1
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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2
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Züblin P, Zeller A, Moulis C, Remaud-Simeon M, Yao Y, Mezzenga R. Expanding the Enzymatic Polymerization Landscape by Lipid Mesophase Soft Nanoconfinement. Angew Chem Int Ed Engl 2024; 63:e202312880. [PMID: 37962302 DOI: 10.1002/anie.202312880] [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] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
Soft nanoconfinement can increase chemical reactivity in nature and has therefore led to considerable interest in transferring this universal feature to artificial biological systems. However, little is known about the underlying principles of soft nanoconfinement responsible for the enhancement of biochemical reactions. Herein we demonstrate how enzymatic polymerization can be expanded, optimized, and engineered when carried out under soft nanoconfinement mediated by lipidic mesophases. By systematically varying the water content in the mesophase and thus the diameter of the confined water nanochannels, we show higher efficiency, turnover rate, and degrees of polymerization as compared to the bulk aqueous solution, all controlled by soft nanoconfinement effects. Furthermore, we exploit the unique properties of unfreezing soft nanoconfined water to perform the first enzymatic polymerization at -20 °C in pure aqueous media. These results underpin lipidic mesophases as a versatile host system for chemical reactions and promote them as an original and unexplored platform for enzymatic polymerization.
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Affiliation(s)
- Patrick Züblin
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Adrian Zeller
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Claire Moulis
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Av. de Rangueil, 31400, Toulouse, France
| | - Magali Remaud-Simeon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Av. de Rangueil, 31400, Toulouse, France
| | - Yang Yao
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
- Department of Materials, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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3
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Zhang Y, Liu J, Hu G, Hu X, Yang J, Zhang H. Fusion enzyme design based on the "channelization" cascade theory and homogenous dextran product improvement. Int J Biol Macromol 2022; 222:652-660. [PMID: 36174857 DOI: 10.1016/j.ijbiomac.2022.09.222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
Abstract
Homogeneous low molecular weight dextran can be used to improve microcirculation and expand blood volume. However, the synthesis and separation of low molecular weight dextran are chemically difficult and environmentally unfriendly. Here, a one-step strategy for the synthesis of homogeneous low molecular weight dextran was developed. Dextransucrase and dextranase were fused by the addition of different length linker peptides. An artificial bifunctional enzyme was created to directly convert sucrose into low molecular weight dextran (13,050 Da), and the related substrate channel mechanism was found. The substrate channel adaptability was studied by changing the length of the linker and its corresponding product behavior. Compared with the mixture of two free enzymes, the residence lag time demonstrates the degree of substrate channelization of a series of fusion enzymes. And found that the highest channelization degree is not equal to produce homogenous dextran. Whereas a fusion enzyme with the appropriate linker (the one with the best substrate channel adaptation) will produce dextran with a homogeneous molecular weight. By studying the temperature dynamics of the fusion enzyme to adjust the two-stage catalytic efficiency of the fusion enzyme, we have increased the yield of low molecular weight homogeneous dextran (Yield of 62 %).
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Affiliation(s)
- Yuxin Zhang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jiali Liu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Ganpeng Hu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Xueqin Hu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
| | - Jingwen Yang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
| | - Hongbin Zhang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
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4
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Zhang YX, Yang JW, Wu YY, Hu XQ, Zhang HB. The stability improvement of dextransucrase by artificial extension modification of the V domain of the enzyme. Enzyme Microb Technol 2021; 151:109919. [PMID: 34649690 DOI: 10.1016/j.enzmictec.2021.109919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 11/16/2022]
Abstract
Improving enzyme stability is very important for enzyme applications. Structural modification is a reliable and effective method to improve the characteristics of protein. By artificially extending the C-terminus, 6 domain modification variants of different sizes were constructed, and a new enzyme species with high stability was obtained. Experimental results affirmed that high stability can be achieved by decreasing the degree of domain freedom. The optimum temperatures of domain modification variants were improved by 10 °C compared with the original enzyme. Specifically, compared with the original enzyme, the half-life of the variant dexYG-fdx (D-F) was increased to 280% under 35 °C and 200% under 45 °C, and the pH tolerance range was wider. Further structural simulations and molecular docking studies provided a reasonable explanation (The increased domain reduced the degree of freedom of the enzyme terminal to some extent) for this variant to increase stability and produce dextran. This study can provide valuable information for increasing the characteristics of recombinant dextransucrase.
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Affiliation(s)
- Yu-Xin Zhang
- School of Food and Bioengineering, Hefei University of Technology, Tunxi Road No.193, Hefei, Anhui, 230009, China.
| | - Jing-Wen Yang
- School of Food and Bioengineering, Hefei University of Technology, Tunxi Road No.193, Hefei, Anhui, 230009, China.
| | - Yuan-Yuan Wu
- School of Food and Bioengineering, Hefei University of Technology, Tunxi Road No.193, Hefei, Anhui, 230009, China.
| | - Xue-Qin Hu
- School of Food and Bioengineering, Hefei University of Technology, Tunxi Road No.193, Hefei, Anhui, 230009, China.
| | - Hong-Bin Zhang
- School of Food and Bioengineering, Hefei University of Technology, Tunxi Road No.193, Hefei, Anhui, 230009, China.
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5
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Wang T, Jiang Z, Wang Y, Wu H, Fang Y, Dong W, Wu B, Ma J, Jiang M. Low Molar Mass Dextran: One-Step Synthesis With Dextransucrase by Site-Directed Mutagenesis and its Potential of Iron-Loading. Front Bioeng Biotechnol 2021; 9:747602. [PMID: 34568303 PMCID: PMC8458854 DOI: 10.3389/fbioe.2021.747602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022] Open
Abstract
Iron dextran is a common anti-anemia drug, and it requires low molar mass dextran as substrate. In this work, we selected 11 amino acid residues in domain A/B of DSR-MΔ2 within a 5-angstrom distance from sucrose for site-directed mutagenesis by molecular docking. Mutation of Q634 did not affect the enzyme catalytic activity, but showed an obvious impact on the ratio of low molecular weight dextran (L-dextran, 3,000–5,000 Da) and relatively higher molecular weight dextran (H-dextran, around 10,000 Da). L-dextran was the main product synthesized by DSR-MΔ2 Q634A, and its average molecular weight was 3,951 Da with a polydispersity index <1.3. The structural characterization of this homopolysaccharide revealed that it was a dextran, with 86.0% α(1→6) and 14.0% α(1→4) glycosidic linkages. Moreover, L-dextran was oxidized with NaOH and chelated with ferric trichloride, and an OL-dextran-iron complex was synthesized with a high iron-loading potential of 33.5% (w/w). Altogether, mutation of amino acids near the sucrose binding site of dextransucrase can affect the chain elongation process, making it possible to modulate dextran size.
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Affiliation(s)
- Tingting Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhiming Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yiya Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hao Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yan Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Bin Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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6
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Molina M, Cioci G, Moulis C, Séverac E, Remaud-Siméon M. Bacterial α-Glucan and Branching Sucrases from GH70 Family: Discovery, Structure-Function Relationship Studies and Engineering. Microorganisms 2021; 9:microorganisms9081607. [PMID: 34442685 PMCID: PMC8398850 DOI: 10.3390/microorganisms9081607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/12/2023] Open
Abstract
Glucansucrases and branching sucrases are classified in the family 70 of glycoside hydrolases. They are produced by lactic acid bacteria occupying very diverse ecological niches (soil, buccal cavity, sourdough, intestine, dairy products, etc.). Usually secreted by their producer organisms, they are involved in the synthesis of α-glucans from sucrose substrate. They contribute to cell protection while promoting adhesion and colonization of different biotopes. Dextran, an α-1,6 linked linear α-glucan, was the first microbial polysaccharide commercialized for medical applications. Advances in the discovery and characterization of these enzymes have remarkably enriched the available diversity with new catalysts. Research into their molecular mechanisms has highlighted important features governing their peculiarities thus opening up many opportunities for engineering these catalysts to provide new routes for the transformation of sucrose into value-added molecules. This article reviews these different aspects with the ambition to show how they constitute the basis for promising future developments.
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7
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Zhao L, Ma Z, Yin J, Shi G, Ding Z. Biological strategies for oligo/polysaccharide synthesis: biocatalyst and microbial cell factory. Carbohydr Polym 2021; 258:117695. [PMID: 33593568 DOI: 10.1016/j.carbpol.2021.117695] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 12/21/2022]
Abstract
Oligosaccharides and polysaccharides constitute the principal components of carbohydrates, which are important biomacromolecules that demonstrate considerable bioactivities. However, the variety and structural complexity of oligo/polysaccharides represent a major challenge for biological and structural explorations. To access structurally defined oligo/polysaccharides, biological strategies using glycoenzyme biocatalysts have shown remarkable synthetic potential attributed to their regioselectivity and stereoselectivity that allow mild, structurally controlled reaction without addition of protecting groups necessary in chemical strategies. This review summarizes recent biotechnological approaches of oligo/polysaccharide synthesis, which mainly includes in vitro enzymatic synthesis and cell factory synthesis. We have discussed the important factors involved in the production of nucleotide sugars. Furthermore, the strategies established in the cell factory and enzymatic syntheses are summarized, and we have highlighted concepts like metabolic flux rebuilding and regulation, enzyme engineering, and route design as important strategies. The research challenges and prospects are also outlined and discussed.
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Affiliation(s)
- Liting Zhao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.
| | - Zhongbao Ma
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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8
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Moulis C, Guieysse D, Morel S, Séverac E, Remaud-Siméon M. Natural and engineered transglycosylases: Green tools for the enzyme-based synthesis of glycoproducts. Curr Opin Chem Biol 2020; 61:96-106. [PMID: 33360622 DOI: 10.1016/j.cbpa.2020.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/22/2023]
Abstract
An increasing number of transglycosylase-based processes provide access to oligosaccharides or glycoconjugates, some of them reaching performance levels compatible with industrial developments. Nevertheless, the full potential of transglycosylases has not been explored because of the challenges in transforming a glycoside hydrolase into an efficient transglycosylase. Advances in studying enzyme structure/function relationships, screening enzyme activity, and generating synthetic libraries guided by computational protein design or machine learning methods should considerably accelerate the development of these catalysts. The time has now come for researchers to uncover their possibilities and learn how to design and precisely refine their activity to respond more rapidly to the growing demand for well-defined glycosidic structures.
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Affiliation(s)
- Claire Moulis
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, Toulouse, Cedex 04, F-31077, France.
| | - David Guieysse
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, Toulouse, Cedex 04, F-31077, France
| | - Sandrine Morel
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, Toulouse, Cedex 04, F-31077, France
| | - Etienne Séverac
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, Toulouse, Cedex 04, F-31077, France
| | - Magali Remaud-Siméon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135, Avenue de Rangueil, Toulouse, Cedex 04, F-31077, France.
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9
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Raga-Carbajal E, Díaz-Vilchis A, Rojas-Trejo SP, Rudiño-Piñera E, Olvera C. The molecular basis of the nonprocessive elongation mechanism in levansucrases. J Biol Chem 2020; 296:100178. [PMID: 33303628 PMCID: PMC7948499 DOI: 10.1074/jbc.ra120.015853] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
Levansucrases (LSs) synthesize levan, a β2-6-linked fructose polymer, by successively transferring the fructosyl moiety from sucrose to a growing acceptor molecule. Elucidation of the levan polymerization mechanism is important for using LSs in the production of size-defined products for application in the food and pharmaceutical industries. For a deeper understanding of the levan synthesis reaction, we determined the crystallographic structure of Bacillus subtilis LS (SacB) in complex with a levan-type fructooligosaccharide and utilized site-directed mutagenesis to identify residues involved in substrate binding. The presence of a levanhexaose molecule in the central catalytic cavity allowed us to identify five substrate-binding subsites (−1, +1, +2, +3, and +4). Mutants affecting residues belonging to the identified acceptor subsites showed similar substrate affinity (Km) values to the wildtype (WT) Km value but had a lower turnover number and transfructosylation/hydrolysis ratio. Of importance, compared with the WT, the variants progressively yielded smaller-sized low-molecular-weight levans, as the affected subsites that were closer to the catalytic site, but without affecting their ability to synthesized high-molecular-weight levans. Furthermore, an additional oligosaccharide-binding site 20 Å away from the catalytic pocket was identified, and its potential participation in the elongation mechanism is discussed. Our results clarify, for the first time, the interaction of the enzyme with an acceptor/product oligosaccharide and elucidate the molecular basis of the nonprocessive levan elongation mechanism of LSs.
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Affiliation(s)
- Enrique Raga-Carbajal
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adelaida Díaz-Vilchis
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Sonia P Rojas-Trejo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Clarita Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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10
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Li X, Wang X, Meng X, Dijkhuizen L, Liu W. Structures, physico-chemical properties, production and (potential) applications of sucrose-derived α-d-glucans synthesized by glucansucrases. Carbohydr Polym 2020; 249:116818. [DOI: 10.1016/j.carbpol.2020.116818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 10/23/2022]
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11
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Yang G, Miton CM, Tokuriki N. A mechanistic view of enzyme evolution. Protein Sci 2020; 29:1724-1747. [PMID: 32557882 PMCID: PMC7380680 DOI: 10.1002/pro.3901] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
Abstract
New enzyme functions often evolve through the recruitment and optimization of latent promiscuous activities. How do mutations alter the molecular architecture of enzymes to enhance their activities? Can we infer general mechanisms that are common to most enzymes, or does each enzyme require a unique optimization process? The ability to predict the location and type of mutations necessary to enhance an enzyme's activity is critical to protein engineering and rational design. In this review, via the detailed examination of recent studies that have shed new light on the molecular changes underlying the optimization of enzyme function, we provide a mechanistic perspective of enzyme evolution. We first present a global survey of the prevalence of activity-enhancing mutations and their distribution within protein structures. We then delve into the molecular solutions that mediate functional optimization, specifically highlighting several common mechanisms that have been observed across multiple examples. As distinct protein sequences encounter different evolutionary bottlenecks, different mechanisms are likely to emerge along evolutionary trajectories toward improved function. Identifying the specific mechanism(s) that need to be improved upon, and tailoring our engineering efforts to each sequence, may considerably improve our chances to succeed in generating highly efficient catalysts in the future.
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Affiliation(s)
- Gloria Yang
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Charlotte M. Miton
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Nobuhiko Tokuriki
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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12
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Molina M, Moulis C, Monties N, Guieysse D, Morel S, Cioci G, Remaud-Siméon M. A specific oligosaccharide-binding site in the alternansucrase catalytic domain mediates alternan elongation. J Biol Chem 2020; 295:9474-9489. [PMID: 32409580 PMCID: PMC7363119 DOI: 10.1074/jbc.ra120.013028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/05/2020] [Indexed: 01/28/2023] Open
Abstract
Microbial α-glucans produced by GH70 (glycoside hydrolase family 70) glucansucrases are gaining importance because of the mild conditions for their synthesis from sucrose, their biodegradability, and their current and anticipated applications that largely depend on their molar mass. Focusing on the alternansucrase (ASR) from Leuconostoc citreum NRRL B-1355, a well-known glucansucrase catalyzing the synthesis of both high- and low-molar-mass alternans, we searched for structural traits in ASR that could be involved in the control of alternan elongation. The resolution of five crystal structures of a truncated ASR version (ASRΔ2) in complex with different gluco-oligosaccharides pinpointed key residues in binding sites located in the A and V domains of ASR. Biochemical characterization of three single mutants and three double mutants targeting the sugar-binding pockets identified in domain V revealed an involvement of this domain in alternan binding and elongation. More strikingly, we found an oligosaccharide-binding site at the surface of domain A, distant from the catalytic site and not previously identified in other glucansucrases. We named this site surface-binding site (SBS) A1. Among the residues lining the SBS-A1 site, two (Gln700 and Tyr717) promoted alternan elongation. Their substitution to alanine decreased high-molar-mass alternan yield by a third, without significantly impacting enzyme stability or specificity. We propose that the SBS-A1 site is unique to alternansucrase and appears to be designed to bind alternating structures, acting as a mediator between the catalytic site and the sugar-binding pockets of domain V and contributing to a processive elongation of alternan chains.
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Affiliation(s)
- Manon Molina
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Claire Moulis
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nelly Monties
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - David Guieysse
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Sandrine Morel
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Gianluca Cioci
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Magali Remaud-Siméon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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13
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Claverie M, Cioci G, Vuillemin M, Bondy P, Remaud-Simeon M, Moulis C. Processivity of dextransucrases synthesizing very-high-molar-mass dextran is mediated by sugar-binding pockets in domain V. J Biol Chem 2020; 295:5602-5613. [PMID: 32161118 PMCID: PMC7186162 DOI: 10.1074/jbc.ra119.011995] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/30/2020] [Indexed: 11/06/2022] Open
Abstract
The dextransucrase DSR-OK from the Gram-positive bacterium Oenococcus kitaharae DSM17330 produces a dextran of the highest molar mass reported to date (∼109 g/mol). In this study, we selected a recombinant form, DSR-OKΔ1, to identify molecular determinants involved in the sugar polymerization mechanism and that confer its ability to produce a very-high-molar-mass polymer. In domain V of DSR-OK, we identified seven putative sugar-binding pockets characteristic of glycoside hydrolase 70 (GH70) glucansucrases that are known to be involved in glucan binding. We investigated their role in polymer synthesis through several approaches, including monitoring of dextran synthesis, affinity assays, sugar binding pocket deletions, site-directed mutagenesis, and construction of chimeric enzymes. Substitution of only two stacking aromatic residues in two consecutive sugar-binding pockets (variant DSR-OKΔ1-Y1162A-F1228A) induced quasi-complete loss of very-high-molar-mass dextran synthesis, resulting in production of only 10-13 kg/mol polymers. Moreover, the double mutation completely switched the semiprocessive mode of DSR-OKΔ1 toward a distributive one, highlighting the strong influence of these pockets on enzyme processivity. Finally, the position of each pocket relative to the active site also appeared to be important for polymer elongation. We propose that sugar-binding pockets spatially closer to the catalytic domain play a major role in the control of processivity. A deep structural characterization, if possible with large-molar-mass sugar ligands, would allow confirming this hypothesis.
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Affiliation(s)
- Marion Claverie
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Gianluca Cioci
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marlène Vuillemin
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Pauline Bondy
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Magali Remaud-Simeon
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Claire Moulis
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France.
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