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Liu J, Feng X, Liang L, Sun L, Meng D. Enzymatic biosynthesis of D-galactose derivatives: Advances and perspectives. Int J Biol Macromol 2024; 267:131518. [PMID: 38615865 DOI: 10.1016/j.ijbiomac.2024.131518] [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: 02/01/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
D-Galactose derivatives, including galactosyl-conjugates and galactose-upgrading compounds, provide various physiological benefits and find applications in industries such as food, cosmetics, feed, pharmaceuticals. Many research on galactose derivatives focuses on identification, characterization, development, and mechanistic aspects of their physiological function, providing opportunities and challenges for the development of practical approaches for synthesizing galactose derivatives. This study focuses on recent advancements in enzymatic biosynthesis of galactose derivatives. Various strategies including isomerization, epimerization, transgalactosylation, and phosphorylation-dephosphorylation were extensively discussed under the perspectives of thermodynamic feasibility, theoretical yield, cost-effectiveness, and by-product elimination. Specifically, the enzymatic phosphorylation-dephosphorylation cascade is a promising enzymatic synthesis route for galactose derivatives because it can overcome the thermodynamic equilibrium of isomerization and utilize cost-effective raw materials. The study also elucidates the existing challenges and future trends in enzymatic biosynthesis of galactose derivatives. Collectively, this review provides a real-time summary aimed at promoting the practical biosynthesis of galactose derivatives through enzymatic catalysis.
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Affiliation(s)
- Juanjuan Liu
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Xinming Feng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China
| | - Likun Liang
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Liqin Sun
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China.
| | - Dongdong Meng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China.
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2
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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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3
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Hirano R, Sakanaka M, Yoshimi K, Sugimoto N, Eguchi S, Yamauchi Y, Nara M, Maeda S, Ami Y, Gotoh A, Katayama T, Iida N, Kato T, Ohno H, Fukiya S, Yokota A, Nishimoto M, Kitaoka M, Nakai H, Kurihara S. Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile. Gut Microbes 2021; 13:1973835. [PMID: 34553672 PMCID: PMC8475593 DOI: 10.1080/19490976.2021.1973835] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 02/04/2023] Open
Abstract
Certain existing prebiotics meant to facilitate the growth of beneficial bacteria in the intestine also promote the growth of other prominent bacteria. Therefore, the growth-promoting effects of β-galactosides on intestinal bacteria were analyzed. Galactosyl-β1,4-l-rhamnose (Gal-β1,4-Rha) selectively promoted the growth of Bifidobacterium. Bifidobacterium longum subsp. longum 105-A (JCM 31944) has multiple solute-binding proteins belonging to ATP-binding cassette transporters for sugars. Each strain in the library of 11 B. longum subsp. longum mutants, in which each gene of the solute-binding protein was disrupted, was cultured in a medium containing Gal-β1,4-Rha as the sole carbon source, and only the BL105A_0502 gene-disruption mutant showed delayed and reduced growth compared to the wild-type strain. BL105A_0502 homolog is highly conserved in bifidobacteria. In a Gal-β1,4-Rha-containing medium, Bifidobacterium longum subsp. infantis JCM 1222T, which possesses BLIJ_2090, a homologous protein to BL105A_0502, suppressed the growth of enteric pathogen Clostridioides difficile, whereas the BLIJ_2090 gene-disrupted mutant did not. In vivo, administration of B. infantis and Gal-β1,4-Rha alleviated C. difficile infection-related weight loss in mice. We have successfully screened Gal-β1,4-Rha as a next-generation prebiotic candidate that specifically promotes the growth of beneficial bacteria without promoting the growth of prominent bacteria and pathogens.
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Affiliation(s)
- Rika Hirano
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Mikiyasu Sakanaka
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | | | - Syogo Eguchi
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Misaki Nara
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Shingo Maeda
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yuta Ami
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takane Katayama
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Noriho Iida
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Tamotsu Kato
- Laboratory for Intestinal Ecosystem, Riken Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, Riken Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Satoru Fukiya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Atsushi Yokota
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mamoru Nishimoto
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Motomitsu Kitaoka
- Faculty of Agriculture, Niigata University, Niigata, Japan
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Shin Kurihara
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
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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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Nishimoto M. Large scale production of lacto- N-biose I, a building block of type I human milk oligosaccharides, using sugar phosphorylases. Biosci Biotechnol Biochem 2019; 84:17-24. [PMID: 31566084 DOI: 10.1080/09168451.2019.1670047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human milk oligosaccharides (HMOs) have drawn attention for their contribution to the explosive bifidobacterial growth in the intestines of neonates. We found that bifidobacteria can efficiently metabolize lacto-N-biose I (LNB), the major building blocks of HMOs, and we have developed a method to synthesize LNB by applying this system. We produced LNB on a kilogram scale by the method. This proved that, among the enterobacteria, only bifidobacteria can assimilate LNB, and provided the data that supported the explosive growth of bifidobacteria in neonates. Furthermore, we were also able to reveal the structure of LNB crystal and the low stability for heating at neutral pH, which has not been clarified so far. In this paper, using bifidobacteria and LNB as examples, I describe the research on oligosaccharide synthesis that was conducted by utilizing a sugar metabolism.Abbreviations: LNB: lacto-N-biose I; GNB: galacto-N-biose; HMOs: human milk oligosaccharides; GLNBP: GNB/LNB phosphorylase; NahK: N-acetylhexosamine 1-kinase; GalT: UDP-glucose-hexose-1-phosphate uridylyltransferase; GalE: UDP-glucose 4-epimerase; SP: sucrose phosphorylase.
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Affiliation(s)
- Mamoru Nishimoto
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
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6
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Pergolizzi G, Kuhaudomlarp S, Kalita E, Field RA. Glycan Phosphorylases in Multi-Enzyme Synthetic Processes. Protein Pept Lett 2017; 24:696-709. [PMID: 28799504 PMCID: PMC5688430 DOI: 10.2174/0929866524666170811125109] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/24/2017] [Accepted: 06/20/2017] [Indexed: 12/22/2022]
Abstract
Glycoside phosphorylases catalyse the reversible synthesis of glycosidic bonds by glycosylation with concomitant release of inorganic phosphate. The equilibrium position of such reactions can render them of limited synthetic utility, unless coupled with a secondary enzymatic step where the reaction lies heavily in favour of product. This article surveys recent works on the combined use of glycan phosphorylases with other enzymes to achieve synthetically useful processes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH. United Kingdom
| | - Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH. United Kingdom
| | - Eeshan Kalita
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH. United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH. United Kingdom
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7
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Kitaoka M. Diversity of phosphorylases in glycoside hydrolase families. Appl Microbiol Biotechnol 2015; 99:8377-90. [PMID: 26293338 DOI: 10.1007/s00253-015-6927-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/05/2015] [Indexed: 01/02/2023]
Abstract
Phosphorylases are useful catalysts for the practical preparation of various sugars. The number of known specificities was 13 in 2002 and is now 30. The drastic increase in available genome sequences has facilitated the discovery of novel activities. Most of these novel phosphorylase activities have been identified through the investigations of glycoside hydrolase families containing known phosphorylases. Here, the diversity of phosphorylases in each family is described in detail.
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Affiliation(s)
- Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
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8
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Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 2015; 10:e0118285. [PMID: 26035711 PMCID: PMC4452783 DOI: 10.1371/journal.pone.0118285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
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Affiliation(s)
- Elsa Petit
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Maddalena V. Coppi
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - James C. Hayes
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Andrew C. Tolonen
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Genoscope, Unité Mixte de Recherche (UMR)-8030, National Center for Scientific Research (CNRS), Evry, France
| | - Thomas Warnick
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - William G. Latouf
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danielle Amisano
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Amy Biddle
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Supratim Mukherjee
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Natalia Ivanova
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Athanassios Lykidis
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Nikos Kyrpides
- Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Unité mixte de recherche (UMR)-6098, National Center for Scientific Research (CNRS), and Universités d’Aix-Marseille I and II, Marseille, France
| | - Joanne Lau
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Danny J. Schnell
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan B. Leschine
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Jeffrey L. Blanchard
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America
- Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
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9
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Puchart V. Glycoside phosphorylases: Structure, catalytic properties and biotechnological potential. Biotechnol Adv 2015; 33:261-76. [DOI: 10.1016/j.biotechadv.2015.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 12/20/2022]
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10
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O'Neill EC, Field RA. Enzymatic synthesis using glycoside phosphorylases. Carbohydr Res 2015; 403:23-37. [PMID: 25060838 PMCID: PMC4336185 DOI: 10.1016/j.carres.2014.06.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 05/29/2014] [Accepted: 06/09/2014] [Indexed: 01/10/2023]
Abstract
Carbohydrate phosphorylases are readily accessible but under-explored catalysts for glycoside synthesis. Their use of accessible and relatively stable sugar phosphates as donor substrates underlies their potential. A wide range of these enzymes has been reported of late, displaying a range of preferences for sugar donors, acceptors and glycosidic linkages. This has allowed this class of enzymes to be used in the synthesis of diverse carbohydrate structures, including at the industrial scale. As more phosphorylase enzymes are discovered, access to further difficult to synthesise glycosides will be enabled. Herein we review reported phosphorylase enzymes and the glycoside products that they have been used to synthesise.
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Affiliation(s)
- Ellis C O'Neill
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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11
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Liu Y, Nishimoto M, Kitaoka M. Facile enzymatic synthesis of sugar 1-phosphates as substrates for phosphorylases using anomeric kinases. Carbohydr Res 2015; 401:1-4. [DOI: 10.1016/j.carres.2014.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 11/24/2022]
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12
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Boutard M, Cerisy T, Nogue PY, Alberti A, Weissenbach J, Salanoubat M, Tolonen AC. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass. PLoS Genet 2014; 10:e1004773. [PMID: 25393313 PMCID: PMC4230839 DOI: 10.1371/journal.pgen.1004773] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/24/2014] [Indexed: 12/16/2022] Open
Abstract
Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.
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Affiliation(s)
- Magali Boutard
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Tristan Cerisy
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Pierre-Yves Nogue
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | | | | | - Marcel Salanoubat
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Andrew C. Tolonen
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
- * E-mail:
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13
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Nakajima M, Yoshida R, Miyanaga A, Taguchi H. Crystallization and preliminary X-ray diffraction analysis of Lin1840, a putative β-glucosidase from Listeria innocua. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1398-401. [PMID: 25286948 DOI: 10.1107/s2053230x14018597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/14/2014] [Indexed: 11/11/2022]
Abstract
Lin1840 is a putative β-glucosidase that is predicted to be involved in 1,2-β-glucan metabolism since the lin1839 gene encoding a 1,2-β-oligoglucan phosphorylase and the lin1840 gene are located in the same gene cluster. Here, Lin1840 was crystallized. The crystals of Lin1840 diffracted to beyond 1.8 Å resolution. The crystal belonged to space group I121, with unit-cell parameters a = 89.75, b = 95.10, c = 215.00 Å, α = 90.00, β = 96.34, γ = 90.00°.
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Affiliation(s)
- Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ryuta Yoshida
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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14
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Viborg AH, Fredslund F, Katayama T, Nielsen SK, Svensson B, Kitaoka M, Lo Leggio L, Abou Hachem M. A β1-6/β1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of β-galactoside catabolism within Bifidobacterium. Mol Microbiol 2014; 94:1024-1040. [PMID: 25287704 DOI: 10.1111/mmi.12815] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2014] [Indexed: 12/20/2022]
Abstract
The Bifidobacterium genus harbours several health promoting members of the gut microbiota. Bifidobacteria display metabolic specialization by preferentially utilizing dietary or host-derived β-galactosides. This study investigates the biochemistry and structure of a glycoside hydrolase family 42 (GH42) β-galactosidase from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 (BlGal42A). BlGal42A displays a preference for undecorated β1-6 and β1-3 linked galactosides and populates a phylogenetic cluster with close bifidobacterial homologues implicated in the utilization of N-acetyl substituted β1-3 galactosides from human milk and mucin. A long loop containing an invariant tryptophan in GH42, proposed to bind substrate at subsite + 1, is identified here as specificity signature within this clade of bifidobacterial enzymes. Galactose binding at the subsite - 1 of the active site induced conformational changes resulting in an extra polar interaction and the ordering of a flexible loop that narrows the active site. The amino acid sequence of this loop provides an additional specificity signature within this GH42 clade. The phylogenetic relatedness of enzymes targeting β1-6 and β1-3 galactosides likely reflects structural differences between these substrates and β1-4 galactosides, containing an axial galactosidic bond. These data advance our molecular understanding of the evolution of sub-specificities that support metabolic specialization in the gut niche.
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Affiliation(s)
- Alexander Holm Viborg
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
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15
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Nakajima M, Toyoizumi H, Abe K, Nakai H, Taguchi H, Kitaoka M. 1,2-β-Oligoglucan phosphorylase from Listeria innocua. PLoS One 2014; 9:e92353. [PMID: 24647662 PMCID: PMC3960220 DOI: 10.1371/journal.pone.0092353] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/20/2014] [Indexed: 01/27/2023] Open
Abstract
We characterized recombinant Lin1839 protein (Lin1839r) belonging to glycoside hydrolase family 94 from Listeria innocua. Lin1839r catalyzed the synthesis of a series of 1,2-β-oligoglucans (Sopn: n denotes degree of polymerization) using sophorose (Sop2) as the acceptor and α-d-glucose 1-phosphate (Glc1P) as the donor. Lin1839r recognized glucose as a very weak acceptor substrate to form polymeric 1,2-β-glucan. The degree of polymerization of the 1,2-β-glucan gradually decreased with long-term incubation to generate a series of Sopns. Kinetic analysis of the phosphorolytic reaction towards sophorotriose revealed that Lin1839r followed a sequential Bi Bi mechanism. The kinetic parameters of the phosphorolysis of sophorotetraose and sophoropentaose were similar to those of sophorotriose, although the enzyme did not exhibit significant phosphorolytic activity on Sop2. These results indicate that the Lin1839 protein is a novel inverting phosphorylase that catalyzes reversible phosphorolysis of 1,2-β-glucan with a degree of polymerization of ≥3. We propose 1,2-β-oligoglucan: phosphate α-glucosyltransferase as the systematic name and 1,2-β-oligoglucan phosphorylase as the short name for this Lin1839 protein.
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Affiliation(s)
- Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Toyoizumi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Koichi Abe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyuki Nakai
- Graduate School of Science & Technology, Niigata University, Niigata, Niigata, Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- * E-mail:
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16
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2-O-α-D-glucosylglycerol phosphorylase from Bacillus selenitireducens MLS10 possessing hydrolytic activity on β-D-glucose 1-phosphate. PLoS One 2014; 9:e86548. [PMID: 24466148 PMCID: PMC3899277 DOI: 10.1371/journal.pone.0086548] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 02/07/2023] Open
Abstract
The glycoside hydrolase family (GH) 65 is a family of inverting phosphorylases that act on α-glucosides. A GH65 protein (Bsel_2816) from Bacillus selenitireducens MLS10 exhibited inorganic phosphate (Pi)-dependent hydrolysis of kojibiose at the rate of 0.43 s−1. No carbohydrate acted as acceptor for the reverse phosphorolysis using β-d-glucose 1-phosphate (βGlc1P) as donor. During the search for a suitable acceptor, we found that Bsel_2816 possessed hydrolytic activity on βGlc1P with a kcat of 2.8 s−1; moreover, such significant hydrolytic activity on sugar 1-phosphate had not been reported for any inverting phosphorylase. The H218O incorporation experiment and the anomeric analysis during the hydrolysis of βGlc1P revealed that the hydrolysis was due to the glucosyl-transferring reaction to a water molecule and not a phosphatase-type reaction. Glycerol was found to be the best acceptor to generate 2-O-α-d-glucosylglycerol (GG) at the rate of 180 s−1. Bsel_2816 phosphorolyzed GG through sequential Bi-Bi mechanism with a kcat of 95 s−1. We propose 2-O-α-d-glucopyranosylglycerol: phosphate β-d-glucosyltransferase as the systematic name and 2-O-α-d-glucosylglycerol phosphorylase as the short name for Bsel_2816. This is the first report describing a phosphorylase that utilizes polyols, and not carbohydrates, as suitable acceptor substrates.
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17
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Nihira T, Nishimoto M, Nakai H, Ohtsubo K, Kitaoka M. Characterization of Two α-1,3-Glucoside Phosphorylases from Clostridium phytofermentans. J Appl Glycosci (1999) 2014. [DOI: 10.5458/jag.jag.jag-2013_013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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18
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Viborg AH, Katayama T, Abou Hachem M, Andersen MC, Nishimoto M, Clausen MH, Urashima T, Svensson B, Kitaoka M. Distinct substrate specificities of three glycoside hydrolase family 42 -galactosidases from Bifidobacterium longum subsp. infantis ATCC 15697. Glycobiology 2013; 24:208-16. [DOI: 10.1093/glycob/cwt104] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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19
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Koyama Y, Hidaka M, Nishimoto M, Kitaoka M. Directed evolution to enhance thermostability of galacto-N-biose/lacto-N-biose I phosphorylase. Protein Eng Des Sel 2013; 26:755-61. [PMID: 24065834 DOI: 10.1093/protein/gzt049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) is the key enzyme in the enzymatic production of lacto-N-biose I. For the purpose of industrial use, we improved the thermostability of GLNBP by evolutionary engineering in which five substitutions in the amino acid sequence were selected from a random mutagenesis GLNBP library constructed using error-prone polymerase chain reaction. Among them, C236Y and D576V mutants showed considerably improved thermostability. Structural analysis of C236Y revealed that the hydroxyl group of Tyr236 forms a hydrogen bond with the carboxyl group of E319. The C236Y and D576V mutations together contributed to the thermostability. The C236Y/D576V mutant exhibited 20°C higher thermostability than the wild type.
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Affiliation(s)
- Yoshiyuki Koyama
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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Nihira T, Suzuki E, Kitaoka M, Nishimoto M, Ohtsubo K, Nakai H. Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. J Biol Chem 2013; 288:27366-27374. [PMID: 23943617 DOI: 10.1074/jbc.m113.469080] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a TonB-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-mannosidase, β-N-acetylhexosaminidase, exo-α-sialidase, and endo-β-N-acetylglucosaminidase), and a phosphorylase (BT1033) with unknown function. It was demonstrated that BT1033 catalyzed the reversible phosphorolysis of β-1,4-D-mannosyl-N-acetyl-D-glucosamine in a typical sequential Bi Bi mechanism. These results indicate that BT1033 plays a crucial role as a key enzyme in the N-glycan catabolism where β-1,4-D-mannosyl-N-acetyl-D-glucosamine is liberated from N-glycans by sequential glycoside hydrolase-catalyzed reactions, transported into the cell, and intracellularly converted into α-D-mannose 1-phosphate and N-acetyl-D-glucosamine. In addition, intestinal anaerobic bacteria such as Bacteroides fragilis, Bacteroides helcogenes, Bacteroides salanitronis, Bacteroides vulgatus, Prevotella denticola, Prevotella dentalis, Prevotella melaninogenica, Parabacteroides distasonis, and Alistipes finegoldii were also suggested to possess the similar metabolic pathway for N-glycans. A notable feature of the new metabolic pathway for N-glycans is the more efficient use of ATP-stored energy, in comparison with the conventional pathway where β-mannosidase and ATP-dependent hexokinase participate, because it is possible to directly phosphorylate the D-mannose residue of β-1,4-D-mannosyl-N-acetyl-D-glucosamine to enter glycolysis. This is the first report of a metabolic pathway for N-glycans that includes a phosphorylase. We propose 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase as the systematic name and β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase as the short name for BT1033.
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Affiliation(s)
- Takanori Nihira
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Erika Suzuki
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Mamoru Nishimoto
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Ken'ichi Ohtsubo
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan.
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21
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Hamura K, Saburi W, Matsui H, Mori H. Modulation of acceptor specificity of Ruminococcus albus cellobiose phosphorylase through site-directed mutagenesis. Carbohydr Res 2013; 379:21-5. [PMID: 23845516 DOI: 10.1016/j.carres.2013.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 11/30/2022]
Abstract
Cellobiose phosphorylase (EC 2.4.1.20, CBP) catalyzes the reversible phosphorolysis of cellobiose to α-D-glucose 1-phosphate (Glc1P) and d-glucose. Cys485, Tyr648, and Glu653 of CBP from Ruminococcus albus, situated at the +1 subsite, were mutated to modulate acceptor specificity. C485A, Y648F, and Y648V were active enough for analysis. Their acceptor specificities were compared with the wild type based on the apparent kinetic parameters determined in the presence of 10 mM Glc1P. C485A showed higher preference for D-glucosamine than the wild type. Apparent kcat/Km values of Y648F for D-mannose and 2-deoxy-D-glucose were 8.2- and 4.0-fold higher than those of the wild type, respectively. Y648V had synthetic activity toward N-acetyl-D-glucosamine, while the other variants did not. The oligosaccharide production in the presence of the same concentrations of wild type and each mutant was compared. C485A produced 4-O-β-D-glucopyranosyl-D-glucosamine from 10 mM Glc1P and D-glucosamine at a rate similar to the wild type. Y648F and Y648V produced 4-O-β-D-glucopyranosyl-D-mannose and 4-O-β-D-glucopyranosyl-N-acetyl-D-glucosamine much more rapidly than the wild type when D-mannose and N-acetyl-D-glucosamine were used as acceptors, respectively. After a 4h reaction, the amounts of 4-O-β-D-glucopyranosyl-D-mannose and 4-O-β-D-glucopyranosyl-N-acetyl-D-glucosamine produced by Y648F and Y648V were 5.9- and 12-fold higher than the wild type, respectively.
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Affiliation(s)
- Ken Hamura
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, Japan
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22
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Recent development of phosphorylases possessing large potential for oligosaccharide synthesis. Curr Opin Chem Biol 2013; 17:301-9. [PMID: 23403067 DOI: 10.1016/j.cbpa.2013.01.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/15/2013] [Indexed: 11/24/2022]
Abstract
Phosphorylases are one group of carbohydrate active enzymes involved in the cleavage and formation of glycosidic linkages together with glycoside hydrolases and sugar nucleotide-dependent glycosyltransferases. Noticeably, the catalyzed phosphorolysis is reversible, making phosphorylases suitable catalysts for efficient synthesis of particular oligosaccharides from a donor sugar 1-phosphate and suitable carbohydrate acceptors with strict regioselectivity. Although utilization of phosphorylases for oligosaccharide synthesis has been limited because only few different enzymes are known, recently the number of reported phosphorylases has gradually increased, providing the variation making these enzymes useful tools for efficient synthesis of diverse oligosaccharides.
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23
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Nihira T, Saito Y, Kitaoka M, Nishimoto M, Otsubo K, Nakai H. Characterization of a laminaribiose phosphorylase from Acholeplasma laidlawii PG-8A and production of 1,3-β-D-glucosyl disaccharides. Carbohydr Res 2012; 361:49-54. [PMID: 22982171 DOI: 10.1016/j.carres.2012.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/06/2012] [Accepted: 08/13/2012] [Indexed: 11/18/2022]
Abstract
We identified a glycoside hydrolase family 94 homolog (ACL0729) from Acholeplasma laidlawii PG-8A as a laminaribiose (1,3-β-D-glucobiose) phosphorylase (EC 2.4.1.31). The recombinant ACL0729 produced in Escherichia coli catalyzed phosphorolysis of laminaribiose with inversion of the anomeric configuration in a typical sequential bi bi mechanism releasing α-D-glucose 1-phosphate and D-glucose. Laminaritriose (1,3-β-D-glucotriose) was not an efficient substrate for ACL0729. The phosphorolysis is reversible, enabling synthesis of 1,3-β-D-glucosyl disaccharides by reverse phosphorolysis with strict regioselectivity from α-D-glucose 1-phosphate as the donor and suitable monosaccharide acceptors (D-glucose, 2-deoxy-D-arabino-hexopyranose, D-xylose, D-glucuronic acid, 1,5-anhydro-D-glucitol, and D-mannose) with C-3 and C-4 equatorial hydroxyl groups. The D-glucose and 2-deoxy-D-arabino-hexopyranose caused significantly strong competitive substrate inhibition compared with other glucobiose phosphorylases reported, in which the acceptor competitively inhibited the binding of the donor substrate. By contrast, none of the examined disaccharides served as acceptor in the synthetic reaction.
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Affiliation(s)
- Takanori Nihira
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
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24
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Identification of Bacillus selenitireducens MLS10 maltose phosphorylase possessing synthetic ability for branched α-D-glucosyl trisaccharides. Carbohydr Res 2012; 360:25-30. [PMID: 22940176 DOI: 10.1016/j.carres.2012.07.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 11/21/2022]
Abstract
We discovered an inverting maltose phosphorylase (Bsel2056) belonging to glycoside hydrolase family 65 from Bacillus selenitireducens MLS10, which possesses synthetic ability for α-D-glucosyl disaccharides and trisaccharides through the reverse phosphorolysis with β-D-glucose 1-phosphate as the donor. Bsel2056 showed the flexibility for monosaccharide acceptors with alternative C2 substituent (2-amino-2-deoxy-D-glucose, 2-deoxy-D-arabino-hexose, 2-acetamido-2-deoxy-D-glucose, D-mannose), resulting in production of 1,4-α-D-glucosyl disaccharides with strict regioselectivity. In addition, Bsel2056 synthesized two maltose derivatives possessing additional D-glucosyl residue bound to C2 position of the D-glucose residue at the reducing end, 1,4-α-D-glucopyranosyl-[1,2-α-D-glucopyranosyl]-D-glucose and 1,4-α-D-glucopyranosyl-[1,2-β-D-glucopyranosyl]-D-glucose, from 1,2-α-D-glucopyranosyl-D-glucose (kojibiose) and 1,2-β-D-glucopyranosyl-D-glucose (sophorose), respectively, as the acceptors. These results suggested that Bsel2056 possessed a binding space to accommodate the bulky C2 substituent of D-glucose.
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Abstract
Intestinal colonization of bifidobacteria is important for the health of infants. Human milk oligosaccharides (HMO) have been identified as growth factors for bifidobacteria. Recently, a bifidobacterial enzymatic system to metabolize HMO was identified. 1,3-β-Galactosyl-N-acetylhexosamine phosphorylase (GLNBP, EC 2.4.1.211), which catalyzes the reversible phosphorolysis of galacto-N-biose (GNB) (Galβ1→3GalNAc)] and lacto-N-biose I (LNB) (Galβ1→3GlcNAc), is a key enzyme to explain the metabolism of HMO. Infant-type bifidobacteria possess the intracellular pathway to specifically metabolize GNB and LNB (GNB/LNB pathway). Bifidobacterium bifidum possesses extracellular enzymes to liberate LNB from HMO. However, Bifidobacterium longum subsp. infantis imports intact HMO to be hydrolyzed by intracellular enzymes. Bifidobacterial enzymes related to the metabolism of HMO are useful tools for preparing compounds related to HMO. For instance, LNB and GNB were produced from sucrose and GlcNAc/GalNAc in 1 pot using 4 bifidobacterial enzymes, including GLNBP. LNB is expected to be a selective bifidus factor for infant-type strains.
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Affiliation(s)
- Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
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26
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Nishimoto M, Hidaka M, Nakajima M, Fushinobu S, Kitaoka M. Identification of amino acid residues that determine the substrate preference of 1,3-β-galactosyl-N-acetylhexosamine phosphorylase. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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3-O-α-D-glucopyranosyl-L-rhamnose phosphorylase from Clostridium phytofermentans. Carbohydr Res 2011; 350:94-7. [PMID: 22277537 DOI: 10.1016/j.carres.2011.12.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 12/15/2011] [Accepted: 12/19/2011] [Indexed: 11/21/2022]
Abstract
We found an unreported activity of phosphorylase catalyzed by a protein (Cphy1019) belonging to glycoside hydrolase family 65 (GH65) from Clostridium phytofermentans. The recombinant Cphy1019 produced in Escherichia coli did not phosphorolyze α-linked glucobioses, such as trehalose (α1-α1), kojibiose (α1-2), nigerose (α1-3), and maltose (α1-4), which are typical substrates for GH65 enzymes. In reverse phosphorolysis, Cphy1019 utilized only l-rhamnose as the acceptor among various sugars examined with β-d-glucose 1-phosphate as the donor. The reaction product was determined to be 3-O-α-d-glucopyranosyl-l-rhamnose, indicating strict α1-3 regioselectivity. We propose 3-O-α-d-glucopyranosyl-l-rhamnose: phosphate β-d-glucosyltransferase as the systematic name and 3-O-α-d-glucopyranosyl-l-rhamnose phosphorylase as the short name for this novel GH65 phosphorylase.
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28
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Engineering of cellobiose phosphorylase for glycoside synthesis. J Biotechnol 2011; 156:253-60. [DOI: 10.1016/j.jbiotec.2011.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 07/06/2011] [Accepted: 07/11/2011] [Indexed: 01/23/2023]
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29
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Discovery of nigerose phosphorylase from Clostridium phytofermentans. Appl Microbiol Biotechnol 2011; 93:1513-22. [PMID: 21808968 DOI: 10.1007/s00253-011-3515-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/15/2011] [Accepted: 07/24/2011] [Indexed: 10/17/2022]
Abstract
A novel phosphorylase from Clostridium phytofermentans belonging to the glycoside hydrolase family (GH) 65 (Cphy1874) was characterized. The recombinant Cphy1874 protein produced in Escherichia coli showed phosphorolytic activity on nigerose in the presence of inorganic phosphate, resulting in the release of D-glucose and β-D-glucose 1-phosphate (β-G1P) with the inversion of the anomeric configuration. Kinetic parameters of the phosphorolytic activity on nigerose were k(cat) = 67 s(-1) and K(m) = 1.7 mM. This enzyme did not phosphorolyze substrates for the typical GH65 enzymes such as trehalose, maltose, and trehalose 6-phosphate except for a weak phosphorolytic activity on kojibiose. It showed the highest reverse phosphorolytic activity in the reverse reaction using D-glucose as the acceptor and β-G1P as the donor, and the product was mostly nigerose at the early stage of the reaction. The enzyme also showed reverse phosphorolytic activity, in a decreasing order, on D-xylose, 1,5-anhydro-D-glucitol, D-galactose, and methyl-α-D-glucoside. All major products were α-1,3-glucosyl disaccharides, although the reaction with D-xylose and methyl-α-D-glucoside produced significant amounts of α-1,2-glucosides as by-products. We propose 3-α-D-glucosyl-D-glucose:phosphate β-D-glucosyltransferase as the systematic name and nigerose phosphorylase as the short name for this Cphy1874 protein.
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Chen C, Chao C, Soetaert W, Wim S, Desmet T, Tom D. Characterization of β-galactoside phosphorylases with diverging acceptor specificities. Enzyme Microb Technol 2011; 49:59-65. [PMID: 22112272 DOI: 10.1016/j.enzmictec.2011.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 03/29/2011] [Accepted: 03/30/2011] [Indexed: 11/25/2022]
Abstract
Glycoside phosphorylases are a special group of carbohydrate-active enzymes, with characteristics in between those of glycoside hydrolases and glycosyl transferases. The phosphorylases from family GH-112 are exceptional because they employ galactose-1-phosphate instead of glucose-1-phosphate as glycosyl donor. Different acceptor specificities have been observed in this family, ranging from l-rhamnose to GlcNAc, GalNAc and a combination of the latter. Three new phosphorylases from previously unexplored branches of the phylogenetic tree of family GH-112 have now been characterized to shed more light on this divergence in acceptor specificity. The enzymes from Erysipelothrix rhusiopathiae and Streptobacillus moniliformis were found to prefer GalNAc as acceptor, while that from Anaerococcus prevotii displays similar activities on GalNAc and GlcNAc. These results confirm the correlation between the amino acid residue at position 162 and the enzyme's specificity, i.e. a threonine in the former group and a valine in the latter. However, mutagenesis of residue 162 did not allow the rational transformation of the substrate preference, as the substitution of valine by threonine in the enzyme from Bifidobacterium longum did not tighten its specificity towards GalNAc. Unexpectedly, introducing an isoleucine at position 162 increased the preference for GlcNAc as acceptor, which illustrates that the structure-function relationships in β-galactoside phosphorylases are not yet completely understood. Several other positions have also been examined by mutational analysis but true determinants of the acceptor specificity in family GH-112 could not be identified.
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Affiliation(s)
- Chao Chen
- Centre for Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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31
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Li B, Nihira T, Nakai H, Nishimoto M, Kitaoka M. An Enzymatic Colorimetric Quantification of Orthophosphate. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2011_002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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32
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Thermal decomposition of β-d-galactopyranosyl-(1→3)-2-acetamido-2-deoxy-d-hexopyranoses under neutral conditions. Carbohydr Res 2010; 345:1901-8. [DOI: 10.1016/j.carres.2010.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/03/2010] [Accepted: 06/09/2010] [Indexed: 11/19/2022]
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33
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Practical preparation of D-galactosyl-beta1-->4-L-rhamnose employing the combined action of phosphorylases. Biosci Biotechnol Biochem 2010; 74:1652-5. [PMID: 20699582 DOI: 10.1271/bbb.100263] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
D-Galactosyl-beta1-->4-L-rhamnose (GalRha) was produced enzymatically from 1.1 M sucrose and 1.0 M L-rhamnose by the concomitant actions of four enzymes (sucrose phosphorylase, UDP-glucose-hexose 1-phosphate uridylyltransferase, UDP-glucose 4-epimerase, and D-galactosyl-beta1-->4-L-rhamnose phosphorylase) in the presence of 1.0 mM UDP-glucose and 30 mM inorganic phosphate. The accumulation of GalRha in 1 liter of the reaction mixture reached 230 g (the reaction yield was 71% from L-rhamnose). Sucrose and fructose in the reaction mixture were removed by yeast treatment, but isolation of GalRha by crystallization after yeast treatment was unsuccessful. Finally, 49 g of GalRha was isolated from part of the reaction mixture with yeast treatment by gel-filtration chromatography.
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34
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Nakajima M, Nishimoto M, Kitaoka M. Characterization of d-galactosyl-β1→4-l-rhamnose phosphorylase from Opitutus terrae. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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