1
|
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.
Collapse
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
| |
Collapse
|
2
|
Guo Z, Wang L, Rao D, Liu W, Xue M, Fu Q, Lu M, Su L, Chen S, Wang B, Wu J. Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77. J Chem Inf Model 2023; 63:6118-6128. [PMID: 37768640 DOI: 10.1021/acs.jcim.3c00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Amylomaltases (AMs) play important roles in glycogen and maltose metabolism. However, the molecular mechanism is elusive. Here, we investigated the conformational dynamics of the 250s loop and catalytic mechanism of Thermus aquaticus TaAM using path-metadynamics and QM/MM MD simulations. The results demonstrate that the transition of the 250s loop from an open to closed conformation promotes polysaccharide sliding, leading to the ideal positioning of the acid/base. Furthermore, the conformational dynamics can also modulate the selectivity of hydrolysis and transglycosylation. The closed conformation of the 250s loop enables the tight packing of the active site for transglycosylation, reducing the energy penalty and efficiently preventing the penetration of water into the active site. Conversely, the partially closed conformation for hydrolysis results in a loosely packed active site, destabilizing the transition state. These computational findings guide mutation experiments and enable the identification of mutants with an improved disproportionation/hydrolysis ratio. The present mechanism is in line with experimental data, highlighting the critical role of conformational dynamics in regulating the catalytic reactivity of GHs.
Collapse
Affiliation(s)
- Zhiyong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Deming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Miaomiao Xue
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Qisheng Fu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Mengwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| |
Collapse
|
3
|
Guo Z, Wang L, Su L, Chen S, Xia W, André I, Rovira C, Wang B, Wu J. A Single Hydrogen Bond Controls the Selectivity of Transglycosylation vs Hydrolysis in Family 13 Glycoside Hydrolases. J Phys Chem Lett 2022; 13:5626-5632. [PMID: 35704841 DOI: 10.1021/acs.jpclett.2c01136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Converting glycoside hydrolases (GHs) from hydrolytic to synthetic enzymes via transglycosylation is a long-standing goal for the biosynthesis of complex carbohydrates. However, the molecular determinants for the selectivity of transglycosylation (T) vs hydrolysis (H) are still not fully unraveled. Herein, we show experimentally that mutation of one active site residue can switch the enzyme activity between hydrolysis and transglycosylation in two highly homologous GHs. Further QM/MM simulations reveal that the mutation modulates the T vs H reaction barriers via the presence/absence of a single H-bond with the nucleophile Asp. Such a H-bond controls the product selectivity via a dual effect: on one hand, it facilitates the breaking of the glycosyl-enzyme intermediate. On the other, it displaces the sugar acceptor, resulting in a reduced affinity and significant steric repulsion for transglycosylation. These findings expand our understanding of the molecular mechanisms that modulate the T/H balance in GHs.
Collapse
Affiliation(s)
- Zhiyong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Wei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31400, France
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, People's Republic of China
| |
Collapse
|
4
|
Coines J, Cuxart I, Teze D, Rovira C. Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases. J Phys Chem B 2022; 126:802-812. [PMID: 35073079 PMCID: PMC8819650 DOI: 10.1021/acs.jpcb.1c09536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Glycoside hydrolases
and glycosyltransferases are the main classes
of enzymes that synthesize and degrade carbohydrates, molecules essential
to life that are a challenge for classical chemistry. As such, considerable
efforts have been made to engineer these enzymes and make them pliable
to human needs, ranging from directed evolution to rational design,
including mechanism engineering. Such endeavors fall short and are
unreported in numerous cases, while even success is a necessary but
not sufficient proof that the chemical rationale behind the design
is correct. Here we review some of the recent work in CAZyme mechanism
engineering, showing that computational simulations are instrumental
to rationalize experimental data, providing mechanistic insight into
how native and engineered CAZymes catalyze chemical reactions. We
illustrate this with two recent studies in which (i) a glycoside hydrolase
is converted into a glycoside phosphorylase and (ii) substrate specificity
of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.
Collapse
Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Cuxart
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - David Teze
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| |
Collapse
|
5
|
Yu XQ, Yang JW, Ding XJ, Liu LH, Hu XQ, Zhang HB. Analysis of the Effect of N555 Mutations on the Product Specificity of Dextransucrase Using Caffeic Acid Phenethyl Ester as an Acceptor Substrate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5774-5782. [PMID: 33978404 DOI: 10.1021/acs.jafc.1c00822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioglycosylation is an efficient strategy to improve biological activities and physicochemical properties of natural compounds to develop structural modifications of drugs. In this study, an N555 residue was identified as a candidate for site-directed mutagenesis through sequence alignment with GTF180ΔN. Caffeic acid phenethyl ester (CAPE) was used as an acceptor substrate. Two generated mutants, N555Q and N555E, demonstrated significant specificity of distribution of products. Under identical conditions, the conversion rates of diglycoside products (CAPE-2G) generated by the N555E (80.8%) and N555Q (84.5%) mutants were 3.30- and 3.46-fold higher than those generated by the original enzyme (24.4%). The structural simulation results demonstrated that a new hydrogen bond was formed between the N555 residue and CAPE, and the N555 residue was closely related to substrate elongation. These results provide a reference for subsequent studies. Suitable mutants for transfer of diglycosides have important application potential in the food and pharmaceutical industries.
Collapse
Affiliation(s)
- Xiao-Qin Yu
- Department of Pharmaceutical Engineering, School of Food and Biological Engineering, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| | - Jing-Wen Yang
- Department of Pharmaceutical Engineering, School of Food and Biological Engineering, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| | - Xiao-Jie Ding
- Department of Pharmaceutical Engineering, School of Food and Biological Engineering, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| | - Lan-Hua Liu
- Instrumental Analysis Center, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| | - Xue-Qin Hu
- Department of Pharmaceutical Engineering, School of Food and Biological Engineering, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| | - Hong-Bin Zhang
- Department of Pharmaceutical Engineering, School of Food and Biological Engineering, Hefei University of Technology, 193# Tunxi Road, Hefei 230009, Anhui Province, P. R. China
| |
Collapse
|
6
|
Marneth K, van den Elst H, Cramer‐Blok A, Codee J, Overkleeft HS, Aerts JMFG, Ubbink M, Ben Bdira F. Tuning the Transglycosylation Reaction of a GH11 Xylanase by a Delicate Enhancement of its Thumb Flexibility. Chembiochem 2021; 22:1743-1749. [PMID: 33534182 PMCID: PMC8251542 DOI: 10.1002/cbic.202000856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Glycoside hydrolases (GHs) are attractive tools for multiple biotechnological applications. In conjunction with their hydrolytic function, GHs can perform transglycosylation under specific conditions. In nature, oligosaccharide synthesis is performed by glycosyltransferases (GTs); however, the industrial use of GTs is limited by their instability in solution. A key difference between GTs and GHs is the flexibility of their binding site architecture. We have used the xylanase from Bacillus circulans (BCX) to study the interplay between active-site flexibility and transglycosylation. Residues of the BCX "thumb" were substituted to increase the flexibility of the enzyme binding site. Replacement of the highly conserved residue P116 with glycine shifted the balance of the BCX enzymatic reaction toward transglycosylation. The effects of this point mutation on the structure and dynamics of BCX were investigated by NMR spectroscopy. The P116G mutation induces subtle changes in the configuration of the thumb and enhances the millisecond dynamics of the active site. Based on our findings, we propose the remodelling of the GH enzymes glycon site flexibility as a strategy to improve the transglycosylation efficiency of these biotechnologically important catalysts.
Collapse
Affiliation(s)
- Kim Marneth
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hans van den Elst
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Anneloes Cramer‐Blok
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen Codee
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Pallister E, Gray CJ, Flitsch SL. Enzyme promiscuity of carbohydrate active enzymes and their applications in biocatalysis. Curr Opin Struct Biol 2020; 65:184-192. [PMID: 32942240 DOI: 10.1016/j.sbi.2020.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022]
Abstract
The application of biocatalysis for the synthesis of glycans and glycoconjugates is a well-established and successful strategy, both for small and large scale synthesis. Compared to chemical synthesis, is has the advantage of high selectivity, but biocatalysis had been largely limited to natural glycans both in terms of reactivity and substrates. This review describes recent advances in exploiting enzyme promiscuity to expand the range of substrates and reactions that carbohydrate active enzymes (CAZymes) can catalyse. The main focus is on formation and hydrolysis of glycosidic linkages, including sugar kinases, reactions that are central to glycobiotechnology. In addition, biocatalysts that generate sugar analogues and modify carbohydrates, such as oxidases, transaminases and acylases are reviewed. As carbohydrate active enzymes become more accessible and protein engineering strategies become faster, the application of biocatalysis in the generation of a wide range of glycoconjugates, beyond natural structures is expected to expand.
Collapse
Affiliation(s)
- Edward Pallister
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| |
Collapse
|
9
|
Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [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: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
Collapse
|
10
|
Qin Z, Li S, Huang X, Kong W, Yang X, Zhang S, Cao L, Liu Y. Improving Galactooligosaccharide Synthesis Efficiency of β-Galactosidase Bgal1-3 by Reshaping the Active Site with an Intelligent Hydrophobic Amino Acid Scanning. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11158-11166. [PMID: 31537069 DOI: 10.1021/acs.jafc.9b04774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are ongoing interests in improving the galactooligosaccharide (GOS) synthesis efficiency of β-galactosidase by protein engineering. In this study, an intelligent double-hydrophobic amino acid scanning strategy was proposed and employed to target nine residues forming the glycon-binding site (-1 subsite) of β-galactosidase Bgal1-3. Two mutants C510V and H512I with significantly improved GOS synthesis efficiency were obtained. When 40% (w/v) lactose was used as a substrate, Bgal1-3 reached a maximum GOS yield of 45.3% at 16 h, while the mutants reached higher yields in a much shorter time (59.1% at 10 h for C510V, 51.5% at 2 h for H512I). When skim milk was treated with these enzymes, more GOS was produced (19.9 g/L for C510V, 12.7 g/L for H512I) than that for Bgal1-3 (10.3 g/L) at a lactose conversion of 90%. These results validated hydrophobicity scanning as an efficient method to engineer β-galactosidases into promising catalysts for the preparation of GOS and GOS-enriched milk.
Collapse
Affiliation(s)
- Zongmin Qin
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Shuifeng Li
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Xin Huang
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Wei Kong
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Xiangpeng Yang
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Sufang Zhang
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Lichuang Cao
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| | - Yuhuan Liu
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea , Sun Yat-Sen University , Guangzhou 510275 , P. R. China
| |
Collapse
|
11
|
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.
Collapse
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
| | | |
Collapse
|
12
|
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.
Collapse
|
13
|
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]
|
14
|
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: 43] [Impact Index Per Article: 6.1] [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.
Collapse
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
| |
Collapse
|
15
|
David B, Irague R, Jouanneau D, Daligault F, Czjzek M, Sanejouand YH, Tellier C. Internal Water Dynamics Control the Transglycosylation/Hydrolysis Balance in the Agarase (AgaD) of Zobellia galactanivorans. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00348] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benoit David
- UFIP,
CNRS, Université de Nantes, 44322 Nantes, France
| | - Romain Irague
- UFIP,
CNRS, Université de Nantes, 44322 Nantes, France
| | - Diane Jouanneau
- Integrative
Biology of Marine Models, CNRS, UPMC Univ Paris 06, Sorbonne Université, 29680 Roscoff, France
| | | | - Mirjam Czjzek
- Integrative
Biology of Marine Models, CNRS, UPMC Univ Paris 06, Sorbonne Université, 29680 Roscoff, France
| | | | | |
Collapse
|