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Charoenwongpaiboon T, Charoenwongphaibun C, Wangpaiboon K, Panpetch P, Wanichacheva N, Pichyangkura R. Endo- and exo-levanases from Bacillus subtilis HM7: Catalytic components, synergistic cooperation, and application in fructooligosaccharide synthesis. Int J Biol Macromol 2024; 271:132508. [PMID: 38782321 DOI: 10.1016/j.ijbiomac.2024.132508] [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: 01/01/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Levan-type fructooligosaccharides (LFOS) exhibit significant biological activities and selectively promote the growth of certain beneficial bacteria. Levanase is an important enzyme for LFOS production. In this study, two isoforms of levanases, exo- and endo-type depolymerizing enzymes, from Bacillus subtilis HM7 isolated from Dynastes hercules larvae excrement were cloned, expressed, and characterized. The synergistic effect on the levan hydrolysis and kinetic properties of both isoforms were evaluated, indicating their cooperation in levan metabolism, where the endo-levanase catalyzes a rate-limiting step. In addition, homology models and molecular dynamics simulations revealed the key amino residues of the enzymes for levan binding and catalysis. It was found that both isoforms possessed distinct binding residues in the active sites, suggesting the importance of the specificity of the enzymes. Finally, we demonstrated the potential of endo-type levanase in LFOS synthesis using a one-pot reaction with levansucrase. Overall, this study fills the knowledge gap in understanding levanase's mechanism, making an important contribution to the fields of food science and biotechnology.
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Affiliation(s)
| | - Chonnipha Charoenwongphaibun
- Division of Chemistry, Department of Physical and Material Sciences, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Sean, Nakhon Pathom 73140, Thailand
| | - Karan Wangpaiboon
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pawinee Panpetch
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nantanit Wanichacheva
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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2
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Versluys M, Porras-Domínguez JR, Voet A, Struyf T, Van den Ende W. Insights in inulin binding and inulin oligosaccharide formation by novel multi domain endo-inulinases from Botrytis cinerea. Carbohydr Polym 2024; 328:121690. [PMID: 38220320 DOI: 10.1016/j.carbpol.2023.121690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/09/2023] [Accepted: 12/10/2023] [Indexed: 01/16/2024]
Abstract
World-wide, pathogenic fungi such as Botrytis cinerea cause tremendous yield losses in terms of food production and post-harvest food decay. Many fungi produce inulin-type oligosaccharides (IOSs) from inulin through endo-inulinases which typically show a two domain structure. B.cinerea lacks a two domain endo-inulinase but contains a three domain structure instead. Genome mining revealed three and four domain (d4) enzymes in the fungal kingdom. Here, three and two domain enzymes were compared in their capacity to produce IOSs from inulin. Hill kinetics were observed in three domain enzymes as compared to Michaelis-Menten kinetics in two domain enzymes, suggesting that the N-terminal extension functions as a carbohydrate binding module. Analysis of the IOS product profiles generated from purified GF6, GF12, GF16 and GF18 inulins and extensive sugar docking approaches led to enhanced insights in the active site functioning, revealing subtle differences between the endo-inulinases from Aspergillus niger and B. cinerea. Improved insights in structure-function relationships in fungal endo-inulinases offer opportunities to develop superior enzymes for the production of specific IOS formulations to improve plant and animal health (priming agents, prebiotics).
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Affiliation(s)
- Maxime Versluys
- Laboratory of Molecular Plant Biology and KU Leuven Plant Institute, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Jaime Ricardo Porras-Domínguez
- Laboratory of Molecular Plant Biology and KU Leuven Plant Institute, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium.
| | - Arnout Voet
- Laboratory of Biochemistry, Molecular and Structural Biology, KU Leuven, Celestijnenlaan 200g, 3001 Leuven, Belgium.
| | - Tom Struyf
- Laboratory of Molecular Plant Biology and KU Leuven Plant Institute, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium.
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology and KU Leuven Plant Institute, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium.
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3
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Wu X, Wu Z, Ju X, Fan Y, Yang C, Han Y, Chen W, Tang D, Lv C, Cao Q, Wang J, Zhang K. IbInvInh2, a novel invertase inhibitor in sweet potato, regulates starch content through post-translational regulation of vacuolar invertase IbβFRUCT2. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107815. [PMID: 37301188 DOI: 10.1016/j.plaphy.2023.107815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/22/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
As a key enzyme in the starch and sugar metabolic pathways in sweet potato (Ipomoea batatas (L.) Lam.), the vacuolar invertase (EC 3.2.1.26) IbβFRUCT2 is involved in partitioning and modulating the starch and sugar components of the storage root. However, the post-translational regulation of its invertase activity remains unclear. In this study, we identified three invertase inhibitors, IbInvInh1, IbInvInh2, and IbInvInh3, as potential interaction partners of IbβFRUCT2. All were found to act as vacuolar invertase inhibitors (VIFs) and belonged to the plant invertase/pectin methyl esterase inhibitor superfamily. Among the three VIFs, IbInvInh2 is a novel VIF in sweet potato and was confirmed to be an inhibitor of IbβFRUCT2. The N-terminal domain of IbβFRUCT2 and the Thr39 and Leu198 sites of IbInvInh2 were predicted to be engaged in their interactions. The transgenic expression of IbInvInh2 in Arabidopsis thaliana plants reduced the starch content of leaves, while its expression in the Ibβfruct2-expressing Arabidopsis plants increased the starch content of leaves, suggesting that the post-translational inhibition of IbβFRUCT2 activity by IbInvInh2 contributes to the regulation of the plant starch content. Taken together, our findings reveal a novel VIF in sweet potato and provide insights into the potential regulatory roles of the VIFs and invertase-VIF interaction in starch metabolism. These insights lay the foundation for using VIFs to improve the starch properties of crops.
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Affiliation(s)
- Xuli Wu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China
| | - Zhengdan Wu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xisan Ju
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Chaobin Yang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China
| | - Yonghui Han
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China
| | - Wanxia Chen
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China
| | - Daobin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, 400715, China
| | - Changwen Lv
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, 400715, China
| | - Qinghe Cao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou, 221131, China
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, 400715, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops in Chongqing, Beibei, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, 400715, China.
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Trapala J, González-Andrade M, Olvera C, Cayetano M, Sanz-Aparicio J, Jimenez-Ortega E, Bustos-Jaimes I, Montiel C. Relevance of aromatic and polar amino acids in the specificity of Inulinase ISO3 from Kluyveromyces marxianus: A molecular dynamics approach with an experimental verification. Int J Biol Macromol 2023; 242:124734. [PMID: 37150366 DOI: 10.1016/j.ijbiomac.2023.124734] [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: 03/02/2023] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
The Inulinase from Kluyveromyces marxianus ISO3 (Inu-ISO3) is an enzyme able to hydrolyze linear fructans such as chicory inulin as well as branched fructans like agavin. This enzyme was cloned and expressed in Komagataella pastoris to study the role of selected aromatic and polar residues in the catalytic pocket by Alanine scanning. Molecular dynamics (MD) simulations and enzyme kinetics analysis were performed to study the functional consequences of these amino acid substitutions. Site-directed mutagenesis was used to construct the mutants of the enzyme after carrying out the MD simulations between Inu-ISO3 and its substrates. Mutation Trp79:Ala resulted in the total loss of activity when fructans were used as substrates, while with sucrose, the activity decreased by 98 %. In contrast, the mutations Phe113:Ala and Gln236:Ala increased the invertase activity when sucrose was used as a substrate. Although these amino acids are not part of the conserved motifs where the catalytic triad is located, they are essential for the enzyme's activity. In silico and experimental approaches corroborate the relevance of these residues for substrate binding and their influence on enzymatic activity.
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Affiliation(s)
- Jonathan Trapala
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico
| | | | - Clarita Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos 62250, Mexico
| | - Maribel Cayetano
- Departamento de Bioquímica, Facultad de Medicina, UNAM, Mexico City 04510, Mexico
| | - Julia Sanz-Aparicio
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Elena Jimenez-Ortega
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Ismael Bustos-Jaimes
- Departamento de Bioquímica, Facultad de Medicina, UNAM, Mexico City 04510, Mexico
| | - Carmina Montiel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico.
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Cen X, Zhang R, He L, Tang X, Wu Q, Zhou J, Huang Z. Deletion of the Loop Linking Two Domains of Exo-Inulinase InuAMN8 Diminished the Enzymatic Thermo-Halo-Alcohol Tolerance. Front Microbiol 2022; 13:924447. [PMID: 35814689 PMCID: PMC9260423 DOI: 10.3389/fmicb.2022.924447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022] Open
Abstract
Inulin is the rich water-soluble storage polysaccharide after starch in nature, and utilization of inulin through hydrolysis of exo-inulinases has attracted much attention. Thermo-halo-alcohol tolerance is essential for exo-inulinase applications, while no report reveals the molecular basis involved in halo-alcohol tolerance of exo-inulinases via experimental data. In this study, two loops of exo-inulinase InuAMN8, including the loop built with 360GHVRLGPQP368 linking domains of Glyco_hydro_32N and Glyco_hydro_32C and another loop built with 169GGAG172 in the catalytic domain, were deleted to generate mutants MutG360Δ9 and MutG169Δ4, respectively. After heterologous expression, purification, and dialysis, InuAMN8, MutG169Δ4, and MutG360Δ9 showed half-lives of 144, 151, and 7 min at 50°C, respectively. InuAMN8 and MutG169Δ4 were very stable, while MutG360Δ9 showed a half-life of approximately 60 min in 5.0% (w/v) NaCl, and they showed half-lives of approximately 60 min in 25.0, 25.0, and 5.0% (w/v) ethanol, respectively. Structural analysis indicated that two cation-π bonds, which contributed to thermal properties of InuAMN8 at high temperatures, broke in MutG360Δ9. Four basic amino acid residues were exposed to the structural surface of MutG360Δ9 and formed positive and neutral electrostatic potential that caused detrimental effects on halo-alcohol tolerance. The study may provide a better understanding of the loop-function relationships that are involved in thermo-halo-alcohol adaptation of enzymes in extreme environment.
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Affiliation(s)
- Xiaolong Cen
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Limei He
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
- *Correspondence: Junpei Zhou, ,
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
- Zunxi Huang,
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He L, Zhang R, Shen J, Miao Y, Zeng C, Tang X, Wu Q, Zhou J, Huang Z. Improving the low-temperature properties of an exo-inulinase via the deletion of a loop fragment located in its catalytic pocket. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2021.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Germec M, Turhan I. Kinetic modeling and sensitivity analysis of inulinase production in large-scale stirred tank bioreactor with sugar beet molasses-based medium. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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8
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de Lima MZT, de Almeida LR, Mera AM, Bernardes A, Garcia W, Muniz JRC. Crystal Structure of a Sucrose-6-phosphate Hydrolase from Lactobacillus gasseri with Potential Applications in Fructan Production and the Food Industry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10223-10234. [PMID: 34449216 DOI: 10.1021/acs.jafc.1c03901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fructooligosaccharides (FOSs) are polymers of fructose with a prebiotic activity because of their production and fermentation by bacteria that inhabit the gastrointestinal tract and are widely used in the industry and new functional foods. Lactobacillus gasseri stands out as an important homofermentative microorganism related to FOS production, and its potential applications in the industry are undeniable. In this study, we report the production and characterization of a sucrose-6-phosphate hydrolase from L. gasseri belonging to the GH32 family. Apo-LgAs32 and LgAs32 complexed with β-d-fructose structures were determined at a resolution of 1.94 and 1.84 Å, respectively. The production of FOS, fructans, 1-kestose, and nystose by the recombinant LgAs32, using sucrose as a substrate, shown in this study is very promising. When compared to its homologous enzyme from Lactobacillus reuteri, the production of 1-kestose by LgAs32 is increased; thus, LgAs32 can be considered as an alternative in fructan production and other industrial applications.
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Affiliation(s)
- Mariana Z T de Lima
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao Carlos, SP 13563-120, Brazil
| | - Leonardo R de Almeida
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao Carlos, SP 13563-120, Brazil
| | - Alain M Mera
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao Carlos, SP 13563-120, Brazil
| | - Amanda Bernardes
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao Carlos, SP 13563-120, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP 09210-580, Brazil
| | - João R C Muniz
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao Carlos, SP 13563-120, Brazil
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The β-Fructofuranosidase from Rhodotorula dairenensis: Molecular Cloning, Heterologous Expression, and Evaluation of Its Transferase Activity. Catalysts 2021. [DOI: 10.3390/catal11040476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The β-fructofuranosidase from the yeast Rhodotorula dairenensis (RdINV) produces a mixture of potential prebiotic fructooligosaccharides (FOS) of the levan-, inulin- and neo-FOS series by transfructosylation of sucrose. In this work, the gene responsible for this activity was characterized and its functionality proved in Pichia pastoris. The amino acid sequence of the new protein contained most of the characteristic elements of β-fructofuranosidases included in the family 32 of the glycosyl hydrolases (GH32). The heterologous yeast produced a protein of about 170 kDa, where N-linked and O-linked carbohydrates constituted about 15% and 38% of the total protein mass, respectively. Biochemical and kinetic properties of the heterologous protein were similar to the native enzyme, including its ability to produce prebiotic sugars. The maximum concentration of FOS obtained was 82.2 g/L, of which 6-kestose represented about 59% (w/w) of the total products synthesized. The potential of RdINV to fructosylate 19 hydroxylated compounds was also explored, of which eight sugars and four alditols were modified. The flexibility to recognize diverse fructosyl acceptors makes this protein valuable to produce novel glycosyl-compounds with potential applications in food and pharmaceutical industries.
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10
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Wang CH, Xiong WP, Huang C, Li XM, Wang QY, Huang RB. Engineering better catalytic activity and acidic adaptation into Kluyveromyces marxianus exoinulinase using site-directed mutagenesis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:2472-2482. [PMID: 33034040 DOI: 10.1002/jsfa.10873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 10/03/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Exoinulinase catalyzes the successive removal of individual fructose moiety from the non-reducing end of the inulin molecule, which is useful for biotechnological applications like producing fructan-based non-grain biomass energy and high-fructose syrup. In this study, an exoinulinase (KmINU) from Kluyveromyces marxianus DSM 5418 was tailored for increased catalytic activity and acidic adaptation for inulin hydrolysis processes by rational site-directed mutagenesis. RESULTS Three mutations, S124Y, N158S and Q215V distal to the catalytic residues of KmINU were designed and heterologously expressed in Pichia pastoris GS115. Compared to the wild-type, S124Y shifted the pH-activity profile towards acidic pH values and increased the catalytic activity and catalytic efficiency by 59% and 99% to 688.4 ± 17.03 s-1 and 568.93 L mmol-1 s-1 , respectively. N158S improved the catalytic activity under acidic pH conditions, giving a maximum value of 464.06 ± 14.06 s-1 on inulin at pH 4.5. Q215V markedly improved the substrate preference for inulin over sucrose by 5.56-fold, and showed catalytic efficiencies of 208.82 and 6.88 L mmol-1 s-1 towards inulin and sucrose, respectively. Molecular modeling and computational docking indicated that structural reorientation may underlie the increased catalytic activity, acidic adaptation and substrate preference. CONCLUSIONS The KmINU mutants may serve as industrially promising candidates for inulin hydrolysis. Protein engineering of exoinulinase here provides a successful example of the extent to which mutating non-conserved substrate recognition and binding residues distal to the active site can be used for industrial enzyme improvements. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Wu-Ping Xiong
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Cheng Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Xiao-Ming Li
- Nanning Sinozyme Biotechnology Co., Ltd, Nanning, China
| | - Qing-Yan Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Ri-Bo Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China
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11
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Singh R, Singh T, Hassan M, Kennedy JF. Updates on inulinases: Structural aspects and biotechnological applications. Int J Biol Macromol 2020; 164:193-210. [DOI: 10.1016/j.ijbiomac.2020.07.078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
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12
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Zhang R, He L, Shen J, Miao Y, Tang X, Wu Q, Zhou J, Huang Z. Improving low-temperature activity and thermostability of exo-inulinase InuAGN25 on the basis of increasing rigidity of the terminus and flexibility of the catalytic domain. Bioengineered 2020; 11:1233-1244. [PMID: 33131413 PMCID: PMC8291790 DOI: 10.1080/21655979.2020.1837476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Enzymes displaying high activity at low temperatures and good thermostability are attracting attention in many studies. However, improving low-temperature activity along with the thermostability of enzymes remains challenging. In this study, the mutant Mut8S, including eight sites (N61E, K156R, P236E, T243K, D268E, T277D, Q390K, and R409D) mutated from the exo-inulinase InuAGN25, was designed on the basis of increasing the number of salt bridges through comparison between the low-temperature-active InuAGN25 and thermophilic exo-inulinases. The recombinant Mut8S, which was expressed in Escherichia coli, was digested by human rhinovirus 3 C protease to remove the amino acid fusion sequence at N-terminus, producing RfsMut8S. Compared with wild-type RfsMInuAGN25, the mutant RfsMut8S showed (1) lower root mean square deviation values, (2) lower root mean square fluctuation (RMSF) values of residues in six regions of the N and C termini but higher RMSF values in five regions of the catalytic pocket, (3) higher activity at 0-40°C, and (4) better thermostability at 50°C. This study proposes a way to increase low-temperature activity along with a thermostability improvement of exo-inulinase on the basis of increasing the rigidity of the terminus and the flexibility of the catalytic domain. These findings may prove useful in formulating rational designs for increasing the thermal performance of enzymes.
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Affiliation(s)
- Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Limei He
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Jidong Shen
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Ying Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, People's Republic of China
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13
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Ma J, Li T, Tan H, Liu W, Yin H. The Important Roles Played in Substrate Binding of Aromatic Amino Acids in Exo-Inulinase From Kluyveromyces cicerisporus CBS 4857. Front Mol Biosci 2020; 7:569797. [PMID: 33102520 PMCID: PMC7545266 DOI: 10.3389/fmolb.2020.569797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/03/2020] [Indexed: 11/13/2022] Open
Abstract
Inulinase is a member of the glycoside hydrolase family 32 (GH32). It catalyzes the randomly hydrolyzation of 2,1-β-D-fructosidic linkages in inulin and plays a role in the production of high-fructose syrup. In this study, detailed roles of the conserved residues W79, F113, M117, R181, C239, and W334 of the exo-inulinase from Kluyveromyces cicerisporus CBS4857 (KcINU1) in substrate binding and stabilization were evaluated by in silico analysis and site-directed mutagenesis. These residues belong to the conserved WG, FSGSMV, RDP, ECP, and WQY regions of the GH32 and are located around the catalytic pocket of KcINU1. Zymogram assay showed relatively weaker band for F113W and similar band for M117A compared to the wild-type enzyme toward inulin and sucrose, whereas all other variants showed no observable stain on the native polyacrylamide gel electrophoresis. These results were further confirmed with the dinitrosalicylic acid colorimetric method. It showed that the residual activities of F113W toward inulin and sucrose were 33.8 ± 3.3% and 96.2 ± 5.5%, respectively, and that of M117A were 103.8 ± 1.3% and 166.5 ± 12%, respectively. Results from fluorescence spectra indicated that there is a significant conformational change that happened in F113W compared to the wild-type enzyme, while M117A exhibited limited impact although the quenching effect was increased.
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Affiliation(s)
- Junyan Ma
- Natural Products and Glyco-Biotechnology Research Group, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Medical College, Dalian University, Dalian, China
| | - Tang Li
- Natural Products and Glyco-Biotechnology Research Group, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haidong Tan
- Natural Products and Glyco-Biotechnology Research Group, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wujun Liu
- Natural Products and Glyco-Biotechnology Research Group, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Heng Yin
- Natural Products and Glyco-Biotechnology Research Group, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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14
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He L, Zhang R, Shen J, Miao Y, Tang X, Wu Q, Zhou J, Huang Z. Removal of N-terminal tail changes the thermostability of the low-temperature-active exo-inulinase InuAGN25. Bioengineered 2020; 11:921-931. [PMID: 32865156 PMCID: PMC8291819 DOI: 10.1080/21655979.2020.1809921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exo-inulinases are members of the glycoside hydrolase family 32 and function by hydrolyzing inulin into fructose with yields up to 90–95%. The N-terminal tail contributes to enzyme thermotolerance, which plays an important role in enzyme applications. However, the role of N-terminal amino acid residues in the thermal performance and structural properties of exo-inulinases remains to be elucidated. In this study, three and six residues of the N-terminus starting from Gln23 of the exo-inulinase InuAGN25 were deleted and expressed in Escherichia coli. After digestion with human rhinovirus 3 C protease to remove the N-terminal amino acid fusion sequence that may affect the thermolability of enzymes, wild-type RfsMInuAGN25 and its mutants RfsMutNGln23Δ3 and RfsMutNGln23Δ6 were produced. Compared with RfsMInuAGN25, thermostability of RfsMutNGln23Δ3 was enhanced while that of RfsMutNGln23Δ6 was slightly reduced. Compared with the N-terminal structures of RfsMInuAGN25 and RfsMutNGln23Δ6, RfsMutNGln23Δ3 had a higher content of (1) the helix structure, (2) salt bridges (three of which were organized in a network), (3) cation–π interactions (one of which anchored the N-terminal tail). These structural properties may account for the improved thermostability of RfsMutNGln23Δ3. The study provides a better understanding of the N-terminus–function relationships that are useful for rational design of thermostability of exo-inulinases.
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Affiliation(s)
- Limei He
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Jidong Shen
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Ying Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
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15
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Trapala J, Bustos-Jaimes I, Manzanares P, Bárzana E, Montiel C. Purification and characterization of an inulinase produced by a Kluyveromyces marxianus strain isolated from blue agave bagasse. Protein Expr Purif 2020; 176:105718. [PMID: 32777449 DOI: 10.1016/j.pep.2020.105718] [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: 04/10/2020] [Revised: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 11/15/2022]
Abstract
Exo-inulinases are versatile enzymes that have gained attention in recent years due to their ability to hydrolyze linear and branched polyfructose chains found in inulines. Agavin, a branched inulin, is found in Agave plant, the raw matter to produce tequila. Our group has isolated several microbial strains from agave bagasse, an agro-industrial residue from tequila production that increases yearly. Strain ISO3, identified as Kluyveromyces marxianus, showed a remarkable activity towards agavin, and from its fermentation liquor an inulinolytic enzyme (Inu-ISO3) was purified. The isolated enzyme is a glycosylated dimeric protein with a molecular mass of ~256 kDa, as determined by DLS and SEC. The enzyme has an isoelectric pH of 4.6 and has both inulinase and invertase activities with an I/S ratio (ratio of activity with agavin to activity with sucrose) of 1.39. The enzyme has temperature and pH optima of 50 °C and 5.5, respectively, and follows hyperbolic kinetics with agavin (kcat of 339 ± 27 s-1 and KM of 11.8 ± 1.5 mM). The remarkable activity of Inu-ISO3 on linear and branched inulin spotlights this enzyme as a potential player in the treatment of agricultural residua for the generation of added-value products.
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Affiliation(s)
- Jonathan Trapala
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Ismael Bustos-Jaimes
- Departamento de Bioquímica, Facultad de Medicina, UNAM, Mexico City 04510, Mexico
| | - Paloma Manzanares
- Centro de Investigaciones Energéticas, Medio Ambientales y Tecnológicas (CIEMAT), Madrid 28040, Spain
| | - Eduardo Bárzana
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Carmina Montiel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico.
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16
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17
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Ilgın M, Germec M, Turhan I. Inulinase production and mathematical modeling from carob extract by using
Aspergillus niger. Biotechnol Prog 2019; 36:e2919. [DOI: 10.1002/btpr.2919] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Merve Ilgın
- Akdeniz UniversityDepartment of Food Engineering Antalya Turkey
| | - Mustafa Germec
- Akdeniz UniversityDepartment of Food Engineering Antalya Turkey
| | - Irfan Turhan
- Akdeniz UniversityDepartment of Food Engineering Antalya Turkey
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18
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Ernits K, Eek P, Lukk T, Visnapuu T, Alamäe T. First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron. Sci Rep 2019; 9:8443. [PMID: 31186460 PMCID: PMC6560043 DOI: 10.1038/s41598-019-44785-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/24/2019] [Indexed: 01/05/2023] Open
Abstract
The endo-levanase BT1760 of a human gut commensal Bacteroides thetaiotaomicron randomly cuts a β-2,6-linked fructan, levan, into fructo-oligosaccharides providing a prebiotic substrate for gut microbiota. Here we introduce the crystal structure of BT1760 at resolution of 1.65 Å. The fold of the enzyme is typical for GH32 family proteins: a catalytic N-terminal five-bladed β-propeller connected with a C-terminal β-sandwich domain. The levantetraose-bound structure of catalytically inactive mutant E221A at 1.90-Å resolution reveals differences in substrate binding between the endo-acting fructanases. A shallow substrate-binding pocket of the endo-inulinase INU2 of Aspergillus ficuum binds at least three fructose residues at its flat bottom. In the levantetraose-soaked crystal of the endo-levanase E221A mutant the ligand was bent into the pond-like substrate pocket with its fructose residues making contacts at −3, −2, −1 and + 1 subsites residing at several pocket depths. Binding of levantetraose to the β-sandwich domain was not detected. The N- and C-terminal modules of BT1760 did not bind levan if expressed separately, the catalytic domain lost its activity and both modules tended to precipitate. We gather that endo-levanase BT1760 requires both domains for correct folding, solubility and stability of the protein.
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Affiliation(s)
- Karin Ernits
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Priit Eek
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Tiit Lukk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Triinu Visnapuu
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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19
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Sakibaev FA, Holyavka MG, Makin SM, Artyukhov VG. An In silico Search for the Sites of Potential Binding with Charged and Hydrophobic Carriers in the Molecules of Endoinulinase from Aspergillus ficuum and Exoinulinase from Aspergillus awamori. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919030199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Qiu Y, Zhu Y, Zhan Y, Zhang Y, Sha Y, Zhan Y, Xu Z, Li S, Feng X, Xu H. Systematic unravelling of the inulin hydrolase from Bacillus amyloliquefaciens for efficient conversion of inulin to poly-(γ-glutamic acid). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:145. [PMID: 31210783 PMCID: PMC6563369 DOI: 10.1186/s13068-019-1485-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Bacillus amyloliquefaciens NB is a newly discovered strain, which produces poly-(γ-glutamic acid) (γ-PGA) from raw extracted inulin of Jerusalem artichoke tubers; however, the underlying mechanisms remain unknown. To address this problem, we identified the inulin hydrolase in wild-type strain B. amyloliquefaciens NB. RESULTS The novel inulin hydrolase (CscA) was discovered from strain NB, with high inulinase activity (987.0 U/mg at 55 °C) and strong resistance at pH values between 8.0 and 11.0, suggesting the potential application of CscA in Jerusalem artichoke biorefinery. CscA exhibited a k cat/K m of (6.93 ± 0.27) × 103 for inulin; its enzymatic activity was stimulated by metal ions, like K+, Mn2+, or Ca2+. Similar to their role in glycoside hydrolase 32 family enzymes, the conserved Asp37, Asp161, and Glu215 residues of CscA contribute to its catalytic activity. Targeted disruption of CscA gene suppressed inulin utilization by strain NB. Overexpression of CscA significantly enhanced the γ-PGA generation by 19.2% through enhancement in inulin consumption. CONCLUSIONS The inulin hydrolase CscA is critical for inulin metabolism in B. amyloliquefaciens and indicates potential application in Jerusalem artichoke biorefinery.
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Affiliation(s)
- Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yijing Zhan
- Nanjing Shineking Biotech Co., Ltd, Nanjing, 210061 China
| | - Yatao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yuanyuan Sha
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yijing Zhan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Zongqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 211816 China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
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21
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Holyavka MG, Makin SM, Kondratyev MS, Abdullatypov AV, Kovaleva TA, Artyukhov VG. Supramolecular Organization of Inulinases from Aspergillus awamori, Aspergillus ficuum and Kluyveromyces marxianus: A Comparative Aspect. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918060155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Hernández‐González M, Pantazopoulou A, Spanoudakis D, Seegers CL, Peñalva MA. Genetic dissection of the secretory route followed by a fungal extracellular glycosyl hydrolase. Mol Microbiol 2018; 109:781-800. [DOI: 10.1111/mmi.14073] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/15/2018] [Accepted: 07/02/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Miguel Hernández‐González
- Department of Cellular and Molecular Biology and WhiteBiotech Interdepartmental Unit Centro de Investigaciones Biológicas CSIC Madrid Spain
| | - Areti Pantazopoulou
- Department of Cellular and Molecular Biology and WhiteBiotech Interdepartmental Unit Centro de Investigaciones Biológicas CSIC Madrid Spain
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago IL USA
| | - Dimitris Spanoudakis
- Department of Cellular and Molecular Biology and WhiteBiotech Interdepartmental Unit Centro de Investigaciones Biológicas CSIC Madrid Spain
| | - Christel L.C. Seegers
- Department of Cellular and Molecular Biology and WhiteBiotech Interdepartmental Unit Centro de Investigaciones Biológicas CSIC Madrid Spain
- Avebe UA Foxhol The Netherlands
| | - Miguel A. Peñalva
- Department of Cellular and Molecular Biology and WhiteBiotech Interdepartmental Unit Centro de Investigaciones Biológicas CSIC Madrid Spain
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23
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Qiu Y, Lei P, Zhang Y, Sha Y, Zhan Y, Xu Z, Li S, Xu H, Ouyang P. Recent advances in bio-based multi-products of agricultural Jerusalem artichoke resources. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:151. [PMID: 29881456 PMCID: PMC5984348 DOI: 10.1186/s13068-018-1152-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/23/2018] [Indexed: 05/30/2023]
Abstract
The Jerusalem artichoke is a perennial plant that belongs to the sunflower family. As a non-grain crop, Jerusalem artichoke possesses a number of desirable characteristics that make it a valuable feedstock for biorefinery, such as inulin content, rapid growth, strong adaptability, and high yields. This review provides a comprehensive introduction to renewable Jerusalem artichoke-based biomass resources and recent advances in bio-based product conversion. Furthermore, we discuss the latest in the development of inulinase-producing microorganisms and enhanced inulin hydrolysis capacity of microbes by genetic engineering, which lead to a more cost-effective Jerusalem artichoke biorefinery. The review is aimed at promoting Jerusalem artichoke industry and new prospects for higher value-added production.
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Affiliation(s)
- Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Peng Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, 210042 China
| | - Yatao Zhang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yuanyuan Sha
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Yijing Zhan
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Zongqi Xu
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
| | - Pingkai Ouyang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816 China
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24
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Holyavka MG, Kayumov AR, Baydamshina DR, Koroleva VA, Trizna EY, Trushin MV, Artyukhov VG. Efficient fructose production from plant extracts by immobilized inulinases from Kluyveromyces marxianus and Helianthus tuberosus. Int J Biol Macromol 2018; 115:829-834. [PMID: 29698764 DOI: 10.1016/j.ijbiomac.2018.04.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 01/01/2023]
Abstract
The enzymatic hydrolysis of poly- and oligosaccharides from plants seems like an advantageous approach for sugars production. Two inulinases producing fructose from plant oligosaccharides were isolated from yeast Kluyveromyces marxianus and plant Helianthus tuberosus. Both enzymes were immobilized on polymeric carriers by using the static adsorption approach. We could save 80.4% of the initial catalytic activity of plant inulinase immobilized on KU-2 cation-exchange resin and 75.5% of yeast enzyme activity adsorbed on AV-17-2P anion-exchange resin. After immobilization, the Km values increased 1.5 and 6 times for enzymes from K. marxianus and H. tuberosus, respectively. The optimal temperatures for catalysis of both enzymes were increased from 48-50 °C up to 70 °C. The activities of both immobilized enzymes remained unchanged after the 10 cycles of 20-min hydrolysis reaction at 70 °C model batch reactor. Sorbents, native and immobilized enzymes did not exhibit any mutagenic or cytotoxic activity.
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Nagaya M, Kimura M, Gozu Y, Sato S, Hirano K, Tochio T, Nishikawa A, Tonozuka T. Crystal structure of a β-fructofuranosidase with high transfructosylation activity from Aspergillus kawachii. Biosci Biotechnol Biochem 2017; 81:1786-1795. [DOI: 10.1080/09168451.2017.1353405] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Abstract
β-Fructofuranosidases belonging to glycoside hydrolase family (GH) 32 are enzymes that hydrolyze sucrose. Some GH32 enzymes also catalyze transfructosylation to produce fructooligosaccharides. We found that Aspergillus kawachii IFO 4308 β-fructofuranosidase (AkFFase) produces fructooligosaccharides, mainly 1-kestose, from sucrose. We determined the crystal structure of AkFFase. AkFFase is composed of an N-terminal small component, a β-propeller catalytic domain, an α-helical linker, and a C-terminal β-sandwich, similar to other GH32 enzymes. AkFFase forms a dimer, and the dimerization pattern is different from those of other oligomeric GH32 enzymes. The complex structure of AkFFase with fructose unexpectedly showed that fructose binds both subsites −1 and +1, despite the fact that the catalytic residues were not mutated. Fructose at subsite +1 interacts with Ile146 and Glu296 of AkFFase via direct hydrogen bonds.
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Affiliation(s)
- Mika Nagaya
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Miyoko Kimura
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yoshifumi Gozu
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Shona Sato
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Katsuaki Hirano
- Research & Development Center, B Food Science Co., Ltd., Chita, Japan
| | - Takumi Tochio
- Research & Development Center, B Food Science Co., Ltd., Chita, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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The importance of the non-active site and non-periodical structure located histidine residue respect to the structure and function of exo-inulinase. Int J Biol Macromol 2017; 98:542-549. [DOI: 10.1016/j.ijbiomac.2017.01.130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/15/2017] [Accepted: 01/30/2017] [Indexed: 11/19/2022]
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Mendoza-Llerenas EO, Pérez DJ, Gómez-Sandoval Z, Escalante-Minakata P, Ibarra-Junquera V, Razo-Hernández RS, Capozzi V, Russo P, Spano G, Fiocco D, Osuna-Castro JA, Moreno A. Lactobacillus plantarum WCFS1 β-Fructosidase: Evidence for an Open Funnel-Like Channel Through the Catalytic Domain with Importance for the Substrate Selectivity. Appl Biochem Biotechnol 2016; 180:1056-1075. [PMID: 27295039 DOI: 10.1007/s12010-016-2152-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
Abstract
β-Fructosidase, a glycoside hydrolase of a biotechnologically important strain, was studied for its biochemical, physicochemical, and three-dimensional structure characteristics. This enzyme was heterologously expressed in Escherichia coli as a C-terminal His-tagged protein (SacB). β-Fructosidase catalyzes the cleavage of glycoside bonds toward certain carbohydrates with β-fructofuranosyl linkages; however, SacB exhibited selectivity toward sucrose and an optimum activity at pH 6.0-6.5 and 37 °C. In such optimum enzymatic activity conditions, the SacB was commonly observed as a monodisperse protein by dynamic light scattering (DLS). As β-fructosidase belongs to glycoside hydrolase family 32 (GH32), a β-sandwich and a five-bladed β-propeller domain are typical predicted folds in its structure. Docking and molecular dynamic simulations revealed for the first time a funnel-like channel perfectly exposed in the β-propeller domain of the Lactobacillus plantarum β-fructosidase (this allows the interaction between its entire catalytic triad and substrates that are larger than sucrose). In contrast, SacB showed a closed central tunnel collaterally induced by its His-tag.
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Affiliation(s)
- Edgar Omar Mendoza-Llerenas
- Facultad de Ciencias Químicas, Universidad de Colima, Carr. Colima-Coquimatlán, km 9, Coquimatlán, Colima, México, C.P. 28400
| | - David Javier Pérez
- Facultad de Ciencias Químicas, Universidad de Colima, Carr. Colima-Coquimatlán, km 9, Coquimatlán, Colima, México, C.P. 28400
| | - Zeferino Gómez-Sandoval
- Facultad de Ciencias Químicas, Universidad de Colima, Carr. Colima-Coquimatlán, km 9, Coquimatlán, Colima, México, C.P. 28400
| | - Pilar Escalante-Minakata
- Laboratorio de Bioingeniería, Universidad de Colima, Carr. Colima-Coquimatlán, km 9, Coquimatlán, Colima, México, C.P. 28400
| | - Vrani Ibarra-Junquera
- Laboratorio de Bioingeniería, Universidad de Colima, Carr. Colima-Coquimatlán, km 9, Coquimatlán, Colima, México, C.P. 28400
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Dinámica de Proteínas y Ácidos Nucleicos, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62209
| | - Vittorio Capozzi
- Dipartimento di Scienze degli Alimenti, Facoltà di Agraria, Università degli Studi di Foggia, via Napoli 25, Foggia, Italy, C.P. 71122
| | - Pasquale Russo
- Dipartimento di Scienze degli Alimenti, Facoltà di Agraria, Università degli Studi di Foggia, via Napoli 25, Foggia, Italy, C.P. 71122
| | - Giuseppe Spano
- Dipartimento di Scienze degli Alimenti, Facoltà di Agraria, Università degli Studi di Foggia, via Napoli 25, Foggia, Italy, C.P. 71122
| | - Daniela Fiocco
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, viale Luigi Pinto 1, Foggia, Italy, C.P. 71100
| | - Juan Alberto Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Autopista Colima-Manzanillo, km 40, Tecomán, Colima, México, C.P. 28100.
| | - Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito exterior Ciudad Universitaria, Ciudad de Mexico, 04510, México.
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Deletion of loop fragment adjacent to active site diminishes the stability and activity of exo-inulinase. Int J Biol Macromol 2016; 92:1234-1241. [DOI: 10.1016/j.ijbiomac.2016.08.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/04/2016] [Accepted: 08/11/2016] [Indexed: 11/20/2022]
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Mohandesi N, Haghbeen K, Ranaei O, Arab SS, Hassani S. Catalytic efficiency and thermostability improvement of Suc2 invertase through rational site-directed mutagenesis. Enzyme Microb Technol 2016; 96:14-22. [PMID: 27871374 DOI: 10.1016/j.enzmictec.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 10/21/2022]
Abstract
Engineering of invertases has come to attention because of increasing demand for possible applications of invertases in various industrial processes. Due to the known physicochemical properties, invertases from micro-organisms such as Saccharomyces cerevisiae carrying SUC2 gene are considered as primary models. To improve thermostability and catalytic efficiency of SUC2 invertase (SInv), six influential residues with Relative Solvent Accessibility<5% were selected through multiple-sequence alignments, molecular modelling, structural and computational analyses. Consequently, SInv and 5 mutants including three mutants with single point substitution [Mut1=P152V, Mut2=S85V and Mut3=K153F)], one mutant with two points [Mut4=S305V-N463V] and one mutant with three points [Mut5=S85V-K153F-T271V] were developed via site-directed mutagenesis and produced using Pichia pastoris as the host. Physicochemical studies on these enzymes indicated that the selected amino acids which were located in the active site region mainly influenced catalytic efficiency. The best improvement belonged to Mut1 (54% increase in Kcat/Km) and Mut3 exhibited the worst effect (90% increase in Km). These results suggest that Pro152 and Lys153 play key role in preparation of the right substrate lodging in the active site of SInv. The best thermostability improvement (16%) was observed for Mut4 in which two hydrophilic residues located on the loops, far from the active site, were replaced by Valines. These results suggest that tactful simultaneous substitution of influential hydrophilic residues in both active site region and peripheral loops with hydrophobic amino acids could result in more thermostable invertases with enhanced catalytic efficiency.
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Affiliation(s)
- Nooshin Mohandesi
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology. P.O. Box: 149651/161, Tehran, Iran
| | - Kamahldin Haghbeen
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology. P.O. Box: 149651/161, Tehran, Iran.
| | - Omid Ranaei
- Department of Biotechnology, Faculty of New Technologies Engineering, Shahid Beheshti University, Tehran, Iran
| | - Seyed Shahriar Arab
- Faculty of Biological Science, Bioinformatics Department, Tarbiat Modares University, Tehran, Iran
| | - Sorour Hassani
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology. P.O. Box: 149651/161, Tehran, Iran
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Immobilization of inulinase from Aspergillus niger on octadecyl substituted nanoporous silica: Inulin hydrolysis in a continuous mode operation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Holyavka M, Artyukhov V, Kovaleva T. Structural and functional properties of inulinases: A review. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1196486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Shen J, Zhang R, Li J, Tang X, Li R, Wang M, Huang Z, Zhou J. Characterization of an exo-inulinase from Arthrobacter: a novel NaCl-tolerant exo-inulinase with high molecular mass. Bioengineered 2016; 6:99-105. [PMID: 25695343 DOI: 10.1080/21655979.2015.1019686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A glycoside hydrolase family 32 exo-inulinase gene was cloned from Arthrobacter sp. HJ7 isolated from saline soil located in Heijing town. The gene encodes an 892-residue polypeptide with a calculated mass of 95.1 kDa and a high total frequency of amino acid residues G, A, and V (30.0%). Escherichia coli BL21 (DE3) cells were used as hosts to express the exo-inulinase gene. The recombinant exo-inulinase (rInuAHJ7) showed an apparently maximal activity at pH 5.0-5.5 and 40-45°C. The addition of 1.0 and 10.0 mM Zn(2+) and Pb(2+) had little or no effect on the enzyme activity. rInuAHJ7 exhibited good salt tolerance, retaining more than 98% inulinase activity at a concentration of 3.0%-20.0% (w/v) NaCl. Fructose was the main product of inulin, levan, and Jerusalem artichoke tubers hydrolyzed by the enzyme. The present study is the first to report the identification and characterization of an Arthrobacter sp exo-inulinase showing a high molecular mass of 95.1 kDa and NaCl tolerance. These results suggest that the exo-inulinase might be an alternative material for potential applications in processing seafood and other foods with high saline contents, such as marine algae, pickles, and sauces.
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Affiliation(s)
- Jidong Shen
- a Engineering Research Center of Sustainable Development and Utilization of Biomass Energy; Ministry of Education ; Yunnan Normal University ; Kunming , PR China
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Ramírez-Escudero M, Gimeno-Pérez M, González B, Linde D, Merdzo Z, Fernández-Lobato M, Sanz-Aparicio J. Structural Analysis of β-Fructofuranosidase from Xanthophyllomyces dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity. J Biol Chem 2016; 291:6843-57. [PMID: 26823463 DOI: 10.1074/jbc.m115.708495] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/06/2022] Open
Abstract
Xanthophyllomyces dendrorhousβ-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement and also a long extension of its C terminus that together with anN-linked glycan mediate the formation of an unusual dimer. The two active sites of the dimer are connected by a long crevice, which might indicate its potential ability to accommodate branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. The inactive D80A mutant was used to obtain complexes with relevant substrates and products, with their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending on the substrate, and thus, a flexible loop (Glu-334-His-343) is essential in binding sucrose and β(2-1)-linked oligosaccharides. Conversely, β(2-6) and neo-type substrates are accommodated mainly by stacking to Trp-105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on α-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements, and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.
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Affiliation(s)
- Mercedes Ramírez-Escudero
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid and
| | - María Gimeno-Pérez
- the Center of Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Beatriz González
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid and
| | - Dolores Linde
- the Center of Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Zoran Merdzo
- the Center of Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - María Fernández-Lobato
- the Center of Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Julia Sanz-Aparicio
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid and
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Maaroufi H, Levesque RC. Glycoside hydrolase family 32 is present in Bacillus subtilis phages. Virol J 2015; 12:157. [PMID: 26438422 PMCID: PMC4595243 DOI: 10.1186/s12985-015-0373-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/03/2015] [Indexed: 01/21/2023] Open
Abstract
Background Glycoside hydrolase family 32 (GH32) enzymes cleave the glycosidic bond between two monosaccharides or between a carbohydrate and an aglycone moiety. GH32 enzymes have been studied in prokaryotes and in eukaryotes but not in viruses. Findings This is the first analysis of GH32 enzymes in Bacillus subtilis phage SP10, ϕNIT1 and SPG24. Phylogenetic analysis, molecular docking and secretability predictions suggest that phage GH32 enzymes function as levan (fructose homopolysaccharide) fructotransferase. Conclusions We showed that viruses also contain GH32 enzymes and that our analyses in silico strongly suggest that these enzymes function as levan fructotransferase. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0373-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Halim Maaroufi
- Institut de biologie intégrative et des systèmes (IBIS), Plate-Forme de Bio-Informatique, Université Laval, Pavillon Charles-Eugène Marchand, 1030 Avenue de la médecine, Québec, Québec, G1V 0A6, Canada.
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS) and Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, G1V 0A6, Canada
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Identification, biochemical characterization, and in-vivo expression of the intracellular invertase BfrA from the pathogenic parasite Leishmania major. Carbohydr Res 2015; 415:31-8. [DOI: 10.1016/j.carres.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 06/12/2015] [Accepted: 07/10/2015] [Indexed: 01/14/2023]
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Mazola Y, Guirola O, Palomares S, Chinea G, Menéndez C, Hernández L, Musacchio A. A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes. J Mol Model 2015; 21:228. [PMID: 26267297 DOI: 10.1007/s00894-015-2772-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/20/2015] [Indexed: 02/02/2023]
Abstract
Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability.
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Affiliation(s)
- Yuliet Mazola
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology (CIGB), Ave. 31 e/ 158 and 190, Playa, P.O. Box 6162, Havana, 10600, Cuba,
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Holyavka MG, Artyukhov VG, Makin SM. Investigation of inulinase permolecular organization from producers of the genus Aspergillus using several computing and experimental methods. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Flores AC, Morlett JA, Rodríguez R. Inulin Potential for Enzymatic Obtaining of Prebiotic Oligosaccharides. Crit Rev Food Sci Nutr 2015; 56:1893-902. [DOI: 10.1080/10408398.2013.807220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Zhou J, Lu Q, Peng M, Zhang R, Mo M, Tang X, Li J, Xu B, Ding J, Huang Z. Cold-active and NaCl-tolerant exo-inulinase from a cold-adapted Arthrobacter sp. MN8 and its potential for use in the production of fructose at low temperatures. J Biosci Bioeng 2015; 119:267-74. [DOI: 10.1016/j.jbiosc.2014.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 07/19/2014] [Accepted: 08/07/2014] [Indexed: 01/09/2023]
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40
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Azhar M, Natalia D, Syukur S, . V, . J. Gene Fragments that Encodes Inulin Hydrolysis Enzyme from Genomic Bacillus licheniformis: Isolation by PCR Technique Using New Primers. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ijbc.2015.59.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Zhou J, Peng M, Zhang R, Li J, Tang X, Xu B, Ding J, Gao Y, Ren J, Huang Z. Characterization of Sphingomonas sp. JB13 exo-inulinase: a novel detergent-, salt-, and protease-tolerant exo-inulinase. Extremophiles 2015; 19:383-93. [PMID: 25575614 DOI: 10.1007/s00792-014-0724-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/11/2014] [Indexed: 11/24/2022]
Abstract
A glycoside hydrolase family 32 exo-inulinase gene was cloned from Sphingomonas sp. JB13 and expressed in Escherichia coli BL21 (DE3). The purified recombinant enzyme (rInuAJB13) showed an apparently optimal activity at pH 5.5 and 55 °C and remained activity at 10-70 °C. The addition of most metal ions and chemical reagents showed little or no effect (retaining more than 76.5 % activity) on the enzyme activity, notably the addition of surfactants SDS, CTAB, Tween 80, and Triton X-100. Most local liquid detergents, including Balin, Walch, Ariel, Tide, Tupperware, and Bluemoon, also showed little or no effect (retaining more than 77.8 % activity) on the enzyme activity. rInuAJB13 exhibited 135.3-163.6 % activity at the NaCl concentration of 1.0-4.5 M. After incubation with up to 57.0 mg mL(-1) trypsin and 90.0 mg mL(-1) proteinase K at 37 °C for 60 min (pH 7.2), rInuAJB13 retained more than 80 % of its initial activity. The enzyme presents a high proportion (28.0 %) of amino acid residues G, A, and V. This paper is the first to report a detergent-, salt-, and protease-tolerant exo-inulinase.
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Affiliation(s)
- Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China
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Flores-Gallegos AC, Morlett-Chávez JA, Aguilar CN, Riutort M, Rodríguez-Herrera R. Gene Encoding Inulinase Isolated from Penicillium citrinum ESS and Its Molecular Phylogeny. Appl Biochem Biotechnol 2014; 175:1358-70. [DOI: 10.1007/s12010-014-1280-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
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Chen M, Lei X, Chen C, Zhang S, Xie J, Wei D. Cloning, Overexpression, and Characterization of a Highly Active Endoinulinase Gene from Aspergillus fumigatus Cl1 for Production of Inulo-Oligosaccharides. Appl Biochem Biotechnol 2014; 175:1153-67. [DOI: 10.1007/s12010-014-1296-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
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A novel low-temperature-active exo-inulinase identified based on Molecular-Activity strategy from Sphingobacterium sp. GN25 isolated from feces of Grus nigricollis. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Seibel J, Jördening HJ, Buchholz K. Extending synthetic routes for oligosaccharides by enzyme, substrate and reaction engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 120:163-93. [PMID: 20182930 DOI: 10.1007/10_2009_54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The integration of all relevant tools for bioreaction engineering has been a recent challenge. This approach should notably favor the production of oligo- and polysaccharides, which is highly complex due to the requirements of regio- and stereoselectivity. Oligosaccharides (OS) and polysaccharides (PS) have found many interests in the fields of food, pharmaceuticals, and cosmetics due to different specific properties. Food, sweeteners, and food ingredients represent important sectors where OS are used in major amounts. Increasing attention has been devoted to the sophisticated roles of OS and glycosylated compounds, at cell or membrane surfaces, and their function, e.g., in infection and cancer proliferation. The challenge for synthesis is obvious, and convenient approaches using cheap and readily available substrates and enzymes will be discussed. We report on new routes for the synthesis of oligosaccharides (OS), with emphasis on enzymatic reactions, since they offer unique properties, proceeding highly regio- and stereoselective in water solution, and providing for high yields in general.
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Affiliation(s)
- Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany,
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Gao J, Xu YY, Yang HM, Xu H, Xue F, Li S, Feng XH. Gene Cloning, Expression, and Characterization of an Exo-inulinase from Paenibacillus polymyxa ZJ-9. Appl Biochem Biotechnol 2014; 173:1419-30. [DOI: 10.1007/s12010-014-0950-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
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Microbial enzymatic production and applications of short-chain fructooligosaccharides and inulooligosaccharides: recent advances and current perspectives. J Ind Microbiol Biotechnol 2014; 41:893-906. [PMID: 24793124 DOI: 10.1007/s10295-014-1452-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/19/2014] [Indexed: 01/02/2023]
Abstract
The industrial production of short-chain fructooligosaccharides (FOS) and inulooligosaccharides is expanding rapidly due to the pharmaceutical importance of these compounds. These compounds, concisely termed prebiotics, have biofunctional properties and hence health benefits if consumed in recommended dosages. Prebiotics can be produced enzymatically from sucrose elongation or via enzymatic hydrolysis of inulin by exoinulinases and endoinulinases acting alone or synergistically. Exoinulinases cleave the non-reducing β-(2, 1) end of inulin-releasing fructose while endoinulinases act on the internal linkages randomly to release inulotrioses (F3), inulotetraoses (F4) and inulopentaoses (F5) as major products. Fructosyltransferases act by cleaving a sucrose molecule and then transferring the liberated fructose molecule to an acceptor molecule such as sucrose or another oligosaccharide to elongate the short-chain fructooligosaccharide. The FOS produced by the action of fructosyltransferases are 1-kestose (GF2), nystose (GF3) and fructofuranosyl nystose (GF4). The production of high yields of oligosaccharides of specific chain length from simple raw materials such as inulin and sucrose is a technical challenge. This paper critically explores recent research trends in the production and application of short-chain oligosaccharides. Inulin and enzyme sources for the production of prebiotics are discussed. The mechanism of FOS chain elongation and also the health benefits associated with prebiotics consumption are discussed in detail.
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Holyavka MG, Kovaleva TA, Grechkina MV, Ostankova IV, Artyukhov VG. Inulinases from various producers: The features of their permolecular organization. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683814010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Functional characterization of a vacuolar invertase from Solanum lycopersicum: post-translational regulation by N-glycosylation and a proteinaceous inhibitor. Biochimie 2013; 101:39-49. [PMID: 24374160 DOI: 10.1016/j.biochi.2013.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/13/2013] [Indexed: 11/22/2022]
Abstract
Plant vacuolar invertases, which belong to family 32 of glycoside hydrolases (GH32), are key enzymes in sugar metabolism. They hydrolyse sucrose into glucose and fructose. The cDNA encoding a vacuolar invertase from Solanum lycopersicum (TIV-1) was cloned and heterologously expressed in Pichia pastoris. The functional role of four N-glycosylation sites in TIV-1 has been investigated by site-directed mutagenesis. Single mutations to Asp of residues Asn52, Asn119 and Asn184, as well as the triple mutant (Asn52, Asn119 and Asn184), lead to enzymes with reduced specific invertase activity and thermostability. Expression of the N516D mutant, as well as of the quadruple mutant (N52D, N119D, N184D and N516D) could not be detected, indicating that these mutations dramatically affected the folding of the protein. Our data indicate that N-glycosylation is important for TIV-1 activity and that glycosylation of N516 is crucial for recombinant enzyme stability. Using a functional genomics approach a new vacuolar invertase inhibitor of S. lycopersicum (SolyVIF) has been identified. SolyVIF cDNA was cloned and heterologously expressed in Escherichia coli. Specific interactions between SolyVIF and TIV-1 were investigated by an enzymatic approach and surface plasmon resonance (SPR). Finally, qRT-PCR analysis of TIV-1 and SolyVIF transcript levels showed a specific tissue and developmental expression. TIV-1 was mainly expressed in flowers and both genes were expressed in senescent leaves.
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