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Singh RP, Niharika J, Thakur R, Wagstaff BA, Kumar G, Kurata R, Patel D, Levy CW, Miyazaki T, Field RA. Utilization of dietary mixed-linkage β-glucans by the Firmicute Blautia producta. J Biol Chem 2023:104806. [PMID: 37172725 DOI: 10.1016/j.jbc.2023.104806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The β-glucans are structurally varied, naturally occurring components of the cell walls and storage materials of a variety of plant and microbial species. In the human diet, mixed-linkage glucans [MLG - β-(1,3/4)-glucans] influence the gut microbiome and the host immune system. Although consumed daily, the molecular mechanism by which human gut Gram-positive bacteria utilize MLG largely remains unknown. In this study, we used Blautia producta ATCC 27340 as a model organism to develop understanding of MLG utilization. B. producta encodes a gene locus comprising a multi-modular cell-anchored endo-glucanase (BpGH16MLG), an ABC transporter, and a glycoside phosphorylase (BpGH94MLG) for utilizing MLG, as evidenced by the up-regulation of expression of the enzyme- and solute binding protein (SBP)-encoding genes in this cluster when the organism is grown on MLG. We determined that recombinant BpGH16MLG cleaved various types of β-glucan, generating oligosaccharides suitable for cellular uptake by B. producta. Cytoplasmic digestion of these oligosaccharides is then performed by recombinant BpGH94MLG and β-glucosidases (BpGH3-AR8MLG and BpGH3-X62MLG). Using targeted deletion, we demonstrated BpSBPMLG is essential for B. producta growth on barley β-glucan. Furthermore, we revealed that beneficial bacteria, such as Roseburia faecis JCM 17581T, Bifidobacterium pseudocatenulatum JCM 1200T, Bifidobacterium adolescentis JCM 1275T, and Bifidobacterium bifidum JCM 1254, can also utilize oligosaccharides resulting from the action of BpGH16MLG. Disentangling the β-glucan utilizing capability of B. producta provides a rational basis on which to consider the probiotic potential of this class of organism.
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Affiliation(s)
- Ravindra Pal Singh
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India.
| | - Jayashree Niharika
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Raksha Thakur
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Ben A Wagstaff
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Gulshan Kumar
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Dhaval Patel
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India
| | - Colin W Levy
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Takatsugu Miyazaki
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Storani A, Guerrero SA, Iglesias AA. Insights to improve the activity of glycosyl phosphorylases from Ruminococcus albus 8 with cello-oligosaccharides. Front Chem 2023; 11:1176537. [PMID: 37090251 PMCID: PMC10119399 DOI: 10.3389/fchem.2023.1176537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
The phosphorolysis of cello-oligosaccharides is a critical process played in the rumen by Ruminococcus albus to degrade cellulose. Cellodextrins, made up of a few glucosyl units, have gained lots of interest by their potential applications. Here, we characterized a cellobiose phosphorylase (RalCBP) and a cellodextrin phosphorylase (RalCDP) from R. albus 8. This latter was further analyzed in detail by constructing a truncated mutant (Ral∆N63CDP) lacking the N-terminal domain and a chimeric protein by fusing a CBM (RalCDP-CBM37). RalCBP showed a typical behavior with high activity on cellobiose. Instead, RalCDP extended its activity to longer soluble or insoluble cello-oligosaccharides. The catalytic efficiency of RalCDP was higher with cellotetraose and cellopentaose as substrates for both reaction directions. Concerning properties of Ral∆N63CDP, results support roles for the N-terminal domain in the conformation of the homo-dimer and conferring the enzyme the capacity to catalyze the phosphorolytic reaction. This mutant exhibited reduced affinity toward phosphate and increased to glucose-1-phosphate. Further, the CBM37 module showed functionality when fused to RalCDP, as RalCDP-CBM37 exhibited an enhanced ability to use insoluble cellulosic substrates. Data obtained from this enzyme's binding parameters to cellulosic polysaccharides agree with the kinetic results. Besides, studies of synthesis and phosphorolysis of cello-saccharides at long-time reactions served to identify the utility of these enzymes. While RalCDP produces a mixture of cello-oligosaccharides (from cellotriose to longer oligosaccharides), the impaired phosphorolytic activity makes Ral∆N63CDP lead mainly toward the synthesis of cellotetraose. On the other hand, RalCDP-CBM37 remarks on the utility of obtaining glucose-1-phosphate from cellulosic compounds.
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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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Zhong C, Nidetzky B. Precision synthesis of reducing-end thiol-modified cellulose enabled by enzyme selection. Polym J 2021. [DOI: 10.1038/s41428-021-00599-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractEnzyme-catalyzed iterative β-1,4-glycosylation of β-glycosides is promising for bottom-up polymerization of reducing-end-modified cello-oligosaccharide chains. Self-assembly of the chains from solution yields crystalline nanocellulose materials with properties that are tunable by the glycoside group used. Cellulose chains with a reducing-end thiol group are of interest to install a controllable pattern of site-selective modifications into the nanocellulose material. Selection of the polymerizing enzyme (cellodextrin phosphorylase; CdP) was pursued here to enhance the synthetic precision of β-1-thio-glucose conversion to generate pure “1-thio-cellulose” (≥95%) unencumbered by plain (unlabeled) cellulose resulting from enzymatic side reactions. The CdP from Clostridium stercorarium (CsCdP) was 21 times more active on β-1-thio-glucose (0.17 U/mg; 45 °C) than the CdP from Clostridium cellulosi (CcCdP), and it lacked hydrolase activity, which is substantial in CcCdP, against the α-d-glucose 1-phosphate donor substrate. The combination of these enzyme properties indicated that CsCdP is a practical catalyst for 1-thio-cellulose synthesis directly from β-1-thio-glucose (8 h; 25 mol% yield) that does not require a second enzyme (cellobiose phosphorylase), which was essential when using the less selective CcCdP. The 1-thio-cellulose chains had an average degree of polymerization of ∼10 and were assembled into highly crystalline cellulose II crystallinity material.
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De Doncker M, De Graeve C, Franceus J, Beerens K, Křen V, Pelantová H, Vercauteren R, Desmet T. Exploration of GH94 Sequence Space for Enzyme Discovery Reveals a Novel Glucosylgalactose Phosphorylase Specificity. Chembiochem 2021; 22:3319-3325. [PMID: 34541742 DOI: 10.1002/cbic.202100401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/15/2021] [Indexed: 11/05/2022]
Abstract
The substantial increase in DNA sequencing efforts has led to a rapid expansion of available sequences in glycoside hydrolase families. The ever-increasing sequence space presents considerable opportunities for the search for enzymes with novel functionalities. In this work, the sequence-function space of glycoside hydrolase family 94 (GH94) was explored in detail, using a combined approach of phylogenetic analysis and sequence similarity networks. The identification and experimental screening of unknown clusters led to the discovery of an enzyme from the soil bacterium Paenibacillus polymyxa that acts as a 4-O-β-d-glucosyl-d-galactose phosphorylase (GGalP), a specificity that has not been reported to date. Detailed characterization of GGalP revealed that its kinetic parameters were consistent with those of other known phosphorylases. Furthermore, the enzyme could be used for production of the rare disaccharides 4-O-β-d-glucosyl-d-galactose and 4-O-β-d-glucosyl-l-arabinose. Our current work highlights the power of rational sequence space exploration in the search for novel enzyme specificities, as well as the potential of phosphorylases for rare disaccharide synthesis.
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Affiliation(s)
- Marc De Doncker
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Chloé De Graeve
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Helena Pelantová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Ronny Vercauteren
- Cargill R&D Centre Europe BVBA, Havenstraat 84, 1800, Vilvoorde, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
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Gabrielli V, Muñoz-García JC, Pergolizzi G, de Andrade P, Khimyak YZ, Field RA, Angulo J. Molecular Recognition of Natural and Non-Natural Substrates by Cellodextrin Phosphorylase from Ruminiclostridium Thermocellum Investigated by NMR Spectroscopy. Chemistry 2021; 27:15688-15698. [PMID: 34436794 PMCID: PMC9293210 DOI: 10.1002/chem.202102039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/08/2022]
Abstract
β‐1→4‐Glucan polysaccharides like cellulose, derivatives and analogues, are attracting attention due to their unique physicochemical properties, as ideal candidates for many different applications in biotechnology. Access to these polysaccharides with a high level of purity at scale is still challenging, and eco‐friendly alternatives by using enzymes in vitro are highly desirable. One prominent candidate enzyme is cellodextrin phosphorylase (CDP) from Ruminiclostridium thermocellum, which is able to yield cellulose oligomers from short cellodextrins and α‐d‐glucose 1‐phosphate (Glc‐1‐P) as substrates. Remarkably, its broad specificity towards donors and acceptors allows the generation of highly diverse cellulose‐based structures to produce novel materials. However, to fully exploit this CDP broad specificity, a detailed understanding of the molecular recognition of substrates by this enzyme in solution is needed. Herein, we provide a detailed investigation of the molecular recognition of ligands by CDP in solution by saturation transfer difference (STD) NMR spectroscopy, tr‐NOESY and protein‐ligand docking. Our results, discussed in the context of previous reaction kinetics data in the literature, allow a better understanding of the structural basis of the broad binding specificity of this biotechnologically relevant enzyme.
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Affiliation(s)
- Valeria Gabrielli
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juan C Muñoz-García
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK
| | - Peterson de Andrade
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK.,Present address, Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, NR4 7TH, UK.,Present address, Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Organic Chemistry, Faculty of Chemistry, University of Seville, 41012, Seville, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, 41092, Sevilla, Spain
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7
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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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8
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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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9
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Nidetzky B, Zhong C. Phosphorylase-catalyzed bottom-up synthesis of short-chain soluble cello-oligosaccharides and property-tunable cellulosic materials. Biotechnol Adv 2020; 51:107633. [PMID: 32966861 DOI: 10.1016/j.biotechadv.2020.107633] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/23/2020] [Accepted: 09/06/2020] [Indexed: 12/13/2022]
Abstract
Cellulose-based materials are produced industrially in countless varieties via top-down processing of natural lignocellulose substrates. By contrast, cellulosic materials are only rarely prepared via bottom up synthesis and oligomerization-induced self-assembly of cellulose chains. Building up a cellulose chain via precision polymerization is promising, however, for it offers tunability and control of the final chemical structure. Synthetic cellulose derivatives with programmable material properties might thus be obtained. Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes iterative β-1,4-glycosylation from α-d-glucose 1-phosphate, with the ability to elongate a diversity of acceptor substrates, including cellobiose, d-glucose and a range of synthetic glycosides having non-sugar aglycons. Depending on the reaction conditions leading to different degrees of polymerization (DP), short-chain soluble cello-oligosaccharides (COS) or insoluble cellulosic materials are formed. Here, we review the characteristics of CdP as bio-catalyst for synthetic applications and show advances in the enzymatic production of COS and reducing end-modified, tailored cellulose materials. Recent studies reveal COS as interesting dietary fibers that could provide a selective prebiotic effect. The bottom-up synthesized celluloses involve chains of DP ≥ 9, as precipitated in solution, and they form ~5 nm thick sheet-like crystalline structures of cellulose allomorph II. Solvent conditions and aglycon structures can direct the cellulose chain self-assembly towards a range of material architectures, including hierarchically organized networks of nanoribbons, or nanorods as well as distorted nanosheets. Composite materials are also formed. The resulting materials can be useful as property-tunable hydrogels and feature site-specific introduction of functional and chemically reactive groups. Therefore, COS and cellulose obtained via bottom-up synthesis can expand cellulose applications towards product classes that are difficult to access via top-down processing of natural materials.
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Affiliation(s)
- 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.
| | - Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz 8010, Austria
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Liu N, Fosses A, Kampik C, Parsiegla G, Denis Y, Vita N, Fierobe HP, Perret S. In vitro and in vivo exploration of the cellobiose and cellodextrin phosphorylases panel in Ruminiclostridium cellulolyticum: implication for cellulose catabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:208. [PMID: 31497068 PMCID: PMC6720390 DOI: 10.1186/s13068-019-1549-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/24/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND In anaerobic cellulolytic micro-organisms, cellulolysis results in the action of several cellulases gathered in extracellular multi-enzyme complexes called cellulosomes. Their action releases cellobiose and longer cellodextrins which are imported and further degraded in the cytosol to fuel the cells. In Ruminiclostridium cellulolyticum, an anaerobic and cellulolytic mesophilic bacteria, three cellodextrin phosphorylases named CdpA, CdpB, and CdpC, were identified in addition to the cellobiose phosphorylase (CbpA) previously characterized. The present study aimed at characterizing them, exploring their implication during growth on cellulose to better understand the life-style of cellulolytic bacteria on such substrate. RESULTS The three cellodextrin phosphorylases from R. cellulolyticum displayed marked different enzymatic characteristics. They are specific for cellodextrins of different lengths and present different k cat values. CdpC is the most active enzyme before CdpA, and CdpB is weakly active. Modeling studies revealed that a mutation of a conserved histidine residue in the phosphate ion-binding pocket in CdpB and CdpC might explain their activity-level differences. The genes encoding these enzymes are scattered over the chromosome of R. cellulolyticum and only the expression of the gene encoding the cellobiose phosphorylase and the gene cdpA is induced during cellulose growth. Characterization of four independent mutants constructed in R. cellulolyticum for each of the cellobiose and cellodextrin phosphorylases encoding genes indicated that only the cellobiose phosphorylase is essential for growth on cellulose. CONCLUSIONS Unexpectedly, the cellobiose phosphorylase but not the cellodextrin phosphorylases is essential for the growth of the model bacterium on cellulose. This suggests that the bacterium adopts a "short" dextrin strategy to grow on cellulose, even though the use of long cellodextrins might be more energy-saving. Our results suggest marked differences in the cellulose catabolism developed among cellulolytic bacteria, which is a result that might impact the design of future engineered strains for biomass-to-biofuel conversion.
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Affiliation(s)
- Nian Liu
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Aurélie Fosses
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Clara Kampik
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | | | - Yann Denis
- Aix-Marseille Univ, CNRS, Plateforme Transcriptome, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Henri-Pierre Fierobe
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Stéphanie Perret
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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11
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Gao Y, Saburi W, Taguchi Y, Mori H. Biochemical characteristics of maltose phosphorylase MalE from Bacillus sp. AHU2001 and chemoenzymatic synthesis of oligosaccharides by the enzyme. Biosci Biotechnol Biochem 2019; 83:2097-2109. [PMID: 31262243 DOI: 10.1080/09168451.2019.1634516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Maltose phosphorylase (MP), a glycoside hydrolase family 65 enzyme, reversibly phosphorolyzes maltose. In this study, we characterized Bacillus sp. AHU2001 MP (MalE) that was produced in Escherichia coli. The enzyme exhibited phosphorolytic activity to maltose, but not to other α-linked glucobioses and maltotriose. The optimum pH and temperature of MalE for maltose-phosphorolysis were 8.1 and 45°C, respectively. MalE was stable at a pH range of 4.5-10.4 and at ≤40°C. The phosphorolysis of maltose by MalE obeyed the sequential Bi-Bi mechanism. In reverse phosphorolysis, MalE utilized d-glucose, 1,5-anhydro-d-glucitol, methyl α-d-glucoside, 2-deoxy-d-glucose, d-mannose, d-glucosamine, N-acetyl-d-glucosamine, kojibiose, 3-deoxy-d-glucose, d-allose, 6-deoxy-d-glucose, d-xylose, d-lyxose, l-fucose, and l-sorbose as acceptors. The kcat(app)/Km(app) value for d-glucosamine and 6-deoxy-d-glucose was comparable to that for d-glucose, and that for other acceptors was 0.23-12% of that for d-glucose. MalE synthesized α-(1→3)-glucosides through reverse phosphorolysis with 2-deoxy-d-glucose and l-sorbose, and synthesized α-(1→4)-glucosides in the reaction with other tested acceptors.
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Affiliation(s)
- Yu Gao
- Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan
| | - Yodai Taguchi
- Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University , Sapporo , Japan
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12
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Zhong C, Luley-Goedl C, Nidetzky B. Product solubility control in cellooligosaccharide production by coupled cellobiose and cellodextrin phosphorylase. Biotechnol Bioeng 2019; 116:2146-2155. [PMID: 31062868 PMCID: PMC6767486 DOI: 10.1002/bit.27008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/18/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
Soluble cellodextrins (linear β‐1,4‐d‐gluco‐oligosaccharides) have interesting applications as ingredients for human and animal nutrition. Their bottom‐up synthesis from glucose is promising for bulk production, but to ensure a completely water‐soluble product via degree of polymerization (DP) control (DP ≤ 6) is challenging. Here, we show biocatalytic production of cellodextrins with DP centered at 3 to 6 (~96 wt.% of total product) using coupled cellobiose and cellodextrin phosphorylase. The cascade reaction, wherein glucose was elongated sequentially from α‐d‐glucose 1‐phosphate (αGlc1‐P), required optimization and control at two main points. First, kinetic and thermodynamic restrictions upon αGlc1‐P utilization (200 mM; 45°C, pH 7.0) were effectively overcome (53% → ≥90% conversion after 10 hrs of reaction) by in situ removal of the phosphate released via precipitation with Mg2+. Second, the product DP was controlled by the molar ratio of glucose/αGlc1‐P (∼0.25; 50 mM glucose) used in the reaction. In optimized conversion, soluble cellodextrins in a total product concentration of 36 g/L were obtained through efficient utilization of the substrates used (glucose: 98%; αGlc1‐P: ∼80%) after 1 hr of reaction. We also showed that, by keeping the glucose concentration low (i.e., 1–10 mM; 200 mM αGlc1‐P), the reaction was shifted completely towards insoluble product formation (DP ∼9–10). In summary, this study provides the basis for an efficient and product DP‐controlled biocatalytic synthesis of cellodextrins from expedient substrates.
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Affiliation(s)
- 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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Meng D, Wei X, Zhang YHPJ, Zhu Z, You C, Ma Y. Stoichiometric Conversion of Cellulosic Biomass by in Vitro Synthetic Enzymatic Biosystems for Biomanufacturing. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02473] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
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14
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Environmentally friendly pathways towards the synthesis of vinyl-based oligocelluloses. Carbohydr Polym 2018; 193:196-204. [DOI: 10.1016/j.carbpol.2018.03.098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 11/22/2022]
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15
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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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16
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Kuhaudomlarp S, Patron NJ, Henrissat B, Rejzek M, Saalbach G, Field RA. Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149. J Biol Chem 2018; 293:2865-2876. [PMID: 29317507 PMCID: PMC5827456 DOI: 10.1074/jbc.ra117.000936] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/22/2017] [Indexed: 12/11/2022] Open
Abstract
Glycoside phosphorylases (EC 2.4.x.x) carry out the reversible phosphorolysis of glucan polymers, producing the corresponding sugar 1-phosphate and a shortened glycan chain. β-1,3-Glucan phosphorylase activities have been reported in the photosynthetic euglenozoan Euglena gracilis, but the cognate protein sequences have not been identified to date. Continuing our efforts to understand the glycobiology of E. gracilis, we identified a candidate phosphorylase sequence, designated EgP1, by proteomic analysis of an enriched cellular protein lysate. We expressed recombinant EgP1 in Escherichia coli and characterized it in vitro as a β-1,3-glucan phosphorylase. BLASTP identified several hundred EgP1 orthologs, most of which were from Gram-negative bacteria and had 37-91% sequence identity to EgP1. We heterologously expressed a bacterial metagenomic sequence, Pro_7066 in E. coli and confirmed it as a β-1,3-glucan phosphorylase, albeit with kinetics parameters distinct from those of EgP1. EgP1, Pro_7066, and their orthologs are classified as a new glycoside hydrolase (GH) family, designated GH149. Comparisons between GH94, EgP1, and Pro_7066 sequences revealed conservation of key amino acids required for the phosphorylase activity, suggesting a phosphorylase mechanism that is conserved between GH94 and GH149. We found bacterial GH149 genes in gene clusters containing sugar transporter and several other GH family genes, suggesting that bacterial GH149 proteins have roles in the degradation of complex carbohydrates. The Bacteroidetes GH149 genes located to previously identified polysaccharide utilization loci, implicated in the degradation of complex carbohydrates. In summary, we have identified a eukaryotic and a bacterial β-1,3-glucan phosphorylase and uncovered a new family of phosphorylases that we name GH149.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Nicola J Patron
- 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; Department of Biological Sciences, King Abdulaziz University, Jeddah 23218, Saudi Arabia
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gerhard Saalbach
- 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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17
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Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD. Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries. BIORESOURCE TECHNOLOGY 2017; 239:496-506. [PMID: 28535986 DOI: 10.1016/j.biortech.2017.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 05/28/2023]
Abstract
Complete hydrolysis of cellulose has been a key characteristic of biomass technology because of the limitation of industrial production hosts to use cellodextrin, the partial hydrolysis product of cellulose. Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin of the enzymatic hydrolysis (via endoglucanase and exoglucanase) of cellulose. Conversion of cellobiose to glucose is executed by β-glucosidase. The complete extracellular hydrolysis of celluloses has several critical barriers in biomass technology. An alternative bioengineering strategy to make the bioprocessing less challenging is to engineer microbes with the abilities to hydrolyze and assimilate the cellulosic-hydrolysate cellodextrin. Microorganisms engineered to metabolize cellobiose rather than the monomeric glucose can provide several advantages for lignocellulose-based biorefineries. This review describes the recent advances and challenges in engineering efficient intracellular cellobiose metabolism in industrial hosts. This review also describes the limitations of and future prospectives in engineering intracellular cellobiose metabolism.
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Affiliation(s)
- Vinuselvi Parisutham
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sathesh-Prabu Chandran
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, KogleAllé, DK2970 Hørsholm, Denmark; Synthetic Biology Engineering Research Center (Synberc), Berkeley, CA 94720, USA
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18
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Wu Y, Mao G, Fan H, Song A, Zhang YHP, Chen H. Biochemical properties of GH94 cellodextrin phosphorylase THA_1941 from a thermophilic eubacterium Thermosipho africanus TCF52B with cellobiose phosphorylase activity. Sci Rep 2017; 7:4849. [PMID: 28687766 PMCID: PMC5501786 DOI: 10.1038/s41598-017-05289-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/26/2017] [Indexed: 11/10/2022] Open
Abstract
A hypothetic gene (THA_1941) encoding a putative cellobiose phosphorylase (CBP) from Thermosipho africanus TCF52B has very low amino acid identities (less than 12%) to all known GH94 enzymes. This gene was cloned and over-expressed in Escherichia coli BL21(DE3). The recombinant protein was hypothesized to be a CBP enzyme and it showed an optimum temperature of 75 °C and an optimum pH of 7.5. Beyond its CBP activity, this enzyme can use cellobiose and long-chain cellodextrins with a degree of polymerization of greater than two as a glucose acceptor, releasing phosphate from glucose 1-phosphate. The catalytic efficiencies (kcat/Km) indicated that cellotetraose and cellopentaose were the best substrates for the phosphorolytic and reverse synthetic reactions, respectively. These results suggested that this enzyme was the first enzyme having both cellodextrin and cellobiose phosphorylases activities. Because it preferred cellobiose and cellodextrins to glucose in the synthetic direction, it was categorized as a cellodextrin phosphorylase (CDP). Due to its unique ability of the reverse synthetic reaction, this enzyme could be a potential catalyst for the synthesis of various oligosaccharides. The speculative function of this CDP in the carbohydrate metabolism of T. africanus TCF52B was also discussed.
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Affiliation(s)
- Yuanyuan Wu
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Guotao Mao
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Haiyan Fan
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Andong Song
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Yi-Heng Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
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19
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Devendran S, Abdel-Hamid AM, Evans AF, Iakiviak M, Kwon IH, Mackie RI, Cann I. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Sci Rep 2016; 6:35342. [PMID: 27748409 PMCID: PMC5066209 DOI: 10.1038/srep35342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/01/2022] Open
Abstract
Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.
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Affiliation(s)
- Saravanan Devendran
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Anton F Evans
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Michael Iakiviak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - In Hyuk Kwon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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20
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Raut MP, Karunakaran E, Mukherjee J, Biggs CA, Wright PC. Influence of Substrates on the Surface Characteristics and Membrane Proteome of Fibrobacter succinogenes S85. PLoS One 2015; 10:e0141197. [PMID: 26492413 PMCID: PMC4619616 DOI: 10.1371/journal.pone.0141197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/06/2015] [Indexed: 12/02/2022] Open
Abstract
Although Fibrobacter succinogenes S85 is one of the most proficient cellulose degrading bacteria among all mesophilic organisms in the rumen of herbivores, the molecular mechanism behind cellulose degradation by this bacterium is not fully elucidated. Previous studies have indicated that cell surface proteins might play a role in adhesion to and subsequent degradation of cellulose in this bacterium. It has also been suggested that cellulose degradation machinery on the surface may be selectively expressed in response to the presence of cellulose. Based on the genome sequence, several models of cellulose degradation have been suggested. The aim of this study is to evaluate the role of the cell envelope proteins in adhesion to cellulose and to gain a better understanding of the subsequent cellulose degradation mechanism in this bacterium. Comparative analysis of the surface (exposed outer membrane) chemistry of the cells grown in glucose, acid-swollen cellulose and microcrystalline cellulose using physico-chemical characterisation techniques such as electrophoretic mobility analysis, microbial adhesion to hydrocarbons assay and Fourier transform infra-red spectroscopy, suggest that adhesion to cellulose is a consequence of an increase in protein display and a concomitant reduction in the cell surface polysaccharides in the presence of cellulose. In order to gain further understanding of the molecular mechanism of cellulose degradation in this bacterium, the cell envelope-associated proteins were enriched using affinity purification and identified by tandem mass spectrometry. In total, 185 cell envelope-associated proteins were confidently identified. Of these, 25 proteins are predicted to be involved in cellulose adhesion and degradation, and 43 proteins are involved in solute transport and energy generation. Our results supports the model that cellulose degradation in F. succinogenes occurs at the outer membrane with active transport of cellodextrins across for further metabolism of cellodextrins to glucose in the periplasmic space and inner cytoplasmic membrane.
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Affiliation(s)
- Mahendra P. Raut
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Esther Karunakaran
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Joy Mukherjee
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Catherine A. Biggs
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C. Wright
- The ChELSI Institute, Dept of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
- * E-mail:
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21
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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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22
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Saburi W, Tanaka Y, Muto H, Inoue S, Odaka R, Nishimoto M, Kitaoka M, Mori H. Functional reassignment of Cellvibrio vulgaris EpiA to cellobiose 2-epimerase and an evaluation of the biochemical functions of the 4-O-β-d-mannosyl-d-glucose phosphorylase-like protein, UnkA. Biosci Biotechnol Biochem 2015; 79:969-77. [DOI: 10.1080/09168451.2015.1012146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
The aerobic soil bacterium Cellvibrio vulgaris has a β-mannan-degradation gene cluster, including unkA, epiA, man5A, and aga27A. Among these genes, epiA has been assigned to encode an epimerase for converting d-mannose to d-glucose, even though the amino acid sequence of EpiA is similar to that of cellobiose 2-epimerases (CEs). UnkA, whose function currently remains unknown, shows a high sequence identity to 4-O-β-d-mannosyl-d-glucose phosphorylase. In this study, we have investigated CE activity of EpiA and the general characteristics of UnkA using recombinant proteins from Escherichia coli. Recombinant EpiA catalyzed the epimerization of the 2-OH group of sugar residue at the reducing end of cellobiose, lactose, and β-(1→4)-mannobiose in a similar manner to other CEs. Furthermore, the reaction efficiency of EpiA for β-(1→4)-mannobiose was 5.5 × 104-fold higher than it was for d-mannose. Recombinant UnkA phosphorolyzed β-d-mannosyl-(1→4)-d-glucose and specifically utilized d-glucose as an acceptor in the reverse reaction, which indicated that UnkA is a typical 4-O-β-d-mannosyl-d-glucose phosphorylase.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuka Tanaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hirohiko Muto
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sota Inoue
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Rei Odaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Mamoru Nishimoto
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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23
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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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24
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Chiku K, Nihira T, Suzuki E, Nishimoto M, Kitaoka M, Ohtsubo K, Nakai H. Discovery of two β-1,2-mannoside phosphorylases showing different chain-length specificities from Thermoanaerobacter sp. X-514. PLoS One 2014; 9:e114882. [PMID: 25500577 PMCID: PMC4264767 DOI: 10.1371/journal.pone.0114882] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022] Open
Abstract
We characterized Teth514_1788 and Teth514_1789, belonging to glycoside hydrolase family 130, from Thermoanaerobacter sp. X-514. These two enzymes catalyzed the synthesis of 1,2-β-oligomannan using β-1,2-mannobiose and d-mannose as the optimal acceptors, respectively, in the presence of the donor α-d-mannose 1-phosphate. Kinetic analysis of the phosphorolytic reaction toward 1,2-β-oligomannan revealed that these enzymes followed a typical sequential Bi Bi mechanism. The kinetic parameters of the phosphorolysis of 1,2-β-oligomannan indicate that Teth514_1788 and Teth514_1789 prefer 1,2-β-oligomannans containing a DP ≥3 and β-1,2-Man2, respectively. These results indicate that the two enzymes are novel inverting phosphorylases that exhibit distinct chain-length specificities toward 1,2-β-oligomannan. Here, we propose 1,2-β-oligomannan:phosphate α-d-mannosyltransferase as the systematic name and 1,2-β-oligomannan phosphorylase as the short name for Teth514_1788 and β-1,2-mannobiose:phosphate α-d-mannosyltransferase as the systematic name and β-1,2-mannobiose phosphorylase as the short name for Teth514_1789.
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Affiliation(s)
- Kazuhiro Chiku
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | | | - Erika Suzuki
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Mamoru Nishimoto
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | | | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, Japan
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Jaito N, Saburi W, Odaka R, Kido Y, Hamura K, Nishimoto M, Kitaoka M, Matsui H, Mori H. Characterization of a thermophilic 4-O-β-D-mannosyl-D-glucose phosphorylase from Rhodothermus marinus. Biosci Biotechnol Biochem 2014; 78:263-70. [PMID: 25036679 DOI: 10.1080/09168451.2014.882760] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
4-O-β-D-Mannosyl-D-glucose phosphorylase (MGP), found in anaerobes, converts 4-O-β-D-mannosyl-D-glucose (Man-Glc) to α-D-mannosyl phosphate and D-glucose. It participates in mannan metabolism with cellobiose 2-epimerase (CE), which converts β-1,4-mannobiose to Man-Glc. A putative MGP gene is present in the genome of the thermophilic aerobe Rhodothermus marinus (Rm) upstream of the gene encoding CE. Konjac glucomannan enhanced production by R. marinus of MGP, CE, and extracellular mannan endo-1,4-β-mannosidase. Recombinant RmMGP catalyzed the phosphorolysis of Man-Glc through a sequential bi-bi mechanism involving ternary complex formation. Its molecular masses were 45 and 222 kDa under denaturing and nondenaturing conditions, respectively. Its pH and temperature optima were 6.5 and 75 °C, and it was stable between pH 5.5-8.3 and below 80 °C. In the reverse reaction, RmMGP had higher acceptor preferences for 6-deoxy-D-glucose and D-xylose than R. albus NE1 MGP. In contrast to R. albus NE1 MGP, RmMGP utilized methyl β-D-glucoside and 1,5-anhydro-D-glucitol as acceptor substrates.
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Affiliation(s)
- Nongluck Jaito
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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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: 34] [Impact Index Per Article: 3.4] [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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Nihira T, Saito Y, Nishimoto M, Kitaoka M, Igarashi K, Ohtsubo K, Nakai H. Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi. FEBS Lett 2013; 587:3556-61. [PMID: 24055472 DOI: 10.1016/j.febslet.2013.09.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/25/2022]
Abstract
A novel phosphorylase was characterized as new member of glycoside hydrolase family 94 from the cellulolytic bacterium Xanthomonas campestris and the fungus Neurospora crassa. The enzyme catalyzed reversible phosphorolysis of cellobionic acid. We propose 4-O-β-D-glucopyranosyl-D-gluconic acid: phosphate α-D-glucosyltransferase as the systematic name and cellobionic acid phosphorylase as the short names for the novel enzyme. Several cellulolytic fungi of the phylum Ascomycota also possess homologous proteins. We, therefore, suggest that the enzyme plays a crucial role in cellulose degradation where cellobionic acid as oxidized cellulolytic product is converted into α-D-glucose 1-phosphate and D-gluconic acid to enter glycolysis and the pentose phosphate pathway, respectively.
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Affiliation(s)
- Takanori Nihira
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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