heude M, Loyer P, Legentil L, Nugier-Chauvin C, Daniellou R, Ferrières V. Exploring the synthetic potency of the first furanothioglycoligase through original remote activation. Org Biomol Chem 2011; 9:8371-8. [DOI: 10.1039/c1ob06227a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Site-Saturation Mutagenesis of Leucine 134 of Bacillus licheniformis Nucleotide Exchange Factor GrpE Reveals the Importance of this Residue to the Co-chaperone Activity. Protein J 2010; 29:365-72. [DOI: 10.1007/s10930-010-9261-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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