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Zhong C, Nidetzky B. Bottom-Up Synthesized Glucan Materials: Opportunities from Applied Biocatalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400436. [PMID: 38514194 DOI: 10.1002/adma.202400436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Linear d-glucans are natural polysaccharides of simple chemical structure. They are comprised of d-glucosyl units linked by a single type of glycosidic bond. Noncovalent interactions within, and between, the d-glucan chains give rise to a broad variety of macromolecular nanostructures that can assemble into crystalline-organized materials of tunable morphology. Structure design and functionalization of d-glucans for diverse material applications largely relies on top-down processing and chemical derivatization of naturally derived starting materials. The top-down approach encounters critical limitations in efficiency, selectivity, and flexibility. Bottom-up approaches of d-glucan synthesis offer different, and often more precise, ways of polymer structure control and provide means of functional diversification widely inaccessible to top-down routes of polysaccharide material processing. Here the natural and engineered enzymes (glycosyltransferases, glycoside hydrolases and phosphorylases, glycosynthases) for d-glucan polymerization are described and the use of applied biocatalysis for the bottom-up assembly of specific d-glucan structures is shown. Advanced material applications of the resulting polymeric products are further shown and their important role in the development of sustainable macromolecular materials in a bio-based circular economy is discussed.
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Affiliation(s)
- Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, Graz, 8010, Austria
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2
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De Doncker M, Vleminckx S, Franceus J, Vercauteren R, Desmet T. Converting Bulk Sugars into Functional Fibers: Discovery and Application of a Thermostable β-1,3-Oligoglucan Phosphorylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10497-10505. [PMID: 38659290 DOI: 10.1021/acs.jafc.4c01990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Despite their broad application potential, the widespread use of β-1,3-glucans has been hampered by the high cost and heterogeneity associated with current production methods. To address this challenge, scalable and economically viable processes are needed for the production of β-1,3-glucans with tailorable molecular mass distributions. Glycoside phosphorylases have shown to be promising catalysts for the bottom-up synthesis of β-1,3-(oligo)glucans since they combine strict regioselectivity with a cheap donor substrate (i.e., α-glucose 1-phosphate). However, the need for an expensive priming substrate (e.g., laminaribiose) and the tendency to produce shorter oligosaccharides still form major bottlenecks. Here, we report the discovery and application of a thermostable β-1,3-oligoglucan phosphorylase originating from Anaerolinea thermophila (AtβOGP). This enzyme combines a superior catalytic efficiency toward glucose as a priming substrate, high thermostability, and the ability to synthesize high molecular mass β-1,3-glucans up to DP 75. Coupling of AtβOGP with a thermostable variant of Bifidobacterium adolescentis sucrose phosphorylase enabled the efficient production of tailorable β-1,3-(oligo)glucans from sucrose, with a near-complete conversion of >99 mol %. This cost-efficient process for the conversion of renewable bulk sugar into β-1,3-(oligo)glucans should facilitate the widespread application of these versatile functional fibers across various industries.
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Affiliation(s)
- Marc De Doncker
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Sofie Vleminckx
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jorick Franceus
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ronny Vercauteren
- Cargill R&D Centre Europe BV, Havenstraat 84, B-1800 Vilvoorde, Belgium
| | - Tom Desmet
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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3
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Zühlke MK, Ficko-Blean E, Bartosik D, Terrapon N, Jeudy A, Jam M, Wang F, Welsch N, Dürwald A, Martin LT, Larocque R, Jouanneau D, Eisenack T, Thomas F, Trautwein-Schult A, Teeling H, Becher D, Schweder T, Czjzek M. Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms. Environ Microbiol 2024; 26:e16624. [PMID: 38757353 DOI: 10.1111/1462-2920.16624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Laminarin, a β(1,3)-glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate-binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin-binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin-binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan-binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin-binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102- and CBM103-containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization.
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Affiliation(s)
- Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Elizabeth Ficko-Blean
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU, UMR7257), CNRS, Marseille, France
| | - Alexandra Jeudy
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Murielle Jam
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Fengqing Wang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Laura Torres Martin
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Robert Larocque
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Diane Jouanneau
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Tom Eisenack
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - François Thomas
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Mirjam Czjzek
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
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4
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Dai R, Ma X, Dingkao R, Huang C, La Y, Li X, Ma X, Wu X, Chu M, Guo X, Pei J, Yan P, Liang C. Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak. Front Microbiol 2023; 14:1124917. [PMID: 37200912 PMCID: PMC10185794 DOI: 10.3389/fmicb.2023.1124917] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear. Methods The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied. Results and Discussion The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.
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Affiliation(s)
- Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Renqing Dingkao
- Animal Husbandry Station, Gannan Tibetan Autonomous Prefecture, Gannan, Gansu, China
| | - Chun Huang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xinyi Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Ping Yan,
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- *Correspondence: Chunnian Liang,
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5
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Tanaka Y, Goto K, Jun L, Nishino K, Ogawa T, Maruta T, Ishikawa T. Identification of glucanases and phosphorylases involved in hypoxic paramylon degradation in Euglena gracilis. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Macdonald S, Pereira JH, Liu F, Tegl G, DeGiovanni A, Wardman JF, Deutsch S, Yoshikuni Y, Adams PD, Withers SG. A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. ACS CENTRAL SCIENCE 2022; 8:430-440. [PMID: 35505869 PMCID: PMC9052796 DOI: 10.1021/acscentsci.1c01570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 05/14/2023]
Abstract
The considerable utility of glycoside phosphorylases (GPs) has led to substantial efforts over the past two decades to expand the breadth of known GP activities. Driven largely by the increase of available genomic DNA sequence data, the gap between the number of sequences in the carbohydrate active enzyme database (CAZy DB) and its functionally characterized members continues to grow. This wealth of sequence data presented an exciting opportunity to explore the ever-expanding CAZy DB to discover new GPs with never-before-described functionalities. Utilizing an in silico sequence analysis of CAZy family GH94, we discovered and then functionally and structurally characterized the new GP β-1,3-N-acetylglucosaminide phosphorylase. This new GP was sourced from the genome of the cell-wall-less Mollicute bacterium, Acholeplasma laidlawii and was found to synthesize β-1,3-linked N-acetylglucosaminide linkages. The resulting poly-β-1,3-N-acetylglucosamine represents a new, previously undescribed biopolymer that completes the set of possible β-linked GlcNAc homopolysaccharides together with chitin (β-1,4) and PNAG (poly-β-1,6-N-acetylglucosamine). The new biopolymer was denoted acholetin, a combination of the genus Acholeplasma and the polysaccharide chitin, and the new GP was thus denoted acholetin phosphorylase (AchP). Use of the reverse phosphorolysis action of AchP provides an efficient method to enzymatically synthesize acholetin, which is a new biodegradable polymeric material.
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Affiliation(s)
- Spencer
S. Macdonald
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jose H. Pereira
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Feng Liu
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Gregor Tegl
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Andy DeGiovanni
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob F. Wardman
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Biochemistry & Molecular Biology, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Samuel Deutsch
- The US Department
of Energy Joint Genome Institute, Lawrence
Berkley National Laboratory, Berkeley, California 94720, United States
| | - Yasuo Yoshikuni
- The US Department
of Energy Joint Genome Institute, Lawrence
Berkley National Laboratory, Berkeley, California 94720, United States
| | - Paul D. Adams
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California
Berkeley, Berkeley, California 94720, United States
| | - Stephen G. Withers
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department
of Biochemistry & Molecular Biology, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- E-mail:
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7
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Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
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8
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Nakamura S, Nihira T, Kurata R, Nakai H, Funane K, Park EY, Miyazaki T. Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J Biol Chem 2021; 297:101366. [PMID: 34728215 PMCID: PMC8626586 DOI: 10.1016/j.jbc.2021.101366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022] Open
Abstract
Glycoside hydrolase family 65 (GH65) comprises glycoside hydrolases (GHs) and glycoside phosphorylases (GPs) that act on α-glucosidic linkages in oligosaccharides. All previously reported bacterial GH65 enzymes are GPs, whereas all eukaryotic GH65 enzymes known are GHs. In addition, to date, no crystal structure of a GH65 GH has yet been reported. In this study, we use biochemical experiments and X-ray crystallography to examine the function and structure of a GH65 enzyme from Flavobacterium johnsoniae (FjGH65A) that shows low amino acid sequence homology to reported GH65 enzymes. We found that FjGH65A does not exhibit phosphorolytic activity, but it does hydrolyze kojibiose (α-1,2-glucobiose) and oligosaccharides containing a kojibiosyl moiety without requiring inorganic phosphate. In addition, stereochemical analysis demonstrated that FjGH65A catalyzes this hydrolytic reaction via an anomer-inverting mechanism. The three-dimensional structures of FjGH65A in native form and in complex with glucose were determined at resolutions of 1.54 and 1.40 Å resolutions, respectively. The overall structure of FjGH65A resembled those of other GH65 GPs, and the general acid catalyst Glu472 was conserved. However, the amino acid sequence forming the phosphate-binding site typical of GH65 GPs was not conserved in FjGH65A. Moreover, FjGH65A had the general base catalyst Glu616 instead, which is required to activate a nucleophilic water molecule. These results indicate that FjGH65A is an α-1,2-glucosidase and is the first bacterial GH found in the GH65 family.
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Affiliation(s)
- Shuntaro Nakamura
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kazumi Funane
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan; Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan; Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan; Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan; Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.
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9
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Sun Y, Debeljak P, Obernosterer I. Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. THE ISME JOURNAL 2021; 15:2933-2946. [PMID: 33941887 PMCID: PMC8443675 DOI: 10.1038/s41396-021-00973-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 02/01/2023]
Abstract
Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Using novel Southern Ocean meta-omics resources including 133 metagenome-assembled genomes (MAGs), we show a mosaic of taxonomy-specific ecological strategies in naturally iron-fertilized and high nutrient low chlorophyll (HNLC) waters. Taxonomic profiling revealed apparent community shifts across contrasting nutrient regimes. Community-level and genome-resolved metatranscriptomics evidenced a moderate association between taxonomic affiliations and iron and carbon-related functional roles. Diverse ecological strategies emerged when considering the central metabolic pathways of individual MAGs. Closely related lineages appear to adapt to distinct ecological niches, based on their distribution and gene regulation patterns. Our in-depth observations emphasize the complex interplay between the genetic repertoire of individual taxa and their environment and how this shapes prokaryotic responses to iron and organic carbon availability in the Southern Ocean.
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Affiliation(s)
- Ying Sun
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France.
| | - Pavla Debeljak
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
- University of Vienna, Department of Functional and Evolutionary Ecology, A-1090, Vienna, Austria
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
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10
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Bulmer GS, de Andrade P, Field RA, van Munster JM. Recent advances in enzymatic synthesis of β-glucan and cellulose. Carbohydr Res 2021; 508:108411. [PMID: 34392134 PMCID: PMC8425183 DOI: 10.1016/j.carres.2021.108411] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/07/2023]
Abstract
Bottom-up synthesis of β-glucans such as callose, fungal β-(1,3)(1,6)-glucan and cellulose, can create the defined compounds that are needed to perform fundamental studies on glucan properties and develop applications. With the importance of β-glucans and cellulose in high-profile fields such as nutrition, renewables-based biotechnology and materials science, the enzymatic synthesis of such relevant carbohydrates and their derivatives has attracted much attention. Here we review recent developments in enzymatic synthesis of β-glucans and cellulose, with a focus on progress made over the last five years. We cover the different types of biocatalysts employed, their incorporation in cascades, the exploitation of enzyme promiscuity and their engineering, and reaction conditions affecting the production as well as in situ self-assembly of (non)functionalised glucans. The recent achievements in the application of glycosyl transferases and β-1,4- and β-1,3-glucan phosphorylases demonstrate the high potential and versatility of these biocatalysts in glucan synthesis in both industrial and academic contexts.
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Affiliation(s)
- Gregory S Bulmer
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Peterson de Andrade
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Jolanda M van Munster
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Scotland's Rural College, Edinburgh, UK.
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11
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Ralton JE, Sernee MF, McConville MJ. Evolution and function of carbohydrate reserve biosynthesis in parasitic protists. Trends Parasitol 2021; 37:988-1001. [PMID: 34266735 DOI: 10.1016/j.pt.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022]
Abstract
Nearly all eukaryotic cells synthesize carbohydrate reserves, such as glycogen, starch, or low-molecular-weight oligosaccharides. However, a number of parasitic protists have lost this capacity while others have lost, and subsequently evolved, entirely new pathways. Recent studies suggest that retention, loss, or acquisition of these pathways in different protists is intimately linked to their lifestyle. In particular, parasites with carbohydrate reserves often establish long-lived chronic infections and/or produce environmental cysts, whereas loss of these pathways is associated with parasites that have highly proliferative and metabolically active life-cycle stages. The evolution of mannogen biosynthesis in Leishmania and related parasites indicates that these pathways have played a role in defining the host range and niches occupied by some protists.
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Affiliation(s)
- Julie E Ralton
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - M Fleur Sernee
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia.
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12
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Klimacek M, Zhong C, Nidetzky B. Kinetic modeling of phosphorylase-catalyzed iterative β-1,4-glycosylation for degree of polymerization-controlled synthesis of soluble cello-oligosaccharides. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:134. [PMID: 34112242 PMCID: PMC8194188 DOI: 10.1186/s13068-021-01982-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/31/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes the iterative β-1,4-glycosylation of cellobiose using α-D-glucose 1-phosphate as the donor substrate. Cello-oligosaccharides (COS) with a degree of polymerization (DP) of up to 6 are soluble while those of larger DP self-assemble into solid cellulose material. The soluble COS have attracted considerable attention for their use as dietary fibers that offer a selective prebiotic function. An efficient synthesis of soluble COS requires good control over the DP of the products formed. A mathematical model of the iterative enzymatic glycosylation would be important to facilitate target-oriented process development. RESULTS A detailed time-course analysis of the formation of COS products from cellobiose (25 mM, 50 mM) and α-D-glucose 1-phosphate (10-100 mM) was performed using the CdP from Clostridium cellulosi. A mechanism-based, Michaelis-Menten type mathematical model was developed to describe the kinetics of the iterative enzymatic glycosylation of cellobiose. The mechanistic model was combined with an empirical description of the DP-dependent self-assembly of the COS into insoluble cellulose. The hybrid model thus obtained was used for kinetic parameter determination from time-course fits performed with constraints derived from initial rate data. The fitted hybrid model provided excellent description of the experimental dynamics of the COS in the DP range 3-6 and also accounted for the insoluble product formation. The hybrid model was suitable to disentangle the complex relationship between the process conditions used (i.e., substrate concentration, donor/acceptor ratio, reaction time) and the reaction output obtained (i.e., yield and composition of soluble COS). Model application to a window-of-operation analysis for the synthesis of soluble COS was demonstrated on the example of a COS mixture enriched in DP 4. CONCLUSIONS The hybrid model of CdP-catalyzed iterative glycosylation is an important engineering tool to study and optimize the biocatalytic synthesis of soluble COS. The kinetic modeling approach used here can be of a general interest to be applied to other iteratively catalyzed enzymatic reactions of synthetic importance.
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Affiliation(s)
- Mario Klimacek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (Acib), Graz, Austria.
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13
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Cordoba J, Perez E, Van Vlierberghe M, Bertrand AR, Lupo V, Cardol P, Baurain D. De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes (Basel) 2021; 12:842. [PMID: 34072576 PMCID: PMC8227486 DOI: 10.3390/genes12060842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
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Affiliation(s)
- Javier Cordoba
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Emilie Perez
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Mick Van Vlierberghe
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Amandine R. Bertrand
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Valérian Lupo
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Pierre Cardol
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Denis Baurain
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
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14
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β-Glucan phosphorylases in carbohydrate synthesis. Appl Microbiol Biotechnol 2021; 105:4073-4087. [PMID: 33970317 PMCID: PMC8140972 DOI: 10.1007/s00253-021-11320-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/02/2023]
Abstract
Abstract β-Glucan phosphorylases are carbohydrate-active enzymes that catalyze the reversible degradation of β-linked glucose polymers, with outstanding potential for the biocatalytic bottom-up synthesis of β-glucans as major bioactive compounds. Their preference for sugar phosphates (rather than nucleotide sugars) as donor substrates further underlines their significance for the carbohydrate industry. Presently, they are classified in the glycoside hydrolase families 94, 149, and 161 (www.cazy.org). Since the discovery of β-1,3-oligoglucan phosphorylase in 1963, several other specificities have been reported that differ in linkage type and/or degree of polymerization. Here, we present an overview of the progress that has been made in our understanding of β-glucan and associated β-glucobiose phosphorylases, with a special focus on their application in the synthesis of carbohydrates and related molecules. Key points • Discovery, characteristics, and applications of β-glucan phosphorylases. • β-Glucan phosphorylases in the production of functional carbohydrates.
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15
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Wangpaiboon K, Sitthiyotha T, Chunsrivirot S, Charoenwongpaiboon T, Pichyangkura R. Unravelling Regioselectivity of Leuconostoc citreum ABK-1 Alternansucrase by Acceptor Site Engineering. Int J Mol Sci 2021; 22:3229. [PMID: 33810084 PMCID: PMC8005217 DOI: 10.3390/ijms22063229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 01/24/2023] Open
Abstract
Alternansucrase (ALT, EC 2.4.1.140) is a glucansucrase that can generate α-(1,3/1,6)-linked glucan from sucrose. Previously, the crystal structure of the first alternansucrase from Leuconostoc citreum NRRL B-1355 was successfully elucidated; it showed that alternansucrase might have two acceptor subsites (W675 and W543) responsible for the formation of alternating linked glucan. This work aimed to investigate the primary acceptor subsite (W675) by saturated mutagenesis using Leuconostoc citreum ABK-1 alternansucrase (LcALT). The substitution of other residues led to loss of overall activity, and formation of an alternan polymer with a nanoglucan was maintained when W675 was replaced with other aromatic residues. Conversely, substitution by nonaromatic residues led to the synthesis of oligosaccharides. Mutations at W675 could potentially cause LcALT to lose control of the acceptor molecule binding via maltose-acceptor reaction-as demonstrated by results from molecular dynamics simulations of the W675A variant. The formation of α-(1,2), α-(1,3), α-(1,4), and α-(1,6) linkages were detected from products of the W675A mutant. In contrast, the wild-type enzyme strictly synthesized α-(1,6) linkage on the maltose acceptor. This study examined the importance of W675 for transglycosylation, processivity, and regioselectivity of glucansucrases. Engineering glucansucrase active sites is one of the essential approaches to green tools for carbohydrate modification.
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Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (S.C.)
| | - Thassanai Sitthiyotha
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand;
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (S.C.)
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand;
| | | | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (S.C.)
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16
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Chabi M, Leleu M, Fermont L, Colpaert M, Colleoni C, Ball SG, Cenci U. Retracing Storage Polysaccharide Evolution in Stramenopila. FRONTIERS IN PLANT SCIENCE 2021; 12:629045. [PMID: 33747010 PMCID: PMC7965971 DOI: 10.3389/fpls.2021.629045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
Abstract
Eukaryotes most often synthesize storage polysaccharides in the cytosol or vacuoles in the form of either alpha (glycogen/starch)- or beta-glucosidic (chrysolaminarins and paramylon) linked glucan polymers. In both cases, the glucose can be packed either in water-soluble (glycogen and chrysolaminarins) or solid crystalline (starch and paramylon) forms with different impacts, respectively, on the osmotic pressure, the glucose accessibility, and the amounts stored. Glycogen or starch accumulation appears universal in all free-living unikonts (metazoa, fungi, amoebozoa, etc.), as well as Archaeplastida and alveolata, while other lineages offer a more complex picture featuring both alpha- and beta-glucan accumulators. We now infer the distribution of these polymers in stramenopiles through the bioinformatic detection of their suspected metabolic pathways. Detailed phylogenetic analysis of key enzymes of these pathways correlated to the phylogeny of Stramenopila enables us to retrace the evolution of storage polysaccharide metabolism in this diverse group of organisms. The possible ancestral nature of glycogen metabolism in eukaryotes and the underlying source of its replacement by beta-glucans are discussed.
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Affiliation(s)
- Malika Chabi
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marie Leleu
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Léa Fermont
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Matthieu Colpaert
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Christophe Colleoni
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Steven G. Ball
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Ugo Cenci
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- *Correspondence: Ugo Cenci,
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17
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Awad FN. Glycoside phosphorylases for carbohydrate synthesis: An insight into the diversity and potentiality. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Škodová-Sveráková I, Prokopchuk G, Peña-Diaz P, Záhonová K, Moos M, Horváth A, Šimek P, Lukeš J. Unique Dynamics of Paramylon Storage in the Marine Euglenozoan Diplonema papillatum. Protist 2020; 171:125717. [PMID: 32087573 DOI: 10.1016/j.protis.2020.125717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/07/2020] [Accepted: 02/02/2020] [Indexed: 10/25/2022]
Abstract
Diplonemids belong to the most diverse and abundant marine protists, which places them among the key players of the oceanic ecosystem. Under in vitro conditions, their best-known representative Diplonema papillatum accumulates in its cytoplasm a crystalline polymer. When grown under the nutrient-poor conditions, but not nutrient-rich conditions, D. papillatum synthesizes a β-1,3-glucan polymer, also known as paramylon. This phenomenon is unexpected, as it is in striking contrast to the accumulation of paramylon in euglenids, since these related flagellates synthesize this polymer solely under nutrient-rich conditions. The capacity of D. papillatum to store an energy source in the form of polysaccharides when the environment is poor in nutrients is unexpected and may contribute to the wide distribution of these protists in the ocean.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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19
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Singh RP, Pergolizzi G, Nepogodiev SA, de Andrade P, Kuhaudomlarp S, Field RA. Preparative and Kinetic Analysis of β-1,4- and β-1,3-Glucan Phosphorylases Informs Access to Human Milk Oligosaccharide Fragments and Analogues Thereof. Chembiochem 2020; 21:1043-1049. [PMID: 31657512 PMCID: PMC7187349 DOI: 10.1002/cbic.201900440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/27/2019] [Indexed: 12/21/2022]
Abstract
The enzymatic synthesis of oligosaccharides depends on the availability of suitable enzymes, which remains a limitation. Without recourse to enzyme engineering or evolution approaches, herein we demonstrate the ability of wild-type cellodextrin phosphorylase (CDP: β-1,4-glucan linkage-dependent) and laminaridextrin phosphorylase (Pro_7066: β-1,3-glucan linkage-dependent) to tolerate a number of sugar-1- phosphate substrates, albeit with reduced kinetic efficiency. In spite of catalytic efficiencies of <1 % of the natural reactions, we demonstrate the utility of given phosphorylase-sugar phosphate pairs to access new-to-nature fragments of human milk oligosaccharides, or analogues thereof, in multi-milligram quantities.
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Affiliation(s)
- Ravindra Pal Singh
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Food and Nutritional Biotechnology DivisionNational Agri-Food Biotechnology Institute (NABI)Main Campus, Sector 81Sahibzada Ajit Singh NagarPunjab140306India
| | - Giulia Pergolizzi
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Sergey A. Nepogodiev
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Peterson de Andrade
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Sakonwan Kuhaudomlarp
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Robert A. Field
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Department of Chemistry and Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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20
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Hasan MT, Sun A, Khatiwada B, McQuade L, Mirzaei M, Te'o J, Hobba G, Sunna A, Nevalainen H. Comparative proteomics investigation of central carbon metabolism in Euglena gracilis grown under predominantly phototrophic, mixotrophic and heterotrophic cultivations. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Garron ML, Henrissat B. The continuing expansion of CAZymes and their families. Curr Opin Chem Biol 2019; 53:82-87. [PMID: 31550558 DOI: 10.1016/j.cbpa.2019.08.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/17/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022]
Abstract
Carbohydrate-active enzymes (CAZymes) catalyze the assembly and breakdown of glycans and glycoconjugates. Some have been discovered, studied and exploited for numerous applications long ago. For instance, amylase and invertase were isolated in the second half of the 19th century and lysozyme was the first enzyme whose 3-D structure was determined. In spite of this early start, the number of families of carbohydrate-active enzymes continues to grow steadily in the early 21st century. This review examines the CAZyme families reported during the last two years and posits that the current expansion will continue in the future, progressively uncovering the massive diversity of glycans whose breakdown requires a large diversity of bespoke enzymes.
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Affiliation(s)
- Marie-Line Garron
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France; INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France; INRA, USC 1408 AFMB, 13288, Marseille, France.
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22
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Inwongwan S, Kruger NJ, Ratcliffe RG, O'Neill EC. Euglena Central Metabolic Pathways and Their Subcellular Locations. Metabolites 2019; 9:E115. [PMID: 31207935 PMCID: PMC6630311 DOI: 10.3390/metabo9060115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. We analysed bioinformatic, biochemical, and proteomic information from a variety of sources to assess the subcellular location of the enzymes of the central metabolic pathways, and we use these assignments to propose a model of the metabolic network of Euglena. Other than photosynthesis, all major pathways present in the chloroplast are also present elsewhere in the cell. Our model demonstrates how Euglena can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ellis C O'Neill
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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23
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Kuhaudomlarp S, Stevenson CEM, Lawson DM, Field RA. The structure of a GH149 β-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-β-(1 → 3)-glucose (laminaribiose) phosphorylase. Proteins 2019; 87:885-892. [PMID: 31134667 PMCID: PMC6771811 DOI: 10.1002/prot.25745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/07/2019] [Accepted: 05/22/2019] [Indexed: 11/08/2022]
Abstract
Glycoside phosphorylases (GPs) with specificity for β-(1 → 3)-gluco-oligosaccharides are potential candidate biocatalysts for oligosaccharide synthesis. GPs with this linkage specificity are found in two families thus far-glycoside hydrolase family 94 (GH94) and the recently discovered glycoside hydrolase family 149 (GH149). Previously, we reported a crystallographic study of a GH94 laminaribiose phosphorylase with specificity for disaccharides, providing insight into the enzyme's ability to recognize its' sugar substrate/product. In contrast to GH94, characterized GH149 enzymes were shown to have more flexible chain length specificity, with preference for substrate/product with higher degree of polymerization. In order to advance understanding of the specificity of GH149 enzymes, we herein solved X-ray crystallographic structures of GH149 enzyme Pro_7066 in the absence of substrate and in complex with laminarihexaose (G6). The overall domain organization of Pro_7066 is very similar to that of GH94 family enzymes. However, two additional domains flanking its catalytic domain were found only in the GH149 enzyme. Unexpectedly, the G6 complex structure revealed an oligosaccharide surface binding site remote from the catalytic site, which, we suggest, may be associated with substrate targeting. As such, this study reports the first structure of a GH149 phosphorylase enzyme acting on β-(1 → 3)-gluco-oligosaccharides and identifies structural elements that may be involved in defining the specificity of the GH149 enzymes.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
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Gissibl A, Sun A, Care A, Nevalainen H, Sunna A. Bioproducts From Euglena gracilis: Synthesis and Applications. Front Bioeng Biotechnol 2019; 7:108. [PMID: 31157220 PMCID: PMC6530250 DOI: 10.3389/fbioe.2019.00108] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/29/2019] [Indexed: 11/24/2022] Open
Abstract
In recent years, the versatile phototrophic protist Euglena gracilis has emerged as an interesting candidate for application-driven research and commercialisation, as it is an excellent source of dietary protein, pro(vitamins), lipids, and the β-1,3-glucan paramylon only found in euglenoids. From these, paramylon is already marketed as an immunostimulatory agent in nutraceuticals. Bioproducts from E. gracilis can be produced under various cultivation conditions discussed in this review, and their yields are relatively high when compared with those achieved in microalgal systems. Future challenges include achieving the economy of large-scale cultivation. Recent insights into the complex metabolism of E. gracilis have highlighted unique metabolic pathways, which could provide new leads for product enhancement by genetic modification of the organism. Also, development of molecular tools for strain improvement are emerging rapidly, making E. gracilis a noteworthy challenger for microalgae such as Chlorella spp. and their products currently on the market.
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Affiliation(s)
- Alexander Gissibl
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
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Macdonald SS, Armstrong Z, Morgan-Lang C, Osowiecka M, Robinson K, Hallam SJ, Withers SG. Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases. Cell Chem Biol 2019; 26:1001-1012.e5. [PMID: 31080075 DOI: 10.1016/j.chembiol.2019.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 01/19/2023]
Abstract
Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.
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Affiliation(s)
- Spencer S Macdonald
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zachary Armstrong
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Magdalena Osowiecka
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Kyle Robinson
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Kuhaudomlarp S, Pergolizzi G, Patron NJ, Henrissat B, Field RA. Unraveling the subtleties of β-(1→3)-glucan phosphorylase specificity in the GH94, GH149, and GH161 glycoside hydrolase families. J Biol Chem 2019; 294:6483-6493. [PMID: 30819804 PMCID: PMC6484121 DOI: 10.1074/jbc.ra119.007712] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Indexed: 12/31/2022] Open
Abstract
Glycoside phosphorylases (GPs) catalyze the phosphorolysis of glycans into the corresponding sugar 1-phosphates and shortened glycan chains. Given the diversity of natural β-(1→3)-glucans and their wide range of biotechnological applications, the identification of enzymatic tools that can act on β-(1→3)-glucooligosaccharides is an attractive area of research. GP activities acting on β-(1→3)-glucooligosaccharides have been described in bacteria, the photosynthetic excavate Euglena gracilis, and the heterokont Ochromonas spp. Previously, we characterized β-(1→3)-glucan GPs from bacteria and E. gracilis, leading to their classification in glycoside hydrolase family GH149. Here, we characterized GPs from Gram-positive bacteria and heterokont algae acting on β-(1→3)-glucooligosaccharides. We identified a phosphorylase sequence from Ochromonas spp. (OcP1) together with its orthologs from other species, leading us to propose the establishment of a new GH family, designated GH161. To establish the activity of GH161 members, we recombinantly expressed a bacterial GH161 gene sequence (PapP) from the Gram-positive bacterium Paenibacillus polymyxa ATCC 842 in Escherichia coli. We found that PapP acts on β-(1→3)-glucooligosaccharide acceptors with a degree of polymerization (DP) ≥ 2. This activity was distinct from that of characterized GH149 β-(1→3)-glucan phosphorylases, which operate on acceptors with DP ≥ 1. We also found that bacterial GH161 genes co-localize with genes encoding β-glucosidases and ATP-binding cassette transporters, highlighting a probable involvement of GH161 enzymes in carbohydrate degradation. Importantly, in some species, GH161 and GH94 genes were present in tandem, providing evidence that GPs from different CAZy families may work sequentially to degrade oligosaccharides.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Giulia Pergolizzi
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Nicola J Patron
- the Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, 163 Avenue de Luminy, 13288 Marseille, France.,CNRS, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France, and.,the Department of Biological Sciences, King Abdulaziz University, Jeddah 23218, Saudi Arabia
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom,
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Gissibl A, Care A, Sun A, Hobba G, Nevalainen H, Sunna A. Development of screening strategies for the identification of paramylon-degrading enzymes. J Ind Microbiol Biotechnol 2019; 46:769-781. [PMID: 30806871 DOI: 10.1007/s10295-019-02157-7] [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: 12/01/2018] [Accepted: 02/17/2019] [Indexed: 10/27/2022]
Abstract
Enzymatic degradation of the β-1,3-glucan paramylon could enable the production of bioactive compounds for healthcare and renewable substrates for biofuels. However, few enzymes have been found to degrade paramylon efficiently and their enzymatic mechanisms remain poorly understood. Thus, the aim of this work was to find paramylon-degrading enzymes and ways to facilitate their identification. Towards this end, a Euglena gracilis-derived cDNA expression library was generated and introduced into Escherichia coli. A flow cytometry-based screening assay was developed to identify E. gracilis enzymes that could hydrolyse the fluorogenic substrate fluorescein di-β-D-glucopyranoside in combination with time-saving auto-induction medium. In parallel, four amino acid sequences of potential E. gracilis β-1,3-glucanases were identified from proteomic data. The open reading frame encoding one of these candidate sequences (light_m.20624) was heterologously expressed in E. coli. Finally, a Congo Red dye plate assay was developed for the screening of enzyme preparations potentially able to degrade paramylon. This assay was validated with enzymes assumed to have paramylon-degrading activity and then used to identify four commercial preparations with previously unknown paramylon degradation ability.
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Affiliation(s)
- Alexander Gissibl
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Angela Sun
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
| | - Graham Hobba
- Agritechnology Pty Ltd, 36 Underwood Road, Borenore, NSW, 2800, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
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28
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Benkoulouche M, Fauré R, Remaud-Siméon M, Moulis C, André I. Harnessing glycoenzyme engineering for synthesis of bioactive oligosaccharides. Interface Focus 2019; 9:20180069. [PMID: 30842872 DOI: 10.1098/rsfs.2018.0069] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2018] [Indexed: 12/13/2022] Open
Abstract
Combined with chemical synthesis, the use of glycoenzyme biocatalysts has shown great synthetic potential over recent decades owing to their remarkable versatility in terms of substrates and regio- and stereoselectivity that allow structurally controlled synthesis of carbohydrates and glycoconjugates. Nonetheless, the lack of appropriate enzymatic tools with requisite properties in the natural diversity has hampered extensive exploration of enzyme-based synthetic routes to access relevant bioactive oligosaccharides, such as cell-surface glycans or prebiotics. With the remarkable progress in enzyme engineering, it has become possible to improve catalytic efficiency and physico-chemical properties of enzymes but also considerably extend the repertoire of accessible catalytic reactions and tailor novel substrate specificities. In this review, we intend to give a brief overview of the advantageous use of engineered glycoenzymes, sometimes in combination with chemical steps, for the synthesis of natural bioactive oligosaccharides or their precursors. The focus will be on examples resulting from the three main classes of glycoenzymes specialized in carbohydrate synthesis: glycosyltransferases, glycoside hydrolases and glycoside phosphorylases.
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Affiliation(s)
- Mounir Benkoulouche
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Régis Fauré
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Magali Remaud-Siméon
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Claire Moulis
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
| | - Isabelle André
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, 135, avenue de Rangueil, 31077 Toulouse cedex 04, France
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29
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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30
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Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms. ISME JOURNAL 2018; 12:2894-2906. [PMID: 30061707 PMCID: PMC6246565 DOI: 10.1038/s41396-018-0243-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/22/2018] [Accepted: 06/30/2018] [Indexed: 01/15/2023]
Abstract
Polysaccharide degradation by heterotrophic microbes is a key process within Earth's carbon cycle. Here, we use environmental proteomics and metagenomics in combination with cultivation experiments and biochemical characterizations to investigate the molecular details of in situ polysaccharide degradation mechanisms during microalgal blooms. For this, we use laminarin as a model polysaccharide. Laminarin is a ubiquitous marine storage polymer of marine microalgae and is particularly abundant during phytoplankton blooms. In this study, we show that highly specialized bacterial strains of the Bacteroidetes phylum repeatedly reached high abundances during North Sea algal blooms and dominated laminarin turnover. These genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases and transporters that belonged to the most abundant proteins in the environmental samples. In vitro experiments with cultured isolates allowed us to determine the functions of in situ expressed key enzymes and to confirm their role in laminarin utilization. It is shown that laminarin consumption of Formosa spp. is paralleled by enhanced uptake of diatom-derived peptides. This study reveals that genome reduction, enzyme fusions, transporters, and enzyme expansion as well as a tight coupling of carbon and nitrogen metabolism provide the tools, which make Formosa spp. so competitive during microalgal blooms.
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Kuhaudomlarp S, Walpole S, Stevenson CEM, Nepogodiev SA, Lawson DM, Angulo J, Field RA. Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy. Chembiochem 2018; 20:181-192. [PMID: 29856496 DOI: 10.1002/cbic.201800260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Indexed: 12/13/2022]
Abstract
Glycoside phosphorylases (GPs) carry out a reversible phosphorolysis of carbohydrates into oligosaccharide acceptors and the corresponding sugar 1-phosphates. The reversibility of the reaction enables the use of GPs as biocatalysts for carbohydrate synthesis. Glycosyl hydrolase family 94 (GH94), which only comprises GPs, is one of the most studied GP families that have been used as biocatalysts for carbohydrate synthesis, in academic research and in industrial production. Understanding the mechanism of GH94 enzymes is a crucial step towards enzyme engineering to improve and expand the applications of these enzymes in synthesis. In this work with a GH94 laminaribiose phosphorylase from Paenibacillus sp. YM-1 (PsLBP), we have demonstrated an enzymatic synthesis of disaccharide 1 (β-d-mannopyranosyl-(1→3)-d-glucopyranose) by using a natural acceptor glucose and noncognate donor substrate α-mannose 1-phosphate (Man1P). To investigate how the enzyme recognises different sugar 1-phosphates, the X-ray crystal structures of PsLBP in complex with Glc1P and Man1P have been solved, providing the first molecular detail of the recognition of a noncognate donor substrate by GPs, which revealed the importance of hydrogen bonding between the active site residues and hydroxy groups at C2, C4, and C6 of sugar 1-phosphates. Furthermore, we used saturation transfer difference NMR spectroscopy to support crystallographic studies on the sugar 1-phosphates, as well as to provide further insights into the PsLBP recognition of the acceptors and disaccharide products.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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