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Liu P, Chen Y, Ma C, Ouyang J, Zheng Z. β-Galactosidase: a traditional enzyme given multiple roles through protein engineering. Crit Rev Food Sci Nutr 2023:1-20. [PMID: 38108277 DOI: 10.1080/10408398.2023.2292282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
β-Galactosidases are crucial carbohydrate-active enzymes that naturally catalyze the hydrolysis of galactoside bonds in oligo- and disaccharides. These enzymes are commonly used to degrade lactose and produce low-lactose and lactose-free dairy products that are beneficial for lactose-intolerant people. β-galactosidases exhibit transgalactosylation activity, and they have been employed in the synthesis of galactose-containing compounds such as galactooligosaccharides. However, most β-galactosidases have intrinsic limitations, such as low transglycosylation efficiency, significant product inhibition effects, weak thermal stability, and a narrow substrate spectrum, which greatly hinder their applications. Enzyme engineering offers a solution for optimizing their catalytic performance. The study of the enzyme's structure paves the way toward explaining catalytic mechanisms and increasing the efficiency of enzyme engineering. In this review, the structure features of β-galactosidases from different glycosyl hydrolase families and the catalytic mechanisms are summarized in detail to offer guidance for protein engineering. The properties and applications of β-galactosidases are discussed. Additionally, the latest progress in β-galactosidase engineering and the strategies employed are highlighted. Based on the combined analysis of structure information and catalytic mechanisms, the ultimate goal of this review is to furnish a thorough direction for β-galactosidases engineering and promote their application in the food and dairy industries.
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Affiliation(s)
- Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, People's Republic of China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Yuehua Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
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2
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Cui J, Wang Y, Zhou A, He S, Mao Z, Cao T, Wang N, Yuan Y. Cloning, Expression, Purification, and Characterization of a Novel β-Galactosidase/α-L-Arabinopyranosidase from Paenibacillus polymyxa KF-1. Molecules 2023; 28:7464. [PMID: 38005185 PMCID: PMC10673005 DOI: 10.3390/molecules28227464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Glycosidases are essential for the industrial production of functional oligosaccharides and many biotech applications. A novel β-galactosidase/α-L-arabinopyranosidase (PpBGal42A) of the glycoside hydrolase family 42 (GH42) from Paenibacillus polymyxa KF-1 was identified and functionally characterized. Using pNPG as a substrate, the recombinant PpBGal42A (77.16 kD) was shown to have an optimal temperature and pH of 30 °C and 6.0. Using pNPαArap as a substrate, the optimal temperature and pH were 40 °C and 7.0. PpBGal42A has good temperature and pH stability. Furthermore, Na+, K+, Li+, and Ca2+ (5 mmol/L) enhanced the enzymatic activity, whereas Mn2+, Cu2+, Zn2+, and Hg2+ significantly reduced the enzymatic activity. PpBGal42A hydrolyzed pNP-β-D-galactoside and pNP-α-L-arabinopyranoside. PpBGal42A liberated galactose from β-1,3/4/6-galactobiose and galactan. PpBGal42A hydrolyzed arabinopyranose at C20 of ginsenoside Rb2, but could not cleave arabinofuranose at C20 of ginsenoside Rc. Meanwhile, the molecular docking results revealed that PpBGal42A efficiently recognized and catalyzed lactose. PpBGal42A hydrolyzes lactose to galactose and glucose. PpBGal42A exhibits significant degradative activity towards citrus pectin when combined with pectinase. Our findings suggest that PpBGal42A is a novel bifunctional enzyme that is active as a β-galactosidase and α-L-arabinopyranosidase. This study expands on the diversity of bifunctional enzymes and provides a potentially effective tool for the food industry.
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Affiliation(s)
- Jing Cui
- Institute of Innovation Science & Technology, Central Laboratory, Changchun Normal University, Changchun 130031, China;
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Andong Zhou
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Shuhui He
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Zihan Mao
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Ting Cao
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Nan Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China; (Y.W.); (A.Z.); (S.H.); (Z.M.); (N.W.)
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3
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Enhanced thermal stability of the β-galactosidase BgaB from Bacillus circulans by cyclization mediated via SpyTag/SpyCatcher interaction and its use in galacto-oligosaccharides synthesis. Int J Biol Macromol 2022; 222:2341-2352. [DOI: 10.1016/j.ijbiomac.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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4
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Lansky S, Salama R, Biarnés X, Shwartstein O, Schneidman-Duhovny D, Planas A, Shoham Y, Shoham G. Integrative structure determination reveals functional global flexibility for an ultra-multimodular arabinanase. Commun Biol 2022; 5:465. [PMID: 35577850 PMCID: PMC9110388 DOI: 10.1038/s42003-022-03054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
AbnA is an extracellular GH43 α-L-arabinanase from Geobacillus stearothermophilus, a key bacterial enzyme in the degradation and utilization of arabinan. We present herein its full-length crystal structure, revealing the only ultra-multimodular architecture and the largest structure to be reported so far within the GH43 family. Additionally, the structure of AbnA appears to contain two domains belonging to new uncharacterized carbohydrate-binding module (CBM) families. Three crystallographic conformational states are determined for AbnA, and this conformational flexibility is thoroughly investigated further using the "integrative structure determination" approach, integrating molecular dynamics, metadynamics, normal mode analysis, small angle X-ray scattering, dynamic light scattering, cross-linking, and kinetic experiments to reveal large functional conformational changes for AbnA, involving up to ~100 Å movement in the relative positions of its domains. The integrative structure determination approach demonstrated here may apply also to the conformational study of other ultra-multimodular proteins of diverse functions and structures.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Omer Shwartstein
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel.
| | - Gil Shoham
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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5
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Aulitto M, Strazzulli A, Sansone F, Cozzolino F, Monti M, Moracci M, Fiorentino G, Limauro D, Bartolucci S, Contursi P. Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase. Microb Cell Fact 2021; 20:71. [PMID: 33736637 PMCID: PMC7977261 DOI: 10.1186/s12934-021-01553-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
Background The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose, is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. Results In this work we have explored the potential of B. coagulans MA-13 as a source of metabolites and enzymes to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra- cellular glycosyl hydrolase (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as β-galactosidase (GH42) and α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism, since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Conclusions Probiotics which are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this work we have proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in treatment of gastrointestinal diseases. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01553-y.
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Affiliation(s)
- Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Ferdinando Sansone
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145, Naples, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145, Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy.,Institute of Biosciences and BioResources-National Research Council of Italy, Naples, Italy
| | - Gabriella Fiorentino
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy
| | - Danila Limauro
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy
| | | | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy. .,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy. .,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy.
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6
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Mangiagalli M, Lotti M. Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation. Mar Drugs 2021; 19:md19010043. [PMID: 33477853 PMCID: PMC7832830 DOI: 10.3390/md19010043] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.
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7
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Xu Y, Wu Q, Bai L, Mu G, Tuo Y, Jiang S, Zhu X, Qian F. Cloning, expression, and bioinformatics analysis and characterization of a β-galactosidase from Bacillus coagulans T242. J Dairy Sci 2021; 104:2735-2747. [PMID: 33455743 DOI: 10.3168/jds.2020-18942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
The activities of β-galactosidases from bacteria and molds are affected by temperature, pH, and other factors in the processing of dairy products, limiting their application, so it is necessary to find alternative lactases. In this study, the β-galactosidase gene from Bacillus coagulans T242 was cloned, co-expressed with a molecular chaperone in Escherichia coli BL21, and subjected to bioinformatic and kinetic analyses and lactase characterization. The results show that the enzyme is a novel thermostable neutral lactase with optimum hydrolytic activity at pH 6.8 and 50°C. The thermal stability and increased lactose hydrolysis activity of β-galactosidase in the presence of Ca2+ indicated its potential application in the dairy industry.
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Affiliation(s)
- Yunpeng Xu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Qiong Wu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Li Bai
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Guangqing Mu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Yanfeng Tuo
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Shujuan Jiang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Xuemei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Fang Qian
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
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8
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Shulami S, Zehavi A, Belakhov V, Salama R, Lansky S, Baasov T, Shoham G, Shoham Y. Cross-utilization of β-galactosides and cellobiose in Geobacillus stearothermophilus. J Biol Chem 2020; 295:10766-10780. [PMID: 32493770 DOI: 10.1074/jbc.ra120.014029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Indexed: 11/06/2022] Open
Abstract
Strains of the Gram-positive, thermophilic bacterium Geobacillus stearothermophilus possess elaborate systems for the utilization of hemicellulolytic polysaccharides, including xylan, arabinan, and galactan. These systems have been studied extensively in strains T-1 and T-6, representing microbial models for the utilization of soil polysaccharides, and many of their components have been characterized both biochemically and structurally. Here, we characterized routes by which G. stearothermophilus utilizes mono- and disaccharides such as galactose, cellobiose, lactose, and galactosyl-glycerol. The G. stearothermophilus genome encodes a phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) for cellobiose. We found that the cellobiose-PTS system is induced by cellobiose and characterized the corresponding GH1 6-phospho-β-glucosidase, Cel1A. The bacterium also possesses two transport systems for galactose, a galactose-PTS system and an ABC galactose transporter. The ABC galactose transport system is regulated by a three-component sensing system. We observed that both systems, the sensor and the transporter, utilize galactose-binding proteins that also bind glucose with the same affinity. We hypothesize that this allows the cell to control the flux of galactose into the cell in the presence of glucose. Unexpectedly, we discovered that G. stearothermophilus T-1 can also utilize lactose and galactosyl-glycerol via the cellobiose-PTS system together with a bifunctional 6-phospho-β-gal/glucosidase, Gan1D. Growth curves of strain T-1 growing in the presence of cellobiose, with either lactose or galactosyl-glycerol, revealed initially logarithmic growth on cellobiose and then linear growth supported by the additional sugars. We conclude that Gan1D allows the cell to utilize residual galactose-containing disaccharides, taking advantage of the promiscuity of the cellobiose-PTS system.
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Affiliation(s)
- Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Valery Belakhov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Timor Baasov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
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9
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Mangiagalli M, Lapi M, Maione S, Orlando M, Brocca S, Pesce A, Barbiroli A, Camilloni C, Pucciarelli S, Lotti M, Nardini M. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement. FEBS J 2020; 288:546-565. [PMID: 32363751 DOI: 10.1111/febs.15354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5 °C and it is stable for several days at 37 °C and even 50 °C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Michela Lapi
- Department of Biosciences, University of Milano, Italy
| | - Serena Maione
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | | | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Italy
| | | | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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10
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Lansky S, Salama R, Shulami S, Lavid N, Sen S, Schapiro I, Shoham Y, Shoham G. Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. J Mol Biol 2020; 432:2099-2120. [PMID: 32067952 DOI: 10.1016/j.jmb.2020.01.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Noa Lavid
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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11
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β-Galactosidases: A great tool for synthesizing galactose-containing carbohydrates. Biotechnol Adv 2020; 39:107465. [DOI: 10.1016/j.biotechadv.2019.107465] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/26/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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12
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A novel glycoside hydrolase family 42 enzyme with bifunctional β-galactosidase and α-L-arabinopyranosidase activities and its synergistic effects with cognate glycoside hydrolases in plant polysaccharides degradation. Int J Biol Macromol 2019; 140:129-139. [DOI: 10.1016/j.ijbiomac.2019.08.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022]
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13
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Structural Insights into the Molecular Evolution of the Archaeal Exo-β-d-Glucosaminidase. Int J Mol Sci 2019; 20:ijms20102460. [PMID: 31109049 PMCID: PMC6566704 DOI: 10.3390/ijms20102460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/16/2022] Open
Abstract
The archaeal exo-β-d-glucosaminidase (GlmA), a thermostable enzyme belonging to the glycosidase hydrolase (GH) 35 family, hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a novel enzyme in terms of its primary structure, as it is homologous to both GH35 and GH42 β-galactosidases. The catalytic mechanism of GlmA is not known. Here, we summarize the recent reports on the crystallographic analysis of GlmA. GlmA is a homodimer, with each subunit comprising three distinct domains: a catalytic TIM-barrel domain, an α/β domain, and a β1 domain. Surprisingly, the structure of GlmA presents features common to GH35 and GH42 β-galactosidases, with the domain organization resembling that of GH42 β-galactosidases and the active-site architecture resembling that of GH35 β-galactosidases. Additionally, the GlmA structure also provides critical information about its catalytic mechanism, in particular, on how the enzyme can recognize glucosamine. Finally, we postulate an evolutionary pathway based on the structure of an ancestor GlmA to extant GH35 and GH42 β-galactosidases.
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14
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Viborg AH, Katayama T, Arakawa T, Abou Hachem M, Lo Leggio L, Kitaoka M, Svensson B, Fushinobu S. Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42. J Biol Chem 2017; 292:21092-21101. [PMID: 29061847 DOI: 10.1074/jbc.m117.792598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/18/2017] [Indexed: 12/30/2022] Open
Abstract
Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-l-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides. However, BlArap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to α-l-arabinopyranosyl-(1,6)-β-d-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus Paeonia, is not hydrolyzed by classical GH42 β-galactosidases. X-ray crystallography revealed a unique Trp345-X12-Trp358 sequence motif at the BlArap42B active site, as compared with a Phe-X12-His motif in classical GH42 β-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Arap lacking this carbon. Automated docking of paeonolide revealed that it can fit into the BlArap42B active site. The Glcp moiety of paeonolide stacks onto the aromatic ring of the Trp252 at subsite +1 and C4-OH is hydrogen bonded with Asp249 Moreover, the aglycone stacks against Phe421 from the neighboring monomer in the BlArap42B trimer, forming a proposed subsite +2. These results further support the notion that evolution of metabolic specialization can be tracked at the structural level in key enzymes facilitating degradation of specific glycans in an ecological niche.
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Affiliation(s)
- Alexander Holm Viborg
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan.,the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Takane Katayama
- the Graduate School of Biostudies, Kyoto University, Koyoto 606-8502, Japan.,the Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Takatoshi Arakawa
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Maher Abou Hachem
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- the Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark, and
| | - Motomitsu Kitaoka
- the Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Birte Svensson
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2400 Kgs. Lyngby, Denmark
| | - Shinya Fushinobu
- From the Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan,
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15
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Lansky S, Zehavi A, Belrhali H, Shoham Y, Shoham G. Structural basis for enzyme bifunctionality – the case of Gan1D fromGeobacillus stearothermophilus. FEBS J 2017; 284:3931-3953. [DOI: 10.1111/febs.14283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | | | - Yuval Shoham
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Gil Shoham
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
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16
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Ravcheev DA, Thiele I. Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. Front Genet 2017; 8:111. [PMID: 28912798 PMCID: PMC5583593 DOI: 10.3389/fgene.2017.00111] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/11/2017] [Indexed: 12/27/2022] Open
Abstract
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense epithelium-attached layer. The outer layer is inhabited by various representatives of the human gut microbiota (HGM). Glycans of the colonic mucus can be used by the HGM as a source of carbon and energy when dietary fibers are not sufficiently available. Both commensals and pathogens can utilize mucin glycans. Commensals are mostly involved in the cleavage of glycans, while pathogens mostly utilize monosaccharides released by commensals. This HGM-derived degradation of the mucus layer increases pathogen susceptibility and causes many other health disorders. Here, we analyzed 397 individual HGM genomes to identify pathways for the cleavage of host-synthetized mucin glycans to monosaccharides as well as for the catabolism of the derived monosaccharides. Our key results are as follows: (i) Genes for the cleavage of mucin glycans were found in 86% of the analyzed genomes, which significantly higher than a previous estimation. (ii) Genes for the catabolism of derived monosaccharides were found in 89% of the analyzed genomes. (iii) Comparative genomic analysis identified four alternative forms of the monosaccharide-catabolizing enzymes and four alternative forms of monosaccharide transporters. (iv) Eighty-five percent of the analyzed genomes may be involved in potential feeding pathways for the monosaccharides derived from cleaved mucin glycans. (v) The analyzed genomes demonstrated different abilities to degrade known mucin glycans. Generally, the ability to degrade at least one type of mucin glycan was predicted for 81% of the analyzed genomes. (vi) Eighty-two percent of the analyzed genomes can form mutualistic pairs that are able to degrade mucin glycans and are not degradable by any of the paired organisms alone. Taken together, these findings provide further insight into the inter-microbial communications of the HGM as well as into host-HGM interactions.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
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17
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Mine S, Watanabe M, Kamachi S, Abe Y, Ueda T. The Structure of an Archaeal β-Glucosaminidase Provides Insight into Glycoside Hydrolase Evolution. J Biol Chem 2017; 292:4996-5006. [PMID: 28130448 DOI: 10.1074/jbc.m116.766535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
The archaeal exo-β-d-glucosaminidase (GlmA) is a dimeric enzyme that hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a member of the glycosidase hydrolase (GH)-A superfamily-subfamily 35 and is a novel enzyme in terms of its primary structure. Here, we present the crystal structure of GlmA in complex with glucosamine at 1.27 Å resolution. The structure reveals that a monomeric form of GlmA shares structural homology with GH42 β-galactosidases, whereas most of the spatial positions of the active site residues are identical to those of GH35 β-galactosidases. We found that upon dimerization, the active site of GlmA changes shape, enhancing its ability to hydrolyze the smaller substrate in a manner similar to that of homotrimeric GH42 β-galactosidase. However, GlmA can differentiate glucosamine from galactose based on one charged residue while using the "evolutionary heritage residue" it shares with GH35 β-galactosidase. Our study suggests that GH35 and GH42 β-galactosidases evolved by exploiting the structural features of GlmA.
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Affiliation(s)
- Shouhei Mine
- From the Biomedical Research Institute (BMD), National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577,
| | - Masahiro Watanabe
- the Research Institute for Sustainable Chemistry (ISC), AIST, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, and
| | - Saori Kamachi
- the Research Institute for Sustainable Chemistry (ISC), AIST, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, and
| | - Yoshito Abe
- the Laboratory of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tadashi Ueda
- the Laboratory of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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18
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Ding H, Zeng Q, Zhou L, Yu Y, Chen B. Biochemical and Structural Insights into a Novel Thermostable β-1,3-Galactosidase from Marinomonas sp. BSi20414. Mar Drugs 2017; 15:md15010013. [PMID: 28075353 PMCID: PMC5295233 DOI: 10.3390/md15010013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/20/2016] [Accepted: 12/24/2016] [Indexed: 12/25/2022] Open
Abstract
A novel β-1,3-galactosidase, designated as MaBGA (β-galactosidase from Marinomonas sp. BSi20414), was successfully purified to homogeneity from Marinomonas sp. BSi20414 isolated from Arctic sea ice by ammonium sulfate precipitation and anion exchange chromatography, resulting in an 8.12-fold increase in specific activity and 9.9% recovery in total activity. MaBGA displayed its maximum activity at pH 6.0 and 60 °C, and maintained at least 90% of its initial activity over the pH range of 5.0-8.0 after incubating for 1 h. It also exhibited considerable thermal stability, which retained 76% of its initial activity after incubating at 50 °C for 6 h. In contrast to other β-galactosidases, MaBGA displayed strict substrate specificity, not only for the glycosyl group, but also for the linkage type. To better understand the structure-function relationship, the encoding gene of MaBGA was obtained and subject to bioinformatics analysis. Multiple alignments and phylogenetic analysis revealed that MaBGA belonged to the glycoside hydrolase family 42 and had closer genetic relationships with thermophilic β-galactosidases of extremophiles. With the aid of homology modeling and molecular docking, we proposed a reasonable explanation for the linkage selectivity of MaBGA from a structural perspective. On account of the robust stability and 1,3-linkage selectivity, MaBGA would be a promising candidate in the biosynthesis of galacto-oligosaccharide with β1-3 linkage.
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Affiliation(s)
- Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Qian Zeng
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Lili Zhou
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China.
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Fan Y, Yi J, Hua X, Feng Y, Yang R, Zhang Y. Structure analysis of a glycosides hydrolase family 42 cold-adapted β-galactosidase from Rahnella sp. R3. RSC Adv 2016. [DOI: 10.1039/c6ra04529d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The β-galactosidase isolated from a psychrotrophic bacterium, Rahnella sp. R3 (R-β-Gal), exhibits high activity at low temperature and has potential in the dairy industry.
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Affiliation(s)
- Yuting Fan
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Jiang Yi
- College of Chemistry and Environmental Engineering
- Shenzhen University
- 518060 Shenzhen
- China
| | - Xiao Hua
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Yinghui Feng
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Yuzhu Zhang
- US Department of Agriculture
- Agriculture Research Service
- Western Regional Research Center
- Albany
- USA
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