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Novak JK, Gardner JG. Galactomannan utilization by Cellvibrio japonicus relies on a single essential α-galactosidase encoded by the aga27A gene. Mol Microbiol 2023; 119:312-325. [PMID: 36604822 DOI: 10.1111/mmi.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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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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Fukui K, Saburi W, Ibuki M, Tsumura K, Mori H. Preliminary evaluation of colorimetric and HPLC-based methods for quantifying β-(1→4)-mannobiose in a crude material. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2021. [DOI: 10.3136/fstr.27.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kensuke Fukui
- Research Institute for Creating the Future, Fuji Oil Holdings Inc
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University
| | | | - Kazunobu Tsumura
- Research Institute for Creating the Future, Fuji Oil Holdings Inc
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University
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Chen Q, Xiao Y, Zhang W, Stressler T, Fischer L, Jiang B, Mu W. Computer-aided search for a cold-active cellobiose 2-epimerase. J Dairy Sci 2020; 103:7730-7741. [PMID: 32684457 DOI: 10.3168/jds.2020-18153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/04/2020] [Indexed: 01/06/2023]
Abstract
Cellobiose 2-epimerase (CE) is a promising industrial enzyme that can catalyze bioconversion of lactose to its high-value derivatives, namely epilactose and lactulose. A need exists in the dairy industry to catalyze lactose bioconversions at low temperatures to avoid microbial growth. We focused on the discovery of cold-active CE in this study. A genome mining method based on computational prediction was used to screen the potential genes encoding cold-active enzymes. The CE-encoding gene from Roseburia intestinalis, with a predicted high structural flexibility, was expressed heterologously in Escherichia coli. The catalytic property of the recombinant enzyme was extensively studied. The optimum temperature and pH of the enzyme were 45°C and 7.0, respectively. The specific activity of this enzyme to catalyze conversion of lactose to epilactose was measured to be 77.3 ± 1.6 U/mg. The kinetic parameters, including turnover number (kcat), Michaelis constant (Km), and catalytic efficiency (kcat/Km) using lactose as a substrate were 117.0 ± 7.7 s-1, 429.9 ± 57.3 mM, and 0.27 mM-1s-1, respectively. In situ production of epilactose was carried out at 8°C: 20.9% of 68.4 g/L lactose was converted into epilactose in 4 h using 0.02 mg/mL (1.5 U/mL, measured at 45°C) of recombinant enzyme. The enzyme discovered by this in silico method is suitable for low-temperature applications.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yaqin Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Timo Stressler
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, 70599 Stuttgart, Germany
| | - Lutz Fischer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, 70599 Stuttgart, Germany
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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5
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Saburi W, Sato S, Hashiguchi S, Muto H, Iizuka T, Mori H. Enzymatic characteristics of d-mannose 2-epimerase, a new member of the acylglucosamine 2-epimerase superfamily. Appl Microbiol Biotechnol 2019; 103:6559-6570. [DOI: 10.1007/s00253-019-09944-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/20/2019] [Accepted: 05/25/2019] [Indexed: 11/30/2022]
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6
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Xiao Y, Chen Q, Guang C, Zhang W, Mu W. An overview on biological production of functional lactose derivatives. Appl Microbiol Biotechnol 2019; 103:3683-3691. [DOI: 10.1007/s00253-019-09755-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 12/30/2022]
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7
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Chen Q, Xiao Y, Zhang W, Zhang T, Jiang B, Stressler T, Fischer L, Mu W. Current research on cellobiose 2-epimerase: Enzymatic properties, mechanistic insights, and potential applications in the dairy industry. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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8
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Discovery and biochemical characterization of a mannose phosphorylase catalyzing the synthesis of novel β-1,3-mannosides. Biochim Biophys Acta Gen Subj 2017; 1861:3231-3237. [DOI: 10.1016/j.bbagen.2017.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/27/2017] [Accepted: 09/18/2017] [Indexed: 11/19/2022]
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Ladevèze S, Laville E, Despres J, Mosoni P, Potocki-Véronèse G. Mannoside recognition and degradation by bacteria. Biol Rev Camb Philos Soc 2016; 92:1969-1990. [PMID: 27995767 DOI: 10.1111/brv.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.
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Affiliation(s)
- Simon Ladevèze
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Elisabeth Laville
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Jordane Despres
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
| | - Pascale Mosoni
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
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10
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Reaction investigation of lactulose-producing cellobiose 2-epimerases under operational relevant conditions. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Saburi W. Functions, structures, and applications of cellobiose 2-epimerase and glycoside hydrolase family 130 mannoside phosphorylases. Biosci Biotechnol Biochem 2016; 80:1294-305. [PMID: 27031293 DOI: 10.1080/09168451.2016.1166934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Carbohydrate isomerases/epimerases are essential in carbohydrate metabolism, and have great potential in industrial carbohydrate conversion. Cellobiose 2-epimerase (CE) reversibly epimerizes the reducing end d-glucose residue of β-(1→4)-linked disaccharides to d-mannose residue. CE shares catalytic machinery with monosaccharide isomerases and epimerases having an (α/α)6-barrel catalytic domain. Two histidine residues act as general acid and base catalysts in the proton abstraction and addition mechanism. β-Mannoside hydrolase and 4-O-β-d-mannosyl-d-glucose phosphorylase (MGP) were found as neighboring genes of CE, meaning that CE is involved in β-mannan metabolism, where it epimerizes β-d-mannopyranosyl-(1→4)-d-mannose to β-d-mannopyranosyl-(1→4)-d-glucose for further phosphorolysis. MGPs form glycoside hydrolase family 130 (GH130) together with other β-mannoside phosphorylases and hydrolases. Structural analysis of GH130 enzymes revealed an unusual catalytic mechanism involving a proton relay and the molecular basis for substrate and reaction specificities. Epilactose, efficiently produced from lactose using CE, has superior physiological functions as a prebiotic oligosaccharide.
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Affiliation(s)
- Wataru Saburi
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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12
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Ye Y, Saburi W, Odaka R, Kato K, Sakurai N, Komoda K, Nishimoto M, Kitaoka M, Mori H, Yao M. Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies. FEBS Lett 2016; 590:828-37. [PMID: 26913570 DOI: 10.1002/1873-3468.12105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/19/2016] [Accepted: 02/08/2016] [Indexed: 11/11/2022]
Abstract
In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.
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Affiliation(s)
- Yuxin Ye
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Rei Odaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Naofumi Sakurai
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Keisuke Komoda
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 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
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.,Department of Pharmacology, Basic Medical College of Zhengzhou University, Zhengzhou, China
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13
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An inverting β-1,2-mannosidase belonging to glycoside hydrolase family 130 from Dyadobacter fermentans. FEBS Lett 2015; 589:3604-10. [PMID: 26476324 DOI: 10.1016/j.febslet.2015.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 11/21/2022]
Abstract
The glycoside hydrolase family (GH) 130 is composed of inverting phosphorylases that catalyze reversible phosphorolysis of β-D-mannosides. Here we report a glycoside hydrolase as a new member of GH130. Dfer_3176 from Dyadobacter fermentans showed no synthetic activity using α-D-mannose 1-phosphate but it released α-D-mannose from β-1,2-mannooligosaccharides with an inversion of the anomeric configuration, indicating that Dfer_3176 is a β-1,2-mannosidase. Mutational analysis indicated that two glutamic acid residues are critical for the hydrolysis of β-1,2-mannotriose. The two residues are not conserved among GH130 phosphorylases and are predicted to assist the nucleophilic attack of a water molecule in the hydrolysis of the β-D-mannosidic bond.
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14
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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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